Starting phenix.real_space_refine on Wed May 15 16:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8s5k_19738/05_2024/8s5k_19738_trim_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 ASP 47": "OD1" <-> "OD2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 538": "OD1" <-> "OD2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D ASP 538": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 514": "OE1" <-> "OE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ASP 249": "OD1" <-> "OD2" Residue "F TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F GLU 366": "OE1" <-> "OE2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 388": "OD1" <-> "OD2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 179": "OD1" <-> "OD2" Residue "H GLU 201": "OE1" <-> "OE2" Residue "H TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 376": "OD1" <-> "OD2" Residue "H PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 504": "OE1" <-> "OE2" Residue "H PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 20.87, per 1000 atoms: 0.33 Number of scatterers: 63696 At special positions: 0 Unit cell: (161.582, 240.038, 150.374, 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 43.06 Conformation dependent library (CDL) restraints added in 4.9 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: 188 helices and 34 sheets defined 37.6% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.37 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 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' 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 122 through 132 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.533A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 328 through 341 Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.969A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 5.243A 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 405 removed outlier: 4.430A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 411 removed outlier: 3.814A pdb=" N HIS A 411 " --> pdb=" O TRP A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 408 through 411' 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 removed outlier: 3.653A pdb=" N ARG A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) 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 504 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 94 through 98 Processing helix chain 'B' and resid 121 through 133 removed outlier: 4.010A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 161 removed outlier: 4.118A pdb=" N GLY B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.888A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' 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 341 Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.690A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.631A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 removed outlier: 3.953A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 408 through 411' 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 removed outlier: 3.749A pdb=" N ARG B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) 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 94 through 98 Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.713A pdb=" N TRP C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.934A 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: 4.067A pdb=" N ILE C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 267 " --> pdb=" O GLY C 263 " (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: 3.754A pdb=" N VAL C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 4.676A 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 405 removed outlier: 4.195A pdb=" N LYS C 405 " --> pdb=" O ASP C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 removed outlier: 4.047A pdb=" N HIS C 411 " --> pdb=" O TRP C 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 411' 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 removed outlier: 3.652A pdb=" N ARG C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) 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 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: 3.859A 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: 3.611A pdb=" N ILE D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 267 " --> pdb=" O GLY D 263 " (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: 3.740A pdb=" N LYS D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN D 362 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 5.040A 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 408 through 411 removed outlier: 4.167A pdb=" N HIS D 411 " --> pdb=" O TRP D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 408 through 411' 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 removed outlier: 3.784A pdb=" N LYS D 441 " --> pdb=" O ILE D 437 " (cutoff:3.500A) 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 545 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 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 227 through 234 removed outlier: 3.842A 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: 3.608A pdb=" N ILE E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS E 267 " --> pdb=" O GLY E 263 " (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: 3.820A pdb=" N LYS E 359 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN E 362 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 4.920A 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 408 through 411 removed outlier: 4.190A pdb=" N HIS E 411 " --> pdb=" O TRP E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 411' 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 439 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 94 through 98 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 184 Processing helix chain 'F' and resid 203 through 213 removed outlier: 3.823A pdb=" N TRP F 208 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.933A 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: 4.134A pdb=" N ILE F 264 " --> pdb=" O THR F 260 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS F 267 " --> pdb=" O GLY F 263 " (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: 3.752A pdb=" N VAL F 356 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 4.703A 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 405 removed outlier: 4.091A pdb=" N LYS F 405 " --> pdb=" O ASP F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 411 removed outlier: 4.031A pdb=" N HIS F 411 " --> pdb=" O TRP F 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 408 through 411' 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 removed outlier: 3.693A pdb=" N ARG F 439 " --> pdb=" O ILE F 435 " (cutoff:3.500A) 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 94 through 98 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 removed outlier: 4.290A pdb=" N ILE G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 161 removed outlier: 4.161A pdb=" N GLY G 153 " --> pdb=" O ASN G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 227 through 244 removed outlier: 3.866A pdb=" N HIS G 232 " --> pdb=" O ASN G 228 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 291 through 293 No H-bonds generated for 'chain 'G' and resid 291 through 293' Processing helix chain 'G' and resid 328 through 341 Processing helix chain 'G' and resid 348 through 363 removed outlier: 3.665A pdb=" N LYS G 359 " --> pdb=" O ALA G 355 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN G 362 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU G 363 " --> pdb=" O LYS G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 380 No H-bonds generated for 'chain 'G' and resid 378 through 380' Processing helix chain 'G' and resid 388 through 394 Processing helix chain 'G' and resid 399 through 404 Processing helix chain 'G' and resid 408 through 411 removed outlier: 4.001A pdb=" N HIS G 411 " --> pdb=" O TRP G 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 408 through 411' 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 removed outlier: 3.754A pdb=" N ARG G 439 " --> pdb=" O ILE G 435 " (cutoff:3.500A) 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 98 No H-bonds generated for 'chain 'H' and resid 95 through 98' 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 184 Processing helix chain 'H' and resid 203 through 213 Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'H' and resid 236 through 243 Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 291 through 293 No H-bonds generated for 'chain 'H' and resid 291 through 293' Processing helix chain 'H' and resid 328 through 341 Processing helix chain 'H' and resid 348 through 363 removed outlier: 3.946A pdb=" N LYS H 359 " --> pdb=" O ALA H 355 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN H 362 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 5.471A 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 405 removed outlier: 4.477A pdb=" N LYS H 405 " --> pdb=" O ASP H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 411 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 removed outlier: 3.726A pdb=" N ARG H 439 " --> pdb=" O ILE H 435 " (cutoff:3.500A) 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: 6.879A pdb=" N MET A 250 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ILE A 373 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL A 252 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG A 276 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA A 253 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE A 278 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 322 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASP A 281 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE A 324 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 217 through 219 removed outlier: 6.879A pdb=" N THR A 141 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARG A 164 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU A 144 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 166 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 187 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N MET A 169 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.457A 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: 6.146A pdb=" N HIS A 513 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL A 530 " --> pdb=" O HIS A 513 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN A 515 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLN A 528 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN A 517 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 5.019A 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 removed outlier: 3.524A pdb=" N VAL A 459 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.803A pdb=" N LEU B 374 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET B 250 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 373 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 252 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG B 276 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA B 253 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE B 278 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS B 322 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASP B 281 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 6.290A 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: 6.594A pdb=" N ARG B 164 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU B 144 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 166 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B 187 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET B 169 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 6.159A 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: 3.802A pdb=" N GLY B 532 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS B 513 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 530 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN B 515 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN B 528 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN B 517 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 5.986A 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 Processing sheet with id= J, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.581A pdb=" N ARG C 164 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLU C 144 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE C 166 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU C 187 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N MET C 169 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.385A 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: 3.729A pdb=" N GLY C 532 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS C 513 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 530 " --> pdb=" O HIS C 513 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN C 515 " --> pdb=" O GLN C 528 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN C 528 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN C 517 " --> pdb=" O GLN C 526 " (cutoff:3.500A) removed outlier: 4.785A 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 removed outlier: 3.728A pdb=" N VAL C 459 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 457 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.679A pdb=" N MET D 250 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ILE D 373 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 252 " --> pdb=" O ILE D 373 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.548A pdb=" N THR D 141 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG D 164 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLU D 144 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 166 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU D 187 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET D 169 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.350A 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 278 through 282 removed outlier: 6.936A pdb=" N LYS D 322 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ASP D 281 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE D 324 " --> pdb=" O ASP D 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.605A pdb=" N GLY D 532 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS D 513 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL D 530 " --> pdb=" O HIS D 513 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN D 515 " --> pdb=" O GLN D 528 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN D 528 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN D 517 " --> pdb=" O GLN D 526 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN D 526 " --> pdb=" O GLN D 517 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 445 through 449 removed outlier: 3.710A pdb=" N VAL D 459 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 457 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 89 through 91 removed outlier: 6.754A pdb=" N MET E 250 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N ILE E 373 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL E 252 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG E 276 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ALA E 253 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 278 " --> pdb=" O ALA E 253 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 322 " --> pdb=" O GLY E 279 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASP E 281 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE E 324 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.544A pdb=" N THR E 141 " --> pdb=" O HIS E 218 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG E 164 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU E 144 " --> pdb=" O ARG E 164 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 166 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU E 187 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N MET E 169 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 189 " --> pdb=" O MET E 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 488 through 490 removed outlier: 3.594A pdb=" N VAL E 511 " --> pdb=" O GLY E 532 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 532 " --> pdb=" O VAL E 511 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N HIS E 513 " --> pdb=" O VAL E 530 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL E 530 " --> pdb=" O HIS E 513 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN E 515 " --> pdb=" O GLN E 528 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN E 528 " --> pdb=" O GLN E 515 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN E 517 " --> pdb=" O GLN E 526 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN E 526 " --> pdb=" O GLN E 517 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 445 through 449 removed outlier: 3.655A pdb=" N VAL E 459 " --> pdb=" O ALA E 446 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 448 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY E 457 " --> pdb=" O VAL E 448 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 89 through 91 removed outlier: 6.625A pdb=" N MET F 250 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N ILE F 373 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL F 252 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG F 276 " --> pdb=" O LEU F 251 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 141 through 145 removed outlier: 6.381A pdb=" N ARG F 164 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLU F 144 " --> pdb=" O ARG F 164 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 166 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU F 187 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N MET F 169 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL F 189 " --> pdb=" O MET F 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 488 through 490 removed outlier: 3.749A pdb=" N GLY F 532 " --> pdb=" O VAL F 511 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N HIS F 513 " --> pdb=" O VAL F 530 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 530 " --> pdb=" O HIS F 513 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLN F 515 " --> pdb=" O GLN F 528 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN F 528 " --> pdb=" O GLN F 515 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN F 517 " --> pdb=" O GLN F 526 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN F 526 " --> pdb=" O GLN F 517 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 445 through 449 removed outlier: 3.685A pdb=" N VAL F 459 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 457 " --> pdb=" O VAL F 448 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 89 through 91 removed outlier: 6.663A pdb=" N MET G 250 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG G 276 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA G 253 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE G 278 " --> pdb=" O ALA G 253 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LYS G 322 " --> pdb=" O GLY G 279 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASP G 281 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE G 324 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 141 through 145 removed outlier: 6.628A pdb=" N ARG G 164 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU G 144 " --> pdb=" O ARG G 164 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE G 166 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU G 187 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N MET G 169 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL G 189 " --> pdb=" O MET G 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 488 through 490 removed outlier: 6.327A pdb=" N HIS G 513 " --> pdb=" O VAL G 530 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N VAL G 530 " --> pdb=" O HIS G 513 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN G 515 " --> pdb=" O GLN G 528 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN G 528 " --> pdb=" O GLN G 515 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 445 through 449 removed outlier: 3.628A pdb=" N VAL G 459 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 89 through 91 Processing sheet with id= AE, first strand: chain 'H' and resid 217 through 219 removed outlier: 6.787A pdb=" N THR H 141 " --> pdb=" O HIS H 218 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG H 164 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU H 144 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE H 166 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU H 187 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N MET H 169 " --> pdb=" O GLU H 187 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL H 189 " --> pdb=" O MET H 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 250 through 254 removed outlier: 6.062A pdb=" N ARG H 276 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA H 253 " --> pdb=" O ARG H 276 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE H 278 " --> pdb=" O ALA H 253 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS H 322 " --> pdb=" O GLY H 279 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ASP H 281 " --> pdb=" O LYS H 322 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE H 324 " --> pdb=" O ASP H 281 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 488 through 490 removed outlier: 6.418A pdb=" N HIS H 513 " --> pdb=" O VAL H 530 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL H 530 " --> pdb=" O HIS H 513 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN H 515 " --> pdb=" O GLN H 528 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN H 528 " --> pdb=" O GLN H 515 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN H 517 " --> pdb=" O GLN H 526 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLN H 526 " --> pdb=" O GLN H 517 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 445 through 449 886 hydrogen bonds defined for protein. 2601 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: 24.53 Time building geometry restraints manager: 45.32 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: 5670 1.32 - 1.56: 26666 1.56 - 1.81: 233 1.81 - 2.05: 79 Bond restraints: 64360 Sorted by residual: bond pdb=" OP4 LLP D 119 " pdb=" P LLP D 119 " ideal model delta sigma weight residual 1.726 1.641 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" OP4 LLP E 119 " pdb=" P LLP E 119 " ideal model delta sigma weight residual 1.726 1.642 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" OP4 LLP C 119 " pdb=" P LLP C 119 " ideal model delta sigma weight residual 1.726 1.642 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" OP4 LLP F 119 " pdb=" P LLP F 119 " ideal model delta sigma weight residual 1.726 1.643 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" OP4 LLP A 119 " pdb=" P LLP A 119 " ideal model delta sigma weight residual 1.726 1.647 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 64355 not shown) Histogram of bond angle deviations from ideal: 85.17 - 104.00: 565 104.00 - 122.83: 108274 122.83 - 141.66: 7897 141.66 - 160.49: 0 160.49 - 179.33: 16 Bond angle restraints: 116752 Sorted by residual: angle pdb=" O LLP E 119 " pdb=" C LLP E 119 " pdb=" N ASP E 120 " ideal model delta sigma weight residual 123.00 85.17 37.83 1.60e+00 3.91e-01 5.59e+02 angle pdb=" O LLP G 119 " pdb=" C LLP G 119 " pdb=" N ASP G 120 " ideal model delta sigma weight residual 123.00 85.40 37.60 1.60e+00 3.91e-01 5.52e+02 angle pdb=" O LLP D 119 " pdb=" C LLP D 119 " pdb=" N ASP D 120 " ideal model delta sigma weight residual 123.00 85.55 37.45 1.60e+00 3.91e-01 5.48e+02 angle pdb=" O LLP F 119 " pdb=" C LLP F 119 " pdb=" N ASP F 120 " ideal model delta sigma weight residual 123.00 91.76 31.24 1.60e+00 3.91e-01 3.81e+02 angle pdb=" O LLP C 119 " pdb=" C LLP C 119 " pdb=" N ASP C 120 " ideal model delta sigma weight residual 123.00 93.04 29.96 1.60e+00 3.91e-01 3.51e+02 ... (remaining 116747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 27304 20.80 - 41.60: 1850 41.60 - 62.39: 571 62.39 - 83.19: 100 83.19 - 103.99: 23 Dihedral angle restraints: 29848 sinusoidal: 16752 harmonic: 13096 Sorted by residual: dihedral pdb=" CA LYS H 384 " pdb=" C LYS H 384 " pdb=" N PHE H 385 " pdb=" CA PHE H 385 " ideal model delta harmonic sigma weight residual 180.00 -155.94 -24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LYS A 384 " pdb=" C LYS A 384 " pdb=" N PHE A 385 " pdb=" CA PHE A 385 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LYS F 384 " pdb=" C LYS F 384 " pdb=" N PHE F 385 " pdb=" CA PHE F 385 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 29845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3271 0.031 - 0.061: 1113 0.061 - 0.092: 268 0.092 - 0.123: 268 0.123 - 0.153: 40 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA PRO D 375 " pdb=" N PRO D 375 " pdb=" C PRO D 375 " pdb=" CB PRO D 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA PRO E 375 " pdb=" N PRO E 375 " pdb=" C PRO E 375 " pdb=" CB PRO E 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA PRO G 375 " pdb=" N PRO G 375 " pdb=" C PRO G 375 " pdb=" CB PRO G 375 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 4957 not shown) Planarity restraints: 9496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LLP E 119 " 0.136 2.00e-02 2.50e+03 2.19e-01 4.78e+02 pdb=" C LLP E 119 " -0.378 2.00e-02 2.50e+03 pdb=" O LLP E 119 " 0.131 2.00e-02 2.50e+03 pdb=" N ASP E 120 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP G 119 " -0.135 2.00e-02 2.50e+03 2.17e-01 4.73e+02 pdb=" C LLP G 119 " 0.376 2.00e-02 2.50e+03 pdb=" O LLP G 119 " -0.132 2.00e-02 2.50e+03 pdb=" N ASP G 120 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LLP D 119 " 0.135 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C LLP D 119 " -0.376 2.00e-02 2.50e+03 pdb=" O LLP D 119 " 0.130 2.00e-02 2.50e+03 pdb=" N ASP D 120 " 0.110 2.00e-02 2.50e+03 ... (remaining 9493 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 2072 2.13 - 2.75: 120430 2.75 - 3.37: 188084 3.37 - 3.98: 238608 3.98 - 4.60: 374988 Nonbonded interactions: 924182 Sorted by model distance: nonbonded pdb=" OE1 GLU F 297 " pdb=" H GLU F 297 " model vdw 1.516 1.850 nonbonded pdb=" O GLN B 415 " pdb="HE21 GLN C 415 " model vdw 1.564 1.850 nonbonded pdb=" O LEU E 268 " pdb=" H CYS E 272 " model vdw 1.570 1.850 nonbonded pdb=" H GLY A 115 " pdb=" OD2 ASP A 120 " model vdw 1.575 1.850 nonbonded pdb=" OE2 GLU D 304 " pdb=" HZ2 LYS D 384 " model vdw 1.588 1.850 ... (remaining 924177 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: 5.400 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: 0.740 Extract box with map and model: 25.990 Check model and map are aligned: 0.370 Set scattering table: 0.460 Process input model: 166.770 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 206.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 0.085 32568 Z= 0.272 Angle : 0.752 37.830 44232 Z= 0.417 Chirality : 0.041 0.153 4960 Planarity : 0.008 0.219 5656 Dihedral : 14.704 103.991 12120 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.04 % Favored : 96.84 % Rotamer: Outliers : 0.15 % Allowed : 10.69 % Favored : 89.16 % 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: 0.58 (0.14), residues: 4016 helix: 0.51 (0.14), residues: 1490 sheet: 0.02 (0.19), residues: 772 loop : 0.71 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.007 0.001 HIS G 232 PHE 0.022 0.001 PHE H 531 TYR 0.012 0.001 TYR C 163 ARG 0.004 0.000 ARG A 317 *********************** 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 253 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 468 LEU cc_start: 0.7433 (mm) cc_final: 0.7206 (mm) REVERT: E 505 MET cc_start: 0.7080 (mmm) cc_final: 0.6867 (mmt) outliers start: 5 outliers final: 5 residues processed: 250 average time/residue: 0.8441 time to fit residues: 334.4576 Evaluate side-chains 240 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 235 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 146 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 0.6980 chunk 303 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 363 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32568 Z= 0.202 Angle : 0.507 7.009 44232 Z= 0.253 Chirality : 0.041 0.155 4960 Planarity : 0.004 0.065 5656 Dihedral : 8.244 86.738 4456 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 0.85 % Allowed : 10.34 % Favored : 88.81 % 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: 0.81 (0.14), residues: 4016 helix: 0.80 (0.14), residues: 1472 sheet: 0.10 (0.19), residues: 764 loop : 0.75 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 390 HIS 0.007 0.001 HIS G 232 PHE 0.013 0.001 PHE B 531 TYR 0.014 0.001 TYR G 233 ARG 0.003 0.000 ARG E 498 *********************** 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 273 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 244 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 25 residues processed: 258 average time/residue: 0.8240 time to fit residues: 341.6984 Evaluate side-chains 258 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain H residue 230 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 302 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 363 optimal weight: 6.9990 chunk 393 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 32568 Z= 0.353 Angle : 0.571 6.849 44232 Z= 0.290 Chirality : 0.043 0.202 4960 Planarity : 0.004 0.075 5656 Dihedral : 8.162 86.594 4456 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.74 % Rotamer: Outliers : 1.29 % Allowed : 11.21 % Favored : 87.50 % 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: 0.36 (0.14), residues: 4016 helix: 0.41 (0.14), residues: 1496 sheet: -0.29 (0.19), residues: 776 loop : 0.60 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 390 HIS 0.009 0.001 HIS H 232 PHE 0.014 0.001 PHE B 531 TYR 0.015 0.002 TYR C 163 ARG 0.005 0.000 ARG C 317 *********************** 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 277 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 413 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6868 (ttm110) outliers start: 44 outliers final: 33 residues processed: 258 average time/residue: 0.8586 time to fit residues: 355.7539 Evaluate side-chains 254 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 529 MET Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain H residue 461 LEU 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: 1.9990 chunk 40 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 0.8980 chunk 386 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 32568 Z= 0.254 Angle : 0.524 7.371 44232 Z= 0.261 Chirality : 0.041 0.173 4960 Planarity : 0.004 0.068 5656 Dihedral : 7.985 87.237 4456 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.99 % Rotamer: Outliers : 1.29 % Allowed : 11.39 % Favored : 87.32 % 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: 0.47 (0.14), residues: 4016 helix: 0.58 (0.14), residues: 1490 sheet: -0.28 (0.19), residues: 776 loop : 0.60 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 409 HIS 0.006 0.001 HIS H 232 PHE 0.012 0.001 PHE B 531 TYR 0.014 0.001 TYR F 163 ARG 0.005 0.000 ARG G 413 *********************** 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 274 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 413 ARG cc_start: 0.7067 (mtm110) cc_final: 0.6852 (ttm110) REVERT: E 173 MET cc_start: 0.8304 (mmt) cc_final: 0.8049 (mmt) outliers start: 44 outliers final: 35 residues processed: 257 average time/residue: 0.8746 time to fit residues: 359.1078 Evaluate side-chains 257 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 222 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 329 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 347 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 32568 Z= 0.282 Angle : 0.533 7.103 44232 Z= 0.267 Chirality : 0.042 0.180 4960 Planarity : 0.004 0.069 5656 Dihedral : 7.916 88.477 4456 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 1.66 % Allowed : 11.83 % Favored : 86.51 % 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: 0.43 (0.14), residues: 4016 helix: 0.58 (0.14), residues: 1484 sheet: -0.42 (0.19), residues: 756 loop : 0.60 (0.16), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 54 HIS 0.006 0.001 HIS F 203 PHE 0.012 0.001 PHE B 531 TYR 0.015 0.001 TYR F 163 ARG 0.003 0.000 ARG F 548 *********************** 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 288 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.9122 (mmm) cc_final: 0.8497 (mmt) outliers start: 57 outliers final: 46 residues processed: 273 average time/residue: 0.9027 time to fit residues: 391.1837 Evaluate side-chains 260 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 321 optimal weight: 30.0000 chunk 179 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32568 Z= 0.240 Angle : 0.516 7.438 44232 Z= 0.256 Chirality : 0.041 0.172 4960 Planarity : 0.004 0.065 5656 Dihedral : 7.804 88.575 4456 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 1.66 % Allowed : 12.21 % Favored : 86.13 % 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: 0.44 (0.14), residues: 4016 helix: 0.64 (0.14), residues: 1504 sheet: -0.40 (0.19), residues: 768 loop : 0.55 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 54 HIS 0.005 0.001 HIS F 203 PHE 0.011 0.001 PHE B 531 TYR 0.015 0.001 TYR F 163 ARG 0.005 0.000 ARG D 498 *********************** 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 278 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 3.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.9103 (mmm) cc_final: 0.8433 (mmt) REVERT: D 529 MET cc_start: 0.7132 (ptp) cc_final: 0.6380 (ptp) outliers start: 57 outliers final: 52 residues processed: 259 average time/residue: 0.8508 time to fit residues: 352.4712 Evaluate side-chains 272 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain G residue 533 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 0.7980 chunk 43 optimal weight: 20.0000 chunk 220 optimal weight: 0.5980 chunk 282 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 325 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 385 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32568 Z= 0.186 Angle : 0.491 7.700 44232 Z= 0.241 Chirality : 0.041 0.146 4960 Planarity : 0.004 0.059 5656 Dihedral : 7.572 88.522 4456 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 1.43 % Allowed : 12.79 % Favored : 85.78 % 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: 0.65 (0.14), residues: 4016 helix: 0.81 (0.14), residues: 1508 sheet: -0.30 (0.19), residues: 772 loop : 0.69 (0.16), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 54 HIS 0.005 0.001 HIS F 66 PHE 0.010 0.001 PHE B 531 TYR 0.013 0.001 TYR F 163 ARG 0.005 0.000 ARG D 498 *********************** 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 278 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 3.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7024 (tpp) cc_final: 0.6757 (tpp) REVERT: C 382 MET cc_start: 0.9092 (mmm) cc_final: 0.8415 (mmt) outliers start: 49 outliers final: 44 residues processed: 263 average time/residue: 0.8693 time to fit residues: 362.9312 Evaluate side-chains 267 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 190 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32568 Z= 0.205 Angle : 0.500 7.328 44232 Z= 0.245 Chirality : 0.041 0.155 4960 Planarity : 0.004 0.060 5656 Dihedral : 7.413 85.216 4456 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % 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: 0.71 (0.14), residues: 4016 helix: 0.88 (0.14), residues: 1496 sheet: -0.31 (0.19), residues: 772 loop : 0.72 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 54 HIS 0.005 0.001 HIS F 66 PHE 0.010 0.001 PHE B 531 TYR 0.012 0.001 TYR F 163 ARG 0.005 0.000 ARG E 498 *********************** 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 279 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7072 (tpp) cc_final: 0.6802 (tpp) REVERT: C 382 MET cc_start: 0.9103 (mmm) cc_final: 0.8466 (mmt) outliers start: 54 outliers final: 49 residues processed: 262 average time/residue: 0.8542 time to fit residues: 355.1897 Evaluate side-chains 267 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU 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: 0.8980 chunk 359 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 324 optimal weight: 0.0040 chunk 339 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32568 Z= 0.234 Angle : 0.511 7.565 44232 Z= 0.252 Chirality : 0.041 0.166 4960 Planarity : 0.004 0.061 5656 Dihedral : 7.339 85.145 4456 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.38 % Favored : 95.57 % Rotamer: Outliers : 1.58 % Allowed : 12.79 % Favored : 85.63 % 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: 0.67 (0.14), residues: 4016 helix: 0.88 (0.14), residues: 1490 sheet: -0.36 (0.19), residues: 772 loop : 0.68 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 390 HIS 0.005 0.001 HIS F 66 PHE 0.011 0.001 PHE B 531 TYR 0.013 0.001 TYR F 163 ARG 0.008 0.000 ARG B 164 *********************** 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 277 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 223 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.7077 (tpp) cc_final: 0.6808 (tpp) REVERT: C 382 MET cc_start: 0.9116 (mmm) cc_final: 0.8454 (mmt) REVERT: D 120 ASP cc_start: 0.8338 (t0) cc_final: 0.8044 (t70) outliers start: 54 outliers final: 50 residues processed: 262 average time/residue: 0.8733 time to fit residues: 367.8135 Evaluate side-chains 270 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 220 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 1.9990 chunk 379 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 398 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 317 optimal weight: 0.0040 chunk 32 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2058 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= 0.295 Angle : 0.544 9.531 44232 Z= 0.270 Chirality : 0.042 0.189 4960 Planarity : 0.004 0.063 5656 Dihedral : 7.403 86.085 4456 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 1.46 % Allowed : 13.03 % Favored : 85.51 % 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: 0.50 (0.14), residues: 4016 helix: 0.75 (0.14), residues: 1490 sheet: -0.51 (0.19), residues: 772 loop : 0.60 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 390 HIS 0.006 0.001 HIS F 203 PHE 0.013 0.001 PHE E 385 TYR 0.014 0.001 TYR F 163 ARG 0.006 0.000 ARG B 164 ********************** 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 272 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 382 MET cc_start: 0.9132 (mmm) cc_final: 0.8494 (mmt) REVERT: D 120 ASP cc_start: 0.8423 (t0) cc_final: 0.8087 (t70) REVERT: E 505 MET cc_start: 0.7194 (mmm) cc_final: 0.6969 (mmt) outliers start: 50 outliers final: 50 residues processed: 262 average time/residue: 0.8775 time to fit residues: 366.1324 Evaluate side-chains 268 residues out of total 3424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 218 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 384 LYS Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 52 CYS Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 275 CYS Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 502 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 275 CYS Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 423 LEU Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 468 LEU Chi-restraints excluded: chain G residue 171 GLU Chi-restraints excluded: chain G residue 391 MET Chi-restraints excluded: chain G residue 464 MET Chi-restraints excluded: chain H residue 376 ASP Chi-restraints excluded: chain H residue 384 LYS Chi-restraints excluded: chain H residue 392 LEU Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 0.7980 chunk 338 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 326 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.167464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129509 restraints weight = 185243.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.117726 restraints weight = 212542.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114579 restraints weight = 216282.373| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 32568 Z= 0.464 Angle : 0.636 6.680 44232 Z= 0.323 Chirality : 0.045 0.239 4960 Planarity : 0.005 0.068 5656 Dihedral : 7.793 89.928 4455 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 1.52 % Allowed : 13.11 % Favored : 85.37 % 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: -0.08 (0.14), residues: 4016 helix: 0.30 (0.14), residues: 1490 sheet: -0.88 (0.19), residues: 772 loop : 0.28 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 409 HIS 0.008 0.001 HIS F 203 PHE 0.024 0.002 PHE E 385 TYR 0.017 0.002 TYR F 163 ARG 0.006 0.001 ARG B 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9177.06 seconds wall clock time: 160 minutes 57.58 seconds (9657.58 seconds total)