Starting phenix.real_space_refine on Tue Mar 19 15:53:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eow_28487/03_2024/8eow_28487.pdb" } resolution = 3.9 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= 0.004 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15892 2.51 5 N 4116 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 569": "OE1" <-> "OE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 569": "OE1" <-> "OE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "D" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 13.38, per 1000 atoms: 0.54 Number of scatterers: 24628 At special positions: 0 Unit cell: (165.24, 165.24, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4492 8.00 N 4116 7.00 C 15892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 5.1 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 65.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 4.231A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.745A pdb=" N LYS A 137 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.812A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.008A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 241 removed outlier: 3.683A pdb=" N TRP A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 268 removed outlier: 3.536A pdb=" N VAL A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.913A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.910A pdb=" N ILE A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.651A pdb=" N LEU A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.715A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.761A pdb=" N VAL A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.796A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 removed outlier: 3.644A pdb=" N ILE A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 499 removed outlier: 5.304A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 removed outlier: 4.501A pdb=" N ARG A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.762A pdb=" N CYS A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.733A pdb=" N GLU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 removed outlier: 4.014A pdb=" N GLU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.783A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG A 666 " --> pdb=" O HIS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'E' and resid 7 through 10 removed outlier: 3.593A pdb=" N ALA E 10 " --> pdb=" O GLU E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.247A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.627A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 removed outlier: 3.773A pdb=" N ALA E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 removed outlier: 4.231A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.736A pdb=" N LYS D 137 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.809A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.006A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 241 removed outlier: 3.678A pdb=" N TRP D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.530A pdb=" N VAL D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 removed outlier: 3.921A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.910A pdb=" N ILE D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.644A pdb=" N LEU D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 333 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 4.812A pdb=" N ASP D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N HIS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 3.744A pdb=" N VAL D 351 " --> pdb=" O TYR D 347 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.845A pdb=" N ALA D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 436 removed outlier: 3.646A pdb=" N ILE D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 499 removed outlier: 5.301A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 removed outlier: 4.522A pdb=" N ARG D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.765A pdb=" N CYS D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.734A pdb=" N GLU D 551 " --> pdb=" O LYS D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.779A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG D 666 " --> pdb=" O HIS D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 695 Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 4.233A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.727A pdb=" N LYS C 137 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.809A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.005A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 241 removed outlier: 3.677A pdb=" N TRP C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.530A pdb=" N VAL C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 removed outlier: 3.926A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.911A pdb=" N ILE C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.628A pdb=" N LEU C 332 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 333 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 4.820A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HIS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 379 removed outlier: 3.748A pdb=" N VAL C 351 " --> pdb=" O TYR C 347 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 removed outlier: 3.860A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 removed outlier: 3.647A pdb=" N ILE C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 499 removed outlier: 5.300A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 removed outlier: 4.499A pdb=" N ARG C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.767A pdb=" N CYS C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 removed outlier: 3.739A pdb=" N GLU C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.764A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 666 " --> pdb=" O HIS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 695 Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 4.239A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.738A pdb=" N LYS B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.810A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.011A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 241 removed outlier: 3.726A pdb=" N TRP B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.535A pdb=" N VAL B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.925A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.896A pdb=" N ILE B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.705A pdb=" N LEU B 332 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 333 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 4.794A pdb=" N ASP B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 379 removed outlier: 3.790A pdb=" N VAL B 351 " --> pdb=" O TYR B 347 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.869A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 436 removed outlier: 3.615A pdb=" N ILE B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 499 removed outlier: 5.301A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 removed outlier: 4.497A pdb=" N ARG B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.768A pdb=" N CYS B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.739A pdb=" N GLU B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.724A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG B 666 " --> pdb=" O HIS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 695 Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'H' and resid 7 through 10 removed outlier: 3.571A pdb=" N ALA H 10 " --> pdb=" O GLU H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 7 through 10' Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.233A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 3.612A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.867A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 10 removed outlier: 3.568A pdb=" N ALA G 10 " --> pdb=" O GLU G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 10' Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.254A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.623A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 147 removed outlier: 3.712A pdb=" N ALA G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 10 removed outlier: 3.566A pdb=" N ALA F 10 " --> pdb=" O GLU F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 7 through 10' Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.275A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.568A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.625A pdb=" N ALA F 128 " --> pdb=" O MET F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.772A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.582A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.582A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.501A pdb=" N CYS A 640 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 617 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.826A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 607 through 611 removed outlier: 4.125A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU D 32 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU D 32 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'D' and resid 571 through 575 removed outlier: 6.434A pdb=" N ASP D 641 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 617 " --> pdb=" O CYS D 592 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 615 " --> pdb=" O VAL D 594 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 618 " --> pdb=" O TYR D 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.826A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 607 through 611 removed outlier: 4.114A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB7, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.500A pdb=" N CYS C 640 " --> pdb=" O CYS C 575 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 617 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.838A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 607 through 611 removed outlier: 4.125A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.500A pdb=" N CYS B 640 " --> pdb=" O CYS B 575 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 641 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 617 " --> pdb=" O CYS B 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 615 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 618 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.808A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 607 through 611 removed outlier: 4.132A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4332 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: 8.80 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8020 1.34 - 1.46: 6091 1.46 - 1.58: 10881 1.58 - 1.70: 0 1.70 - 1.81: 196 Bond restraints: 25188 Sorted by residual: bond pdb=" CG1 ILE D 456 " pdb=" CD1 ILE D 456 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.36e-01 bond pdb=" CG1 ILE A 456 " pdb=" CD1 ILE A 456 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.82e-01 bond pdb=" CG1 ILE B 456 " pdb=" CD1 ILE B 456 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.80e-01 bond pdb=" CG1 ILE C 456 " pdb=" CD1 ILE C 456 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.75e-01 bond pdb=" CB ASP C 254 " pdb=" CG ASP C 254 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.31e-01 ... (remaining 25183 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.01: 446 106.01 - 113.02: 13644 113.02 - 120.04: 8703 120.04 - 127.05: 11381 127.05 - 134.06: 270 Bond angle restraints: 34444 Sorted by residual: angle pdb=" CA LEU A 331 " pdb=" CB LEU A 331 " pdb=" CG LEU A 331 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" CB MET F 144 " pdb=" CG MET F 144 " pdb=" SD MET F 144 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" CA LEU C 331 " pdb=" CB LEU C 331 " pdb=" CG LEU C 331 " ideal model delta sigma weight residual 116.30 125.96 -9.66 3.50e+00 8.16e-02 7.62e+00 angle pdb=" CA LEU B 292 " pdb=" CB LEU B 292 " pdb=" CG LEU B 292 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU B 331 " pdb=" CB LEU B 331 " pdb=" CG LEU B 331 " ideal model delta sigma weight residual 116.30 125.88 -9.58 3.50e+00 8.16e-02 7.50e+00 ... (remaining 34439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12699 17.11 - 34.22: 1506 34.22 - 51.33: 359 51.33 - 68.44: 49 68.44 - 85.55: 27 Dihedral angle restraints: 14640 sinusoidal: 4764 harmonic: 9876 Sorted by residual: dihedral pdb=" CA GLU C 377 " pdb=" C GLU C 377 " pdb=" N ILE C 378 " pdb=" CA ILE C 378 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU D 377 " pdb=" C GLU D 377 " pdb=" N ILE D 378 " pdb=" CA ILE D 378 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU A 377 " pdb=" C GLU A 377 " pdb=" N ILE A 378 " pdb=" CA ILE A 378 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2300 0.027 - 0.053: 1087 0.053 - 0.080: 404 0.080 - 0.106: 189 0.106 - 0.133: 72 Chirality restraints: 4052 Sorted by residual: chirality pdb=" CA ILE B 442 " pdb=" N ILE B 442 " pdb=" C ILE B 442 " pdb=" CB ILE B 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 442 " pdb=" N ILE A 442 " pdb=" C ILE A 442 " pdb=" CB ILE A 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE D 442 " pdb=" N ILE D 442 " pdb=" C ILE D 442 " pdb=" CB ILE D 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 4049 not shown) Planarity restraints: 4420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 704 " 0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO C 705 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 705 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 705 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 704 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 705 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 705 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 705 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 704 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 705 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " -0.030 5.00e-02 4.00e+02 ... (remaining 4417 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3115 2.75 - 3.29: 25000 3.29 - 3.82: 41242 3.82 - 4.36: 40702 4.36 - 4.90: 73545 Nonbonded interactions: 183604 Sorted by model distance: nonbonded pdb=" O ASN A 290 " pdb=" OG1 THR A 294 " model vdw 2.211 2.440 nonbonded pdb=" OH TYR B 582 " pdb=" OG SER B 590 " model vdw 2.215 2.440 nonbonded pdb=" OH TYR A 582 " pdb=" OG SER A 590 " model vdw 2.216 2.440 nonbonded pdb=" O ASN D 290 " pdb=" OG1 THR D 294 " model vdw 2.216 2.440 nonbonded pdb=" O ASN C 290 " pdb=" OG1 THR C 294 " model vdw 2.216 2.440 ... (remaining 183599 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' } ncs_group { reference = 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.740 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 66.390 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25188 Z= 0.176 Angle : 0.573 9.777 34444 Z= 0.296 Chirality : 0.039 0.133 4052 Planarity : 0.003 0.055 4420 Dihedral : 16.053 85.545 8240 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.35 % Allowed : 30.03 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 3340 helix: 1.98 (0.13), residues: 1932 sheet: -0.99 (0.34), residues: 208 loop : -0.30 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 295 HIS 0.006 0.001 HIS B 364 PHE 0.010 0.001 PHE A 429 TYR 0.016 0.001 TYR C 371 ARG 0.008 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 403 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 529 LEU cc_start: 0.7705 (tt) cc_final: 0.7257 (mm) REVERT: E 12 PHE cc_start: 0.6472 (t80) cc_final: 0.6121 (m-10) REVERT: E 136 VAL cc_start: 0.7633 (t) cc_final: 0.7266 (t) REVERT: D 529 LEU cc_start: 0.7730 (tt) cc_final: 0.7203 (mm) REVERT: C 529 LEU cc_start: 0.7684 (tt) cc_final: 0.7152 (mm) REVERT: B 292 LEU cc_start: 0.8164 (tt) cc_final: 0.7427 (mt) REVERT: H 12 PHE cc_start: 0.6489 (t80) cc_final: 0.6147 (m-10) REVERT: G 12 PHE cc_start: 0.6510 (t80) cc_final: 0.6133 (m-10) REVERT: G 105 LEU cc_start: 0.8069 (tp) cc_final: 0.7830 (tt) REVERT: F 12 PHE cc_start: 0.6482 (t80) cc_final: 0.5927 (m-10) REVERT: F 105 LEU cc_start: 0.7971 (tp) cc_final: 0.7761 (tt) outliers start: 8 outliers final: 8 residues processed: 409 average time/residue: 0.2938 time to fit residues: 201.9673 Evaluate side-chains 390 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 382 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain H residue 92 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 4.9990 chunk 254 optimal weight: 50.0000 chunk 141 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 40.0000 chunk 136 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 101 optimal weight: 40.0000 chunk 160 optimal weight: 20.0000 chunk 196 optimal weight: 0.0020 chunk 305 optimal weight: 8.9990 overall best weight: 4.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS D 583 HIS C 46 ASN C 56 HIS C 583 HIS B 46 ASN B 56 HIS ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25188 Z= 0.408 Angle : 0.646 8.425 34444 Z= 0.344 Chirality : 0.044 0.142 4052 Planarity : 0.004 0.053 4420 Dihedral : 4.635 56.780 3604 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.90 % Allowed : 28.28 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3340 helix: 1.56 (0.13), residues: 1936 sheet: -0.89 (0.34), residues: 208 loop : -0.58 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 222 HIS 0.013 0.002 HIS B 364 PHE 0.018 0.002 PHE B 664 TYR 0.020 0.002 TYR B 423 ARG 0.004 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 379 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8331 (tm-30) REVERT: E 12 PHE cc_start: 0.6489 (t80) cc_final: 0.6143 (m-10) REVERT: E 140 GLU cc_start: 0.5639 (mt-10) cc_final: 0.5289 (mt-10) REVERT: D 476 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 476 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 476 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8346 (tm-30) REVERT: H 12 PHE cc_start: 0.6552 (t80) cc_final: 0.6159 (m-10) REVERT: H 92 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6701 (t80) REVERT: G 12 PHE cc_start: 0.6548 (t80) cc_final: 0.6126 (m-10) REVERT: F 12 PHE cc_start: 0.6568 (t80) cc_final: 0.6016 (m-10) REVERT: F 92 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6363 (t80) outliers start: 135 outliers final: 83 residues processed: 483 average time/residue: 0.2971 time to fit residues: 244.0966 Evaluate side-chains 448 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 363 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 0.3980 chunk 207 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25188 Z= 0.166 Angle : 0.518 7.091 34444 Z= 0.271 Chirality : 0.039 0.140 4052 Planarity : 0.003 0.054 4420 Dihedral : 3.990 55.153 3596 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.02 % Allowed : 31.21 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3340 helix: 1.89 (0.13), residues: 1936 sheet: -0.69 (0.32), residues: 208 loop : -0.43 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 222 HIS 0.004 0.001 HIS B 364 PHE 0.014 0.001 PHE B 429 TYR 0.017 0.001 TYR C 371 ARG 0.003 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 387 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 MET cc_start: 0.7911 (mmp) cc_final: 0.7629 (mmp) REVERT: E 12 PHE cc_start: 0.6519 (t80) cc_final: 0.6150 (m-10) REVERT: H 12 PHE cc_start: 0.6546 (t80) cc_final: 0.6144 (m-10) REVERT: H 89 PHE cc_start: 0.5594 (m-80) cc_final: 0.5386 (m-80) REVERT: H 92 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6410 (t80) REVERT: G 12 PHE cc_start: 0.6574 (t80) cc_final: 0.6130 (m-10) REVERT: F 12 PHE cc_start: 0.6559 (t80) cc_final: 0.5976 (m-10) REVERT: F 92 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6277 (t80) outliers start: 92 outliers final: 57 residues processed: 460 average time/residue: 0.2824 time to fit residues: 219.7358 Evaluate side-chains 442 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 383 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 324 optimal weight: 50.0000 chunk 160 optimal weight: 9.9990 chunk 290 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25188 Z= 0.237 Angle : 0.545 7.197 34444 Z= 0.285 Chirality : 0.040 0.142 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.027 55.759 3596 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 6.21 % Allowed : 29.90 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.15), residues: 3340 helix: 1.89 (0.13), residues: 1936 sheet: -0.56 (0.31), residues: 208 loop : -0.49 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 517 HIS 0.008 0.001 HIS C 364 PHE 0.020 0.001 PHE C 95 TYR 0.015 0.001 TYR B 423 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 380 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 476 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 12 PHE cc_start: 0.6526 (t80) cc_final: 0.6167 (m-10) REVERT: D 476 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 434 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7872 (mt) REVERT: C 476 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 434 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8048 (mt) REVERT: B 476 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8303 (tm-30) REVERT: H 12 PHE cc_start: 0.6490 (t80) cc_final: 0.6140 (m-10) REVERT: H 89 PHE cc_start: 0.5544 (m-80) cc_final: 0.5246 (m-80) REVERT: H 92 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6407 (t80) REVERT: G 12 PHE cc_start: 0.6510 (t80) cc_final: 0.6143 (m-10) REVERT: F 12 PHE cc_start: 0.6538 (t80) cc_final: 0.5986 (m-10) outliers start: 142 outliers final: 108 residues processed: 498 average time/residue: 0.2880 time to fit residues: 243.1865 Evaluate side-chains 487 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 375 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 607 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 3.9990 chunk 184 optimal weight: 50.0000 chunk 4 optimal weight: 0.9980 chunk 241 optimal weight: 30.0000 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 HIS A 583 HIS D 46 ASN D 56 HIS C 56 HIS B 56 HIS B 583 HIS ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 25188 Z= 0.399 Angle : 0.654 8.774 34444 Z= 0.347 Chirality : 0.044 0.143 4052 Planarity : 0.004 0.053 4420 Dihedral : 4.486 55.612 3596 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 8.83 % Allowed : 28.32 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 3340 helix: 1.52 (0.13), residues: 1936 sheet: -0.50 (0.32), residues: 208 loop : -0.70 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 222 HIS 0.013 0.002 HIS C 364 PHE 0.025 0.002 PHE D 95 TYR 0.021 0.002 TYR A 423 ARG 0.004 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 379 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6834 (p90) REVERT: A 305 PRO cc_start: 0.6282 (Cg_endo) cc_final: 0.5885 (Cg_exo) REVERT: A 476 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 570 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8843 (m-10) REVERT: E 12 PHE cc_start: 0.6563 (t80) cc_final: 0.6152 (m-10) REVERT: E 92 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6630 (t80) REVERT: E 140 GLU cc_start: 0.5566 (mt-10) cc_final: 0.5362 (mt-10) REVERT: D 213 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6881 (p90) REVERT: D 305 PRO cc_start: 0.6362 (Cg_endo) cc_final: 0.5964 (Cg_exo) REVERT: D 432 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8388 (p) REVERT: D 476 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 213 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6957 (p90) REVERT: C 476 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 213 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6886 (p90) REVERT: B 476 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8324 (tm-30) REVERT: H 12 PHE cc_start: 0.6569 (t80) cc_final: 0.6137 (m-10) REVERT: H 92 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6348 (t80) REVERT: G 12 PHE cc_start: 0.6596 (t80) cc_final: 0.6140 (m-10) REVERT: F 12 PHE cc_start: 0.6428 (t80) cc_final: 0.5853 (m-10) outliers start: 202 outliers final: 140 residues processed: 554 average time/residue: 0.2785 time to fit residues: 263.2037 Evaluate side-chains 519 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 371 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 325 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25188 Z= 0.156 Angle : 0.538 7.340 34444 Z= 0.276 Chirality : 0.040 0.145 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.069 56.113 3596 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.85 % Allowed : 32.17 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.15), residues: 3340 helix: 1.81 (0.13), residues: 1932 sheet: -0.31 (0.31), residues: 208 loop : -0.52 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 222 HIS 0.004 0.001 HIS C 552 PHE 0.016 0.001 PHE F 141 TYR 0.015 0.001 TYR C 371 ARG 0.002 0.000 ARG D 537 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 407 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6563 (p90) REVERT: A 305 PRO cc_start: 0.6287 (Cg_endo) cc_final: 0.5961 (Cg_exo) REVERT: A 536 MET cc_start: 0.7977 (mmp) cc_final: 0.7642 (mmp) REVERT: E 12 PHE cc_start: 0.6416 (t80) cc_final: 0.6089 (m-10) REVERT: E 92 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6413 (t80) REVERT: D 213 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6622 (p90) REVERT: D 305 PRO cc_start: 0.6394 (Cg_endo) cc_final: 0.6053 (Cg_exo) REVERT: C 213 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6703 (p90) REVERT: B 213 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6630 (p90) REVERT: H 12 PHE cc_start: 0.6517 (t80) cc_final: 0.6112 (m-10) REVERT: H 92 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6324 (t80) REVERT: G 12 PHE cc_start: 0.6478 (t80) cc_final: 0.6088 (m-10) REVERT: F 12 PHE cc_start: 0.6482 (t80) cc_final: 0.5886 (m-10) outliers start: 111 outliers final: 86 residues processed: 493 average time/residue: 0.2854 time to fit residues: 236.6933 Evaluate side-chains 487 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 395 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 607 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 237 optimal weight: 0.0980 chunk 183 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 40.0000 chunk 202 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS C 56 HIS B 56 HIS ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 25188 Z= 0.317 Angle : 0.627 8.249 34444 Z= 0.324 Chirality : 0.043 0.154 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.266 56.534 3596 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.46 % Allowed : 31.73 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3340 helix: 1.67 (0.13), residues: 1936 sheet: -0.18 (0.32), residues: 208 loop : -0.60 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 222 HIS 0.010 0.001 HIS A 364 PHE 0.017 0.002 PHE H 141 TYR 0.019 0.002 TYR A 423 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 391 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 PRO cc_start: 0.6422 (Cg_endo) cc_final: 0.6086 (Cg_exo) REVERT: A 476 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8299 (tm-30) REVERT: E 12 PHE cc_start: 0.6439 (t80) cc_final: 0.6104 (m-10) REVERT: E 92 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6471 (t80) REVERT: D 305 PRO cc_start: 0.6414 (Cg_endo) cc_final: 0.6060 (Cg_exo) REVERT: D 476 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8270 (tm-30) REVERT: C 305 PRO cc_start: 0.6430 (Cg_endo) cc_final: 0.6090 (Cg_exo) REVERT: C 476 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 476 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8357 (tm-30) REVERT: H 12 PHE cc_start: 0.6530 (t80) cc_final: 0.6126 (m-10) REVERT: H 92 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6340 (t80) REVERT: G 12 PHE cc_start: 0.6478 (t80) cc_final: 0.6099 (m-10) REVERT: F 12 PHE cc_start: 0.6388 (t80) cc_final: 0.5833 (m-10) outliers start: 125 outliers final: 103 residues processed: 497 average time/residue: 0.2920 time to fit residues: 245.4913 Evaluate side-chains 494 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 389 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 562 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25188 Z= 0.185 Angle : 0.569 10.154 34444 Z= 0.289 Chirality : 0.040 0.140 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.059 55.587 3596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.81 % Allowed : 32.74 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.15), residues: 3340 helix: 1.83 (0.13), residues: 1932 sheet: -0.15 (0.31), residues: 208 loop : -0.53 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 222 HIS 0.005 0.001 HIS C 364 PHE 0.024 0.001 PHE F 141 TYR 0.013 0.001 TYR A 371 ARG 0.007 0.000 ARG F 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 408 time to evaluate : 2.632 Fit side-chains revert: symmetry clash REVERT: A 305 PRO cc_start: 0.6426 (Cg_endo) cc_final: 0.6096 (Cg_exo) REVERT: A 536 MET cc_start: 0.7931 (mmp) cc_final: 0.7641 (mmp) REVERT: E 12 PHE cc_start: 0.6399 (t80) cc_final: 0.6091 (m-10) REVERT: E 92 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6282 (t80) REVERT: D 305 PRO cc_start: 0.6532 (Cg_endo) cc_final: 0.6196 (Cg_exo) REVERT: D 536 MET cc_start: 0.8042 (mmp) cc_final: 0.7724 (mmp) REVERT: C 305 PRO cc_start: 0.6448 (Cg_endo) cc_final: 0.6126 (Cg_exo) REVERT: C 536 MET cc_start: 0.7909 (mmp) cc_final: 0.7608 (mmp) REVERT: B 213 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6722 (p90) REVERT: B 536 MET cc_start: 0.8008 (mmp) cc_final: 0.7680 (mmp) REVERT: H 12 PHE cc_start: 0.6447 (t80) cc_final: 0.6084 (m-10) REVERT: H 92 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6288 (t80) REVERT: G 12 PHE cc_start: 0.6463 (t80) cc_final: 0.6087 (m-10) REVERT: F 12 PHE cc_start: 0.6321 (t80) cc_final: 0.5790 (m-10) outliers start: 110 outliers final: 96 residues processed: 489 average time/residue: 0.2928 time to fit residues: 242.1070 Evaluate side-chains 502 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 403 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 131 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 10.0000 chunk 310 optimal weight: 50.0000 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 1.9990 chunk 285 optimal weight: 20.0000 chunk 300 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS C 56 HIS ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25188 Z= 0.352 Angle : 0.671 11.831 34444 Z= 0.346 Chirality : 0.044 0.197 4052 Planarity : 0.004 0.057 4420 Dihedral : 4.324 55.832 3596 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.59 % Allowed : 31.99 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3340 helix: 1.63 (0.13), residues: 1952 sheet: -0.13 (0.32), residues: 208 loop : -0.64 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 517 HIS 0.010 0.002 HIS D 364 PHE 0.029 0.002 PHE C 95 TYR 0.021 0.002 TYR D 423 ARG 0.005 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 386 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7018 (p90) REVERT: A 305 PRO cc_start: 0.6455 (Cg_endo) cc_final: 0.6112 (Cg_exo) REVERT: A 476 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8345 (tm-30) REVERT: E 12 PHE cc_start: 0.6406 (t80) cc_final: 0.6112 (m-10) REVERT: E 92 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6421 (t80) REVERT: D 305 PRO cc_start: 0.6534 (Cg_endo) cc_final: 0.6185 (Cg_exo) REVERT: D 476 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 213 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7189 (p90) REVERT: C 305 PRO cc_start: 0.6573 (Cg_endo) cc_final: 0.6219 (Cg_exo) REVERT: C 476 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 213 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7113 (p90) REVERT: B 476 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8398 (tm-30) REVERT: H 12 PHE cc_start: 0.6526 (t80) cc_final: 0.6118 (m-10) REVERT: H 92 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6327 (t80) REVERT: G 12 PHE cc_start: 0.6474 (t80) cc_final: 0.6082 (m-10) REVERT: F 12 PHE cc_start: 0.6359 (t80) cc_final: 0.5797 (m-10) REVERT: F 145 MET cc_start: 0.4035 (mtt) cc_final: 0.3805 (mtt) outliers start: 128 outliers final: 112 residues processed: 491 average time/residue: 0.2963 time to fit residues: 247.0970 Evaluate side-chains 501 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 384 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.6980 chunk 319 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 221 optimal weight: 8.9990 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 0.1980 chunk 266 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25188 Z= 0.158 Angle : 0.594 13.789 34444 Z= 0.297 Chirality : 0.040 0.212 4052 Planarity : 0.003 0.057 4420 Dihedral : 3.986 55.056 3596 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.98 % Allowed : 34.13 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.15), residues: 3340 helix: 1.86 (0.13), residues: 1932 sheet: -0.13 (0.31), residues: 208 loop : -0.49 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 222 HIS 0.004 0.001 HIS D 552 PHE 0.029 0.001 PHE F 141 TYR 0.013 0.001 TYR A 371 ARG 0.004 0.000 ARG C 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 408 time to evaluate : 2.865 Fit side-chains REVERT: A 305 PRO cc_start: 0.6423 (Cg_endo) cc_final: 0.6072 (Cg_exo) REVERT: E 12 PHE cc_start: 0.6381 (t80) cc_final: 0.6061 (m-10) REVERT: E 92 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6075 (t80) REVERT: D 305 PRO cc_start: 0.6501 (Cg_endo) cc_final: 0.6154 (Cg_exo) REVERT: C 305 PRO cc_start: 0.6496 (Cg_endo) cc_final: 0.6165 (Cg_exo) REVERT: H 12 PHE cc_start: 0.6422 (t80) cc_final: 0.6073 (m-10) REVERT: H 92 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6414 (t80) REVERT: G 12 PHE cc_start: 0.6430 (t80) cc_final: 0.6066 (m-10) REVERT: F 12 PHE cc_start: 0.6350 (t80) cc_final: 0.5820 (m-10) outliers start: 91 outliers final: 85 residues processed: 480 average time/residue: 0.2850 time to fit residues: 231.8107 Evaluate side-chains 481 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 394 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 74 optimal weight: 50.0000 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS C 483 ASN ** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.219863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.180900 restraints weight = 36590.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173891 restraints weight = 33989.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.174915 restraints weight = 34731.391| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 25188 Z= 0.333 Angle : 0.683 13.450 34444 Z= 0.349 Chirality : 0.044 0.241 4052 Planarity : 0.004 0.060 4420 Dihedral : 4.220 55.175 3596 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.72 % Allowed : 33.04 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3340 helix: 1.70 (0.13), residues: 1936 sheet: -0.13 (0.32), residues: 208 loop : -0.59 (0.19), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 517 HIS 0.012 0.001 HIS D 364 PHE 0.037 0.002 PHE H 141 TYR 0.019 0.002 TYR A 423 ARG 0.004 0.000 ARG D 677 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.21 seconds wall clock time: 88 minutes 23.04 seconds (5303.04 seconds total)