Starting phenix.real_space_refine on Thu Apr 11 21:46:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2024/6pby_20295.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 15412 2.51 5 N 3964 2.21 5 O 4328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 342": "OD1" <-> "OD2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 342": "OD1" <-> "OD2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ASP 539": "OD1" <-> "OD2" Residue "C ASP 560": "OD1" <-> "OD2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ASP 615": "OD1" <-> "OD2" Residue "C TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C GLU 689": "OE1" <-> "OE2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "C PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 254": "OD1" <-> "OD2" Residue "E PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ASP 283": "OD1" <-> "OD2" Residue "E ASP 342": "OD1" <-> "OD2" Residue "E TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ASP 539": "OD1" <-> "OD2" Residue "E ASP 560": "OD1" <-> "OD2" Residue "E ARG 564": "NH1" <-> "NH2" Residue "E PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 600": "OE1" <-> "OE2" Residue "E ASP 615": "OD1" <-> "OD2" Residue "E TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 666": "NH1" <-> "NH2" Residue "E ARG 675": "NH1" <-> "NH2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E GLU 691": "OE1" <-> "OE2" Residue "E PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 254": "OD1" <-> "OD2" Residue "G PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 264": "OD1" <-> "OD2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G ASP 283": "OD1" <-> "OD2" Residue "G ASP 342": "OD1" <-> "OD2" Residue "G TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "G ARG 493": "NH1" <-> "NH2" Residue "G TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 508": "NH1" <-> "NH2" Residue "G ASP 539": "OD1" <-> "OD2" Residue "G ASP 560": "OD1" <-> "OD2" Residue "G ARG 564": "NH1" <-> "NH2" Residue "G PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 600": "OE1" <-> "OE2" Residue "G ASP 615": "OD1" <-> "OD2" Residue "G TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 666": "NH1" <-> "NH2" Residue "G ARG 675": "NH1" <-> "NH2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G GLU 691": "OE1" <-> "OE2" Residue "G PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "D" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "F" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "H" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 870 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 149 Chain: "C" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "E" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "G" Number of atoms: 5088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5088 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 22, 'TRANS': 652} Chain breaks: 4 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Time building chain proxies: 12.69, per 1000 atoms: 0.53 Number of scatterers: 23832 At special positions: 0 Unit cell: (155, 155, 143, 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 4328 8.00 N 3964 7.00 C 15412 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: 8.90 Conformation dependent library (CDL) restraints added in 4.1 seconds 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6200 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 62.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.367A 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 138 removed outlier: 3.884A pdb=" N GLN A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 334 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.930A 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 550 Processing helix chain 'A' and resid 559 through 568 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: 3.853A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG A 712 " --> pdb=" O HIS A 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.690A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY B 113 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 65 through 75 removed outlier: 3.689A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY D 113 " --> pdb=" O MET D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.734A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP F 20 " --> pdb=" O PHE F 16 " (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 65 through 75 removed outlier: 3.690A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU F 83 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.566A pdb=" N GLY F 113 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.704A pdb=" N ASP H 20 " --> pdb=" O PHE H 16 " (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 65 through 75 removed outlier: 3.690A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 3.609A pdb=" N GLU H 83 " --> pdb=" O THR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.565A pdb=" N GLY H 113 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.735A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE C 21 " --> pdb=" O PHE C 17 " (cutoff:3.500A) removed outlier: 4.367A 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 138 removed outlier: 3.885A pdb=" N GLN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU C 334 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 379 removed outlier: 3.949A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 499 removed outlier: 3.808A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.931A 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 550 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: 3.853A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG C 712 " --> pdb=" O HIS C 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU C 713 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 76 through 90 Processing helix chain 'E' and resid 133 through 138 removed outlier: 3.885A pdb=" N GLN E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 242 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL E 328 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 334 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 379 removed outlier: 3.950A pdb=" N PHE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 400 Processing helix chain 'E' and resid 418 through 435 Processing helix chain 'E' and resid 446 through 499 removed outlier: 3.810A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 521 Processing helix chain 'E' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS E 532 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 545 Processing helix chain 'E' and resid 545 through 550 Processing helix chain 'E' and resid 559 through 568 Processing helix chain 'E' and resid 620 through 625 Processing helix chain 'E' and resid 647 through 657 Processing helix chain 'E' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 696 Processing helix chain 'E' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG E 712 " --> pdb=" O HIS E 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU E 713 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 26 removed outlier: 3.514A pdb=" N ILE G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 67 through 71 Processing helix chain 'G' and resid 76 through 90 Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.884A pdb=" N GLN G 138 " --> pdb=" O THR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 175 through 194 removed outlier: 3.805A pdb=" N VAL G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 242 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 271 Processing helix chain 'G' and resid 283 through 303 removed outlier: 4.041A pdb=" N LYS G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE G 298 " --> pdb=" O THR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 4.196A pdb=" N VAL G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 334 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 removed outlier: 3.799A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 379 removed outlier: 3.951A pdb=" N PHE G 379 " --> pdb=" O ASP G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 400 Processing helix chain 'G' and resid 418 through 435 Processing helix chain 'G' and resid 446 through 499 removed outlier: 3.809A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN G 481 " --> pdb=" O GLN G 477 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 521 Processing helix chain 'G' and resid 524 through 532 removed outlier: 3.931A pdb=" N CYS G 532 " --> pdb=" O VAL G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 545 Processing helix chain 'G' and resid 545 through 550 Processing helix chain 'G' and resid 559 through 568 Processing helix chain 'G' and resid 620 through 625 Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 657 through 668 removed outlier: 3.853A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 696 Processing helix chain 'G' and resid 707 through 720 removed outlier: 4.105A pdb=" N ARG G 712 " --> pdb=" O HIS G 708 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU G 713 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A 45 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE A 30 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS A 643 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 594 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 645 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N CYS A 592 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL A 601 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 610 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 599 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER C 45 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE C 30 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS C 643 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL C 594 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE C 645 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 592 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 606 through 611 removed outlier: 6.573A pdb=" N VAL C 601 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 610 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 599 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU E 32 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER E 45 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE E 30 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 571 through 575 removed outlier: 6.830A pdb=" N HIS E 643 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL E 594 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE E 645 " --> pdb=" O CYS E 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS E 592 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR E 672 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL E 601 " --> pdb=" O VAL E 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE E 610 " --> pdb=" O LEU E 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 599 " --> pdb=" O ILE E 610 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 45 removed outlier: 6.475A pdb=" N LEU G 32 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER G 45 " --> pdb=" O PHE G 30 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE G 30 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 571 through 575 removed outlier: 6.831A pdb=" N HIS G 643 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL G 594 " --> pdb=" O HIS G 643 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 645 " --> pdb=" O CYS G 592 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS G 592 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR G 672 " --> pdb=" O VAL G 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 606 through 611 removed outlier: 6.572A pdb=" N VAL G 601 " --> pdb=" O VAL G 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE G 610 " --> pdb=" O LEU G 599 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 599 " --> pdb=" O ILE G 610 " (cutoff:3.500A) 1512 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: 7.87 Time building geometry restraints manager: 9.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7427 1.34 - 1.46: 5499 1.46 - 1.58: 11250 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 24372 Sorted by residual: bond pdb=" CB ASN G 441 " pdb=" CG ASN G 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.91e+00 bond pdb=" CB ASN E 441 " pdb=" CG ASN E 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN A 441 " pdb=" CG ASN A 441 " ideal model delta sigma weight residual 1.516 1.461 0.055 2.50e-02 1.60e+03 4.83e+00 bond pdb=" CB ASN C 441 " pdb=" CG ASN C 441 " ideal model delta sigma weight residual 1.516 1.462 0.054 2.50e-02 1.60e+03 4.75e+00 bond pdb=" CG1 ILE E 456 " pdb=" CD1 ILE E 456 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 ... (remaining 24367 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.20: 384 105.20 - 112.41: 12560 112.41 - 119.61: 8085 119.61 - 126.82: 11939 126.82 - 134.02: 340 Bond angle restraints: 33308 Sorted by residual: angle pdb=" CA ARG G 387 " pdb=" CB ARG G 387 " pdb=" CG ARG G 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG C 387 " pdb=" CB ARG C 387 " pdb=" CG ARG C 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG E 387 " pdb=" CB ARG E 387 " pdb=" CG ARG E 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA ARG A 387 " pdb=" CB ARG A 387 " pdb=" CG ARG A 387 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CB MET A 366 " pdb=" CG MET A 366 " pdb=" SD MET A 366 " ideal model delta sigma weight residual 112.70 125.57 -12.87 3.00e+00 1.11e-01 1.84e+01 ... (remaining 33303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 12666 17.14 - 34.29: 1162 34.29 - 51.43: 236 51.43 - 68.57: 44 68.57 - 85.72: 12 Dihedral angle restraints: 14120 sinusoidal: 4560 harmonic: 9560 Sorted by residual: dihedral pdb=" CA ILE A 194 " pdb=" C ILE A 194 " pdb=" N LEU A 195 " pdb=" CA LEU A 195 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 194 " pdb=" C ILE C 194 " pdb=" N LEU C 195 " pdb=" CA LEU C 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE E 194 " pdb=" C ILE E 194 " pdb=" N LEU E 195 " pdb=" CA LEU E 195 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2750 0.052 - 0.103: 886 0.103 - 0.155: 240 0.155 - 0.206: 32 0.206 - 0.258: 20 Chirality restraints: 3928 Sorted by residual: chirality pdb=" CB ILE G 140 " pdb=" CA ILE G 140 " pdb=" CG1 ILE G 140 " pdb=" CG2 ILE G 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 140 " pdb=" CA ILE C 140 " pdb=" CG1 ILE C 140 " pdb=" CG2 ILE C 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE A 140 " pdb=" CA ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CG2 ILE A 140 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 3925 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 366 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C MET E 366 " -0.052 2.00e-02 2.50e+03 pdb=" O MET E 366 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA E 367 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C MET G 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET G 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA G 367 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 366 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C MET A 366 " 0.051 2.00e-02 2.50e+03 pdb=" O MET A 366 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA A 367 " -0.018 2.00e-02 2.50e+03 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5864 2.78 - 3.31: 22799 3.31 - 3.84: 40975 3.84 - 4.37: 44736 4.37 - 4.90: 77811 Nonbonded interactions: 192185 Sorted by model distance: nonbonded pdb=" OH TYR A 198 " pdb=" OE1 GLU C 600 " model vdw 2.248 2.440 nonbonded pdb=" OH TYR C 198 " pdb=" OE1 GLU E 600 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR E 198 " pdb=" OE1 GLU G 600 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR G 446 " pdb=" OE1 GLU G 449 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 449 " model vdw 2.298 2.440 ... (remaining 192180 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.380 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 60.080 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 24372 Z= 0.515 Angle : 0.927 12.870 33308 Z= 0.499 Chirality : 0.056 0.258 3928 Planarity : 0.007 0.055 4248 Dihedral : 14.382 85.718 7920 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -3.45 (0.12), residues: 3220 helix: -2.06 (0.09), residues: 1788 sheet: -2.42 (0.28), residues: 228 loop : -2.36 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 222 HIS 0.010 0.002 HIS G 543 PHE 0.032 0.003 PHE E 475 TYR 0.039 0.003 TYR C 464 ARG 0.009 0.001 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8145 (t80) cc_final: 0.7903 (t80) REVERT: A 90 TYR cc_start: 0.7922 (m-80) cc_final: 0.7720 (m-10) REVERT: A 109 PHE cc_start: 0.7947 (m-80) cc_final: 0.7590 (m-10) REVERT: A 344 TYR cc_start: 0.4842 (m-80) cc_final: 0.4347 (m-80) REVERT: A 347 TYR cc_start: 0.4691 (m-80) cc_final: 0.4295 (t80) REVERT: A 376 TYR cc_start: 0.7854 (t80) cc_final: 0.7586 (t80) REVERT: A 519 MET cc_start: 0.7172 (ttm) cc_final: 0.6798 (tmm) REVERT: A 575 CYS cc_start: 0.6318 (m) cc_final: 0.5751 (p) REVERT: B 107 HIS cc_start: 0.6943 (t-90) cc_final: 0.6574 (t-170) REVERT: B 123 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7308 (tm-30) REVERT: D 107 HIS cc_start: 0.6469 (t-90) cc_final: 0.6266 (t70) REVERT: D 123 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7573 (tm-30) REVERT: D 127 GLU cc_start: 0.4810 (tt0) cc_final: 0.4575 (pt0) REVERT: H 123 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 17 PHE cc_start: 0.8111 (t80) cc_final: 0.7869 (t80) REVERT: C 90 TYR cc_start: 0.7921 (m-80) cc_final: 0.7719 (m-10) REVERT: C 109 PHE cc_start: 0.7940 (m-80) cc_final: 0.7557 (m-10) REVERT: C 344 TYR cc_start: 0.4849 (m-80) cc_final: 0.4362 (m-80) REVERT: C 347 TYR cc_start: 0.4735 (m-80) cc_final: 0.4304 (t80) REVERT: C 398 ASP cc_start: 0.7699 (t70) cc_final: 0.7498 (t0) REVERT: C 519 MET cc_start: 0.7129 (ttm) cc_final: 0.6752 (tmm) REVERT: C 575 CYS cc_start: 0.6231 (m) cc_final: 0.5657 (p) REVERT: C 615 ASP cc_start: 0.7418 (m-30) cc_final: 0.7105 (m-30) REVERT: E 17 PHE cc_start: 0.8110 (t80) cc_final: 0.7868 (t80) REVERT: E 109 PHE cc_start: 0.7907 (m-80) cc_final: 0.7550 (m-10) REVERT: E 344 TYR cc_start: 0.4860 (m-80) cc_final: 0.4372 (m-80) REVERT: E 347 TYR cc_start: 0.4745 (m-80) cc_final: 0.4325 (t80) REVERT: E 519 MET cc_start: 0.7114 (ttm) cc_final: 0.6722 (tmm) REVERT: E 575 CYS cc_start: 0.6151 (m) cc_final: 0.5575 (p) REVERT: E 615 ASP cc_start: 0.7511 (m-30) cc_final: 0.7216 (m-30) REVERT: E 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7713 (mm-40) REVERT: G 17 PHE cc_start: 0.8119 (t80) cc_final: 0.7877 (t80) REVERT: G 109 PHE cc_start: 0.7905 (m-80) cc_final: 0.7544 (m-10) REVERT: G 344 TYR cc_start: 0.4850 (m-80) cc_final: 0.4361 (m-80) REVERT: G 347 TYR cc_start: 0.4740 (m-80) cc_final: 0.4325 (t80) REVERT: G 519 MET cc_start: 0.7102 (ttm) cc_final: 0.6709 (tmm) REVERT: G 575 CYS cc_start: 0.6162 (m) cc_final: 0.5580 (p) REVERT: G 615 ASP cc_start: 0.7461 (m-30) cc_final: 0.7150 (m-30) REVERT: G 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7715 (mm-40) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3675 time to fit residues: 285.0821 Evaluate side-chains 331 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.2980 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 165 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 154 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 343 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 667 ASN B 107 HIS F 107 HIS C 93 ASN C 343 HIS C 545 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 667 ASN E 93 ASN E 343 HIS E 545 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 667 ASN G 93 ASN G 343 HIS G 545 ASN ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 667 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5650 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24372 Z= 0.188 Angle : 0.595 13.638 33308 Z= 0.307 Chirality : 0.041 0.159 3928 Planarity : 0.004 0.043 4248 Dihedral : 4.946 15.752 3456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.22 % Allowed : 15.49 % Favored : 82.29 % 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: -1.52 (0.14), residues: 3220 helix: -0.29 (0.11), residues: 1820 sheet: -2.00 (0.30), residues: 204 loop : -1.82 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 222 HIS 0.019 0.001 HIS D 107 PHE 0.015 0.001 PHE B 12 TYR 0.017 0.001 TYR C 464 ARG 0.004 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 399 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8102 (t80) cc_final: 0.7897 (t80) REVERT: A 344 TYR cc_start: 0.4846 (m-80) cc_final: 0.4494 (m-80) REVERT: A 347 TYR cc_start: 0.4618 (m-80) cc_final: 0.4215 (t80) REVERT: A 519 MET cc_start: 0.7150 (ttm) cc_final: 0.6770 (tmm) REVERT: A 575 CYS cc_start: 0.6194 (m) cc_final: 0.5580 (p) REVERT: D 123 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7540 (tm-30) REVERT: D 127 GLU cc_start: 0.5287 (tt0) cc_final: 0.4989 (pt0) REVERT: C 17 PHE cc_start: 0.8107 (t80) cc_final: 0.7905 (t80) REVERT: C 344 TYR cc_start: 0.4821 (m-80) cc_final: 0.4469 (m-80) REVERT: C 347 TYR cc_start: 0.4594 (m-80) cc_final: 0.4233 (t80) REVERT: C 442 ILE cc_start: 0.8152 (mm) cc_final: 0.7862 (mp) REVERT: C 519 MET cc_start: 0.7084 (ttm) cc_final: 0.6639 (tmm) REVERT: C 575 CYS cc_start: 0.6142 (m) cc_final: 0.5507 (p) REVERT: E 17 PHE cc_start: 0.8105 (t80) cc_final: 0.7894 (t80) REVERT: E 333 ARG cc_start: 0.7022 (mtt180) cc_final: 0.6779 (mtt90) REVERT: E 344 TYR cc_start: 0.4836 (m-80) cc_final: 0.4485 (m-80) REVERT: E 347 TYR cc_start: 0.4676 (m-80) cc_final: 0.4220 (t80) REVERT: E 442 ILE cc_start: 0.8153 (mm) cc_final: 0.7861 (mp) REVERT: E 519 MET cc_start: 0.7050 (ttm) cc_final: 0.6611 (tmm) REVERT: E 575 CYS cc_start: 0.6113 (m) cc_final: 0.5494 (p) REVERT: E 651 GLN cc_start: 0.7988 (mt0) cc_final: 0.7724 (mm-40) REVERT: G 17 PHE cc_start: 0.8086 (t80) cc_final: 0.7874 (t80) REVERT: G 333 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6772 (mtt90) REVERT: G 344 TYR cc_start: 0.4828 (m-80) cc_final: 0.4474 (m-80) REVERT: G 347 TYR cc_start: 0.4596 (m-80) cc_final: 0.4243 (t80) REVERT: G 442 ILE cc_start: 0.8157 (mm) cc_final: 0.7876 (mp) REVERT: G 519 MET cc_start: 0.7036 (ttm) cc_final: 0.6594 (tmm) REVERT: G 575 CYS cc_start: 0.6123 (m) cc_final: 0.5495 (p) outliers start: 49 outliers final: 14 residues processed: 430 average time/residue: 0.3013 time to fit residues: 216.1798 Evaluate side-chains 360 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 346 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN F 137 ASN H 137 ASN C 20 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24372 Z= 0.224 Angle : 0.597 12.719 33308 Z= 0.303 Chirality : 0.042 0.176 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.609 15.102 3456 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 17.53 % Favored : 80.71 % 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: -0.65 (0.14), residues: 3220 helix: 0.47 (0.12), residues: 1836 sheet: -1.55 (0.34), residues: 180 loop : -1.60 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 517 HIS 0.009 0.001 HIS D 107 PHE 0.020 0.001 PHE H 68 TYR 0.015 0.001 TYR E 230 ARG 0.003 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 354 time to evaluate : 2.798 Fit side-chains REVERT: A 344 TYR cc_start: 0.4843 (m-80) cc_final: 0.4502 (m-80) REVERT: A 347 TYR cc_start: 0.4596 (m-80) cc_final: 0.4225 (t80) REVERT: A 519 MET cc_start: 0.7137 (ttm) cc_final: 0.6714 (tmm) REVERT: D 123 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7523 (tm-30) REVERT: D 127 GLU cc_start: 0.5116 (tt0) cc_final: 0.4867 (pt0) REVERT: C 344 TYR cc_start: 0.4939 (m-80) cc_final: 0.4598 (m-80) REVERT: C 347 TYR cc_start: 0.4623 (m-80) cc_final: 0.4239 (t80) REVERT: C 519 MET cc_start: 0.7063 (ttm) cc_final: 0.6624 (tmm) REVERT: E 344 TYR cc_start: 0.4946 (m-80) cc_final: 0.4620 (m-80) REVERT: E 347 TYR cc_start: 0.4633 (m-80) cc_final: 0.4254 (t80) REVERT: E 442 ILE cc_start: 0.8097 (mm) cc_final: 0.7880 (mp) REVERT: E 519 MET cc_start: 0.7051 (ttm) cc_final: 0.6612 (tmm) REVERT: G 344 TYR cc_start: 0.4873 (m-80) cc_final: 0.4533 (m-80) REVERT: G 347 TYR cc_start: 0.4627 (m-80) cc_final: 0.4250 (t80) REVERT: G 519 MET cc_start: 0.7039 (ttm) cc_final: 0.6600 (tmm) outliers start: 39 outliers final: 19 residues processed: 375 average time/residue: 0.2976 time to fit residues: 188.3497 Evaluate side-chains 339 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 320 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain G residue 29 ASN Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 84 optimal weight: 0.0970 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 HIS ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 643 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24372 Z= 0.308 Angle : 0.630 13.229 33308 Z= 0.319 Chirality : 0.043 0.190 3928 Planarity : 0.004 0.050 4248 Dihedral : 4.531 16.143 3456 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.45 % Allowed : 18.16 % Favored : 79.39 % 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: -0.28 (0.15), residues: 3220 helix: 0.78 (0.12), residues: 1836 sheet: -1.73 (0.32), residues: 204 loop : -1.39 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 222 HIS 0.007 0.001 HIS E 543 PHE 0.016 0.002 PHE E 452 TYR 0.019 0.002 TYR E 230 ARG 0.007 0.001 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 343 time to evaluate : 2.867 Fit side-chains revert: symmetry clash REVERT: A 344 TYR cc_start: 0.4915 (m-80) cc_final: 0.4613 (m-80) REVERT: A 347 TYR cc_start: 0.4600 (m-80) cc_final: 0.4249 (t80) REVERT: A 519 MET cc_start: 0.7131 (ttm) cc_final: 0.6724 (tmm) REVERT: C 264 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: C 344 TYR cc_start: 0.4885 (m-80) cc_final: 0.4575 (m-80) REVERT: C 347 TYR cc_start: 0.4617 (m-80) cc_final: 0.4242 (t80) REVERT: C 519 MET cc_start: 0.7064 (ttm) cc_final: 0.6627 (tmm) REVERT: E 347 TYR cc_start: 0.4625 (m-80) cc_final: 0.4244 (t80) REVERT: E 519 MET cc_start: 0.7055 (ttm) cc_final: 0.6618 (tmm) REVERT: G 347 TYR cc_start: 0.4624 (m-80) cc_final: 0.4245 (t80) REVERT: G 519 MET cc_start: 0.7022 (ttm) cc_final: 0.6593 (tmm) outliers start: 54 outliers final: 30 residues processed: 378 average time/residue: 0.2983 time to fit residues: 192.3319 Evaluate side-chains 353 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 322 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 645 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 216 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 HIS ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24372 Z= 0.189 Angle : 0.579 12.344 33308 Z= 0.293 Chirality : 0.040 0.160 3928 Planarity : 0.003 0.040 4248 Dihedral : 4.332 15.820 3456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.68 % Allowed : 20.79 % Favored : 77.54 % 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: 0.08 (0.15), residues: 3220 helix: 1.07 (0.12), residues: 1840 sheet: -1.27 (0.35), residues: 180 loop : -1.31 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 222 HIS 0.003 0.001 HIS G 543 PHE 0.016 0.001 PHE A 429 TYR 0.018 0.001 TYR G 344 ARG 0.010 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 359 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 TYR cc_start: 0.4821 (m-80) cc_final: 0.4513 (m-80) REVERT: A 347 TYR cc_start: 0.4660 (m-80) cc_final: 0.4300 (t80) REVERT: A 519 MET cc_start: 0.7016 (ttm) cc_final: 0.6580 (tmm) REVERT: H 127 GLU cc_start: 0.5831 (mm-30) cc_final: 0.5313 (pt0) REVERT: C 336 ARG cc_start: 0.6522 (ttp-110) cc_final: 0.6113 (tpp80) REVERT: C 344 TYR cc_start: 0.4848 (m-80) cc_final: 0.4534 (m-80) REVERT: C 347 TYR cc_start: 0.4674 (m-80) cc_final: 0.4288 (t80) REVERT: C 519 MET cc_start: 0.7013 (ttm) cc_final: 0.6575 (tmm) REVERT: E 347 TYR cc_start: 0.4618 (m-80) cc_final: 0.4223 (t80) REVERT: E 519 MET cc_start: 0.7009 (ttm) cc_final: 0.6569 (tmm) REVERT: G 347 TYR cc_start: 0.4618 (m-80) cc_final: 0.4225 (t80) REVERT: G 519 MET cc_start: 0.7000 (ttm) cc_final: 0.6560 (tmm) outliers start: 37 outliers final: 19 residues processed: 378 average time/residue: 0.3070 time to fit residues: 193.5600 Evaluate side-chains 346 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 327 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.1980 chunk 282 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 313 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 103 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24372 Z= 0.172 Angle : 0.565 12.854 33308 Z= 0.286 Chirality : 0.040 0.162 3928 Planarity : 0.003 0.058 4248 Dihedral : 4.126 15.398 3456 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.26 % Allowed : 21.78 % Favored : 75.95 % 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: 0.31 (0.15), residues: 3220 helix: 1.29 (0.12), residues: 1844 sheet: -1.49 (0.34), residues: 204 loop : -1.20 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 220 HIS 0.002 0.001 HIS E 543 PHE 0.025 0.001 PHE H 68 TYR 0.016 0.001 TYR D 138 ARG 0.006 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 372 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 TYR cc_start: 0.4805 (m-80) cc_final: 0.4491 (m-80) REVERT: A 347 TYR cc_start: 0.4593 (m-80) cc_final: 0.4213 (t80) REVERT: A 483 ASN cc_start: 0.7816 (p0) cc_final: 0.7555 (m110) REVERT: A 519 MET cc_start: 0.7006 (ttm) cc_final: 0.6567 (tmm) REVERT: H 127 GLU cc_start: 0.6069 (mm-30) cc_final: 0.5549 (pt0) REVERT: C 344 TYR cc_start: 0.4728 (m-80) cc_final: 0.4405 (m-80) REVERT: C 347 TYR cc_start: 0.4613 (m-80) cc_final: 0.4224 (t80) REVERT: C 519 MET cc_start: 0.7005 (ttm) cc_final: 0.6573 (tmm) REVERT: E 347 TYR cc_start: 0.4612 (m-80) cc_final: 0.4209 (t80) REVERT: E 519 MET cc_start: 0.7034 (ttm) cc_final: 0.6589 (tmm) REVERT: G 347 TYR cc_start: 0.4638 (m-80) cc_final: 0.4243 (t80) REVERT: G 519 MET cc_start: 0.7027 (ttm) cc_final: 0.6592 (tmm) outliers start: 50 outliers final: 31 residues processed: 406 average time/residue: 0.3048 time to fit residues: 207.3751 Evaluate side-chains 358 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 552 HIS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 552 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 552 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 263 optimal weight: 0.1980 chunk 175 optimal weight: 3.9990 chunk 312 optimal weight: 0.0170 chunk 195 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 1.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24372 Z= 0.210 Angle : 0.582 12.770 33308 Z= 0.293 Chirality : 0.041 0.221 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.081 15.689 3456 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.54 % Allowed : 23.28 % Favored : 74.18 % 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: 0.45 (0.15), residues: 3220 helix: 1.37 (0.12), residues: 1852 sheet: -1.47 (0.34), residues: 204 loop : -1.10 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 220 HIS 0.004 0.001 HIS G 543 PHE 0.047 0.001 PHE C 261 TYR 0.017 0.001 TYR E 230 ARG 0.006 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 346 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 TYR cc_start: 0.4692 (m-80) cc_final: 0.4378 (m-80) REVERT: A 347 TYR cc_start: 0.4598 (m-80) cc_final: 0.4221 (t80) REVERT: A 483 ASN cc_start: 0.7835 (p0) cc_final: 0.7578 (m110) REVERT: A 519 MET cc_start: 0.7013 (ttm) cc_final: 0.6577 (tmm) REVERT: H 127 GLU cc_start: 0.5887 (mm-30) cc_final: 0.5330 (pt0) REVERT: C 344 TYR cc_start: 0.4768 (m-80) cc_final: 0.4445 (m-80) REVERT: C 347 TYR cc_start: 0.4582 (m-80) cc_final: 0.4197 (t80) REVERT: C 519 MET cc_start: 0.7000 (ttm) cc_final: 0.6567 (tmm) REVERT: E 347 TYR cc_start: 0.4614 (m-80) cc_final: 0.4217 (t80) REVERT: E 519 MET cc_start: 0.7045 (ttm) cc_final: 0.6599 (tmm) REVERT: G 336 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.6241 (tpp80) REVERT: G 347 TYR cc_start: 0.4619 (m-80) cc_final: 0.4226 (t80) REVERT: G 519 MET cc_start: 0.6959 (ttm) cc_final: 0.6534 (tmm) outliers start: 56 outliers final: 41 residues processed: 386 average time/residue: 0.3041 time to fit residues: 196.9644 Evaluate side-chains 373 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 332 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 552 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24372 Z= 0.317 Angle : 0.640 14.001 33308 Z= 0.323 Chirality : 0.042 0.221 3928 Planarity : 0.004 0.039 4248 Dihedral : 4.248 16.350 3456 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.35 % Allowed : 22.74 % Favored : 73.91 % 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: 0.44 (0.15), residues: 3220 helix: 1.37 (0.12), residues: 1844 sheet: -1.54 (0.34), residues: 204 loop : -1.07 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 220 HIS 0.006 0.001 HIS C 543 PHE 0.024 0.002 PHE H 68 TYR 0.021 0.002 TYR E 230 ARG 0.005 0.001 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 336 time to evaluate : 2.707 Fit side-chains REVERT: A 336 ARG cc_start: 0.6665 (ttp-110) cc_final: 0.6228 (tpp80) REVERT: A 347 TYR cc_start: 0.4679 (m-80) cc_final: 0.4317 (t80) REVERT: A 519 MET cc_start: 0.7042 (ttm) cc_final: 0.6613 (tmm) REVERT: H 127 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5602 (pt0) REVERT: C 347 TYR cc_start: 0.4666 (m-80) cc_final: 0.4305 (t80) REVERT: C 519 MET cc_start: 0.7013 (ttm) cc_final: 0.6577 (tmm) REVERT: E 336 ARG cc_start: 0.6639 (ttp-110) cc_final: 0.6200 (tpp80) REVERT: E 347 TYR cc_start: 0.4685 (m-80) cc_final: 0.4294 (t80) REVERT: E 519 MET cc_start: 0.7024 (ttm) cc_final: 0.6585 (tmm) REVERT: G 347 TYR cc_start: 0.4718 (m-80) cc_final: 0.4329 (t80) REVERT: G 519 MET cc_start: 0.6987 (ttm) cc_final: 0.6565 (tmm) outliers start: 74 outliers final: 57 residues processed: 391 average time/residue: 0.2960 time to fit residues: 195.3592 Evaluate side-chains 378 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 321 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 645 ILE Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 5.9990 chunk 299 optimal weight: 0.9990 chunk 272 optimal weight: 0.0370 chunk 291 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24372 Z= 0.214 Angle : 0.606 12.919 33308 Z= 0.307 Chirality : 0.041 0.196 3928 Planarity : 0.003 0.040 4248 Dihedral : 4.193 18.146 3456 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.58 % Allowed : 23.96 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 3220 helix: 1.49 (0.12), residues: 1848 sheet: -1.42 (0.34), residues: 204 loop : -1.10 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 220 HIS 0.004 0.001 HIS C 543 PHE 0.039 0.001 PHE E 261 TYR 0.025 0.002 TYR C 55 ARG 0.006 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 351 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ARG cc_start: 0.6603 (ttp-110) cc_final: 0.6228 (tpp80) REVERT: A 347 TYR cc_start: 0.4682 (m-80) cc_final: 0.4312 (t80) REVERT: A 519 MET cc_start: 0.6998 (ttm) cc_final: 0.6570 (tmm) REVERT: H 127 GLU cc_start: 0.5885 (mm-30) cc_final: 0.5347 (pt0) REVERT: C 347 TYR cc_start: 0.4667 (m-80) cc_final: 0.4297 (t80) REVERT: C 519 MET cc_start: 0.6997 (ttm) cc_final: 0.6567 (tmm) REVERT: E 347 TYR cc_start: 0.4681 (m-80) cc_final: 0.4294 (t80) REVERT: E 519 MET cc_start: 0.6993 (ttm) cc_final: 0.6561 (tmm) REVERT: G 336 ARG cc_start: 0.6502 (ttp-110) cc_final: 0.6238 (tpp80) REVERT: G 347 TYR cc_start: 0.4620 (m-80) cc_final: 0.4232 (t80) REVERT: G 519 MET cc_start: 0.6966 (ttm) cc_final: 0.6547 (tmm) outliers start: 57 outliers final: 41 residues processed: 391 average time/residue: 0.3112 time to fit residues: 204.3537 Evaluate side-chains 367 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 326 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 552 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 322 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 24372 Z= 0.359 Angle : 0.677 13.974 33308 Z= 0.343 Chirality : 0.043 0.206 3928 Planarity : 0.004 0.039 4248 Dihedral : 4.335 17.656 3456 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 23.73 % Favored : 73.87 % 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: 0.46 (0.15), residues: 3220 helix: 1.39 (0.12), residues: 1844 sheet: -1.43 (0.34), residues: 204 loop : -1.10 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 220 HIS 0.007 0.001 HIS C 543 PHE 0.036 0.002 PHE C 261 TYR 0.022 0.002 TYR E 230 ARG 0.005 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6440 Ramachandran restraints generated. 3220 Oldfield, 0 Emsley, 3220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 326 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.6341 (tpp80) REVERT: A 347 TYR cc_start: 0.4669 (m-80) cc_final: 0.4297 (t80) REVERT: A 519 MET cc_start: 0.7020 (ttm) cc_final: 0.6596 (tmm) REVERT: H 127 GLU cc_start: 0.5884 (mm-30) cc_final: 0.5380 (pt0) REVERT: C 347 TYR cc_start: 0.4680 (m-80) cc_final: 0.4303 (t80) REVERT: C 519 MET cc_start: 0.7019 (ttm) cc_final: 0.6591 (tmm) REVERT: E 336 ARG cc_start: 0.6534 (ttp-110) cc_final: 0.6165 (tpp80) REVERT: E 347 TYR cc_start: 0.4683 (m-80) cc_final: 0.4318 (t80) REVERT: E 519 MET cc_start: 0.7014 (ttm) cc_final: 0.6585 (tmm) REVERT: G 336 ARG cc_start: 0.6516 (ttp-110) cc_final: 0.6289 (tpp80) REVERT: G 347 TYR cc_start: 0.4689 (m-80) cc_final: 0.4324 (t80) REVERT: G 519 MET cc_start: 0.6958 (ttm) cc_final: 0.6533 (tmm) outliers start: 53 outliers final: 46 residues processed: 363 average time/residue: 0.3088 time to fit residues: 186.6027 Evaluate side-chains 368 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain E residue 462 LEU Chi-restraints excluded: chain E residue 530 GLN Chi-restraints excluded: chain E residue 645 ILE Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 341 LEU Chi-restraints excluded: chain G residue 447 ASP Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 645 ILE Chi-restraints excluded: chain G residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 264 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114444 restraints weight = 51205.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113209 restraints weight = 44547.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114389 restraints weight = 46863.643| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24372 Z= 0.320 Angle : 0.658 13.620 33308 Z= 0.336 Chirality : 0.043 0.188 3928 Planarity : 0.004 0.040 4248 Dihedral : 4.395 17.607 3456 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.08 % Allowed : 25.05 % Favored : 72.87 % 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: 0.46 (0.15), residues: 3220 helix: 1.40 (0.12), residues: 1844 sheet: -1.40 (0.34), residues: 204 loop : -1.11 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 220 HIS 0.006 0.001 HIS A 543 PHE 0.034 0.002 PHE C 261 TYR 0.022 0.002 TYR E 230 ARG 0.005 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.79 seconds wall clock time: 85 minutes 1.10 seconds (5101.10 seconds total)