Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 21:15:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2023/6pby_20295.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2023/6pby_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_2023/6pby_20295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2023/6pby_20295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2023/6pby_20295.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pby_20295/04_2023/6pby_20295.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.36, per 1000 atoms: 0.52 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: 9.99 Conformation dependent library (CDL) restraints added in 3.6 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: 1.46 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: 9.00 Time building geometry restraints manager: 10.74 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.550 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 60.360 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.650 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3726 time to fit residues: 289.6204 Evaluate side-chains 320 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8180 ------------------------------------------------------------------------------- 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: 5.9990 chunk 245 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 545 ASN ** 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 651 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 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 667 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 24372 Z= 0.257 Angle : 0.636 14.651 33308 Z= 0.328 Chirality : 0.042 0.235 3928 Planarity : 0.004 0.040 4248 Dihedral : 5.065 16.000 3456 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.31 % 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: -1.57 (0.14), residues: 3220 helix: -0.36 (0.11), residues: 1824 sheet: -1.85 (0.32), residues: 180 loop : -1.84 (0.17), residues: 1216 *********************** 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 421 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 370 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 15 residues processed: 406 average time/residue: 0.3028 time to fit residues: 204.7530 Evaluate side-chains 349 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 334 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2130 time to fit residues: 9.6069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 294 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 292 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 236 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 552 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 552 HIS ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN E 552 HIS ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN G 552 HIS ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 24372 Z= 0.218 Angle : 0.596 12.788 33308 Z= 0.307 Chirality : 0.041 0.166 3928 Planarity : 0.004 0.040 4248 Dihedral : 4.674 15.676 3456 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.27 % 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: -0.68 (0.14), residues: 3220 helix: 0.43 (0.12), residues: 1832 sheet: -1.59 (0.35), residues: 180 loop : -1.58 (0.18), residues: 1208 *********************** 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 412 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 384 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 404 average time/residue: 0.3058 time to fit residues: 205.1507 Evaluate side-chains 347 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 336 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2076 time to fit residues: 8.2295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 7.9990 chunk 221 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 HIS ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS ** 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS E 651 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 24372 Z= 0.313 Angle : 0.639 14.443 33308 Z= 0.325 Chirality : 0.043 0.169 3928 Planarity : 0.004 0.059 4248 Dihedral : 4.590 15.562 3456 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3220 helix: 0.77 (0.12), residues: 1836 sheet: -1.65 (0.35), residues: 180 loop : -1.41 (0.19), residues: 1204 *********************** 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 386 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 347 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 375 average time/residue: 0.3044 time to fit residues: 191.1121 Evaluate side-chains 348 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 326 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2200 time to fit residues: 12.7512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 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: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.092 24372 Z= 0.451 Angle : 0.723 17.203 33308 Z= 0.365 Chirality : 0.045 0.222 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.774 17.388 3456 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 2.67 % 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: -0.38 (0.15), residues: 3220 helix: 0.64 (0.12), residues: 1844 sheet: -1.91 (0.35), residues: 180 loop : -1.32 (0.19), residues: 1196 *********************** 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 370 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 2.868 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 33 residues processed: 359 average time/residue: 0.3053 time to fit residues: 183.3608 Evaluate side-chains 324 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2169 time to fit residues: 17.1599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 313 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 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: 0.5650 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 24372 Z= 0.244 Angle : 0.617 15.063 33308 Z= 0.311 Chirality : 0.041 0.202 3928 Planarity : 0.004 0.041 4248 Dihedral : 4.500 15.855 3456 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3220 helix: 0.94 (0.12), residues: 1840 sheet: -2.00 (0.33), residues: 204 loop : -1.24 (0.19), residues: 1176 *********************** 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 397 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 358 time to evaluate : 2.932 Fit side-chains outliers start: 39 outliers final: 21 residues processed: 383 average time/residue: 0.3056 time to fit residues: 197.1869 Evaluate side-chains 348 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 327 time to evaluate : 2.835 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2284 time to fit residues: 12.8155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 178 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 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: 0.5649 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 0.067 24372 Z= 0.207 Angle : 0.601 14.179 33308 Z= 0.303 Chirality : 0.041 0.185 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.348 15.946 3456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.95 % 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: 0.15 (0.15), residues: 3220 helix: 1.13 (0.12), residues: 1840 sheet: -1.93 (0.34), residues: 204 loop : -1.14 (0.19), residues: 1176 *********************** 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 381 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 360 time to evaluate : 3.315 Fit side-chains outliers start: 21 outliers final: 9 residues processed: 368 average time/residue: 0.2968 time to fit residues: 184.8012 Evaluate side-chains 339 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 330 time to evaluate : 2.592 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2262 time to fit residues: 7.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 94 optimal weight: 0.0370 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 212 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 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: 0.5651 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 24372 Z= 0.207 Angle : 0.606 13.266 33308 Z= 0.305 Chirality : 0.041 0.234 3928 Planarity : 0.003 0.040 4248 Dihedral : 4.229 16.174 3456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.72 % 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: 0.24 (0.15), residues: 3220 helix: 1.23 (0.12), residues: 1840 sheet: -1.87 (0.34), residues: 204 loop : -1.13 (0.19), residues: 1176 *********************** 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 361 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 345 time to evaluate : 2.958 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 356 average time/residue: 0.3095 time to fit residues: 184.7571 Evaluate side-chains 332 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 327 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2090 time to fit residues: 5.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 275 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 GLN ** 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 24372 Z= 0.215 Angle : 0.618 12.751 33308 Z= 0.311 Chirality : 0.042 0.269 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.169 16.464 3456 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.59 % 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: 0.35 (0.15), residues: 3220 helix: 1.33 (0.12), residues: 1840 sheet: -1.80 (0.34), residues: 204 loop : -1.12 (0.19), residues: 1176 *********************** 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 350 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 337 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 343 average time/residue: 0.2915 time to fit residues: 168.6003 Evaluate side-chains 334 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 328 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2213 time to fit residues: 6.2101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 chunk 187 optimal weight: 20.0000 chunk 145 optimal weight: 0.0470 chunk 213 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 297 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 198 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 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 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 603 GLN ** 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: 0.5653 moved from start: 0.2996 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= 0.184 Angle : 0.617 11.541 33308 Z= 0.310 Chirality : 0.042 0.271 3928 Planarity : 0.003 0.039 4248 Dihedral : 4.094 18.378 3456 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.32 % 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: 0.53 (0.15), residues: 3220 helix: 1.49 (0.12), residues: 1848 sheet: -1.64 (0.34), residues: 204 loop : -1.11 (0.19), residues: 1168 ********************** 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 376 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 369 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 374 average time/residue: 0.3105 time to fit residues: 195.5125 Evaluate side-chains 343 residues out of total 2900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 340 time to evaluate : 3.049 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2823 time to fit residues: 5.9805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 257 optimal weight: 0.0570 chunk 107 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** C 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 ASN ** E 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN ** G 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116408 restraints weight = 51205.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115010 restraints weight = 45740.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116207 restraints weight = 46448.575| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 24372 Z= 0.196 Angle : 0.627 11.158 33308 Z= 0.312 Chirality : 0.041 0.285 3928 Planarity : 0.003 0.038 4248 Dihedral : 4.045 17.855 3456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3220 helix: 1.60 (0.12), residues: 1848 sheet: -1.61 (0.34), residues: 204 loop : -1.11 (0.19), residues: 1168 =============================================================================== Job complete usr+sys time: 4306.02 seconds wall clock time: 79 minutes 18.15 seconds (4758.15 seconds total)