Starting phenix.real_space_refine on Mon Mar 11 10:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yn5_10849/03_2024/6yn5_10849_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.335 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 370 5.16 5 C 36466 2.51 5 N 9500 2.21 5 O 10648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 447": "OD1" <-> "OD2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 643": "NH1" <-> "NH2" Residue "B GLU 668": "OE1" <-> "OE2" Residue "B ARG 670": "NH1" <-> "NH2" Residue "B TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C ARG 670": "NH1" <-> "NH2" Residue "C TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 387": "OE1" <-> "OE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "D TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D GLU 611": "OE1" <-> "OE2" Residue "D ARG 643": "NH1" <-> "NH2" Residue "D ARG 670": "NH1" <-> "NH2" Residue "D TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E ARG 263": "NH1" <-> "NH2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 499": "OE1" <-> "OE2" Residue "E ASP 506": "OD1" <-> "OD2" Residue "E PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 608": "NH1" <-> "NH2" Residue "E PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 668": "OE1" <-> "OE2" Residue "E ARG 670": "NH1" <-> "NH2" Residue "E TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F ARG 141": "NH1" <-> "NH2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 608": "NH1" <-> "NH2" Residue "F ARG 643": "NH1" <-> "NH2" Residue "F TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 698": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 355": "OE1" <-> "OE2" Residue "G TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 447": "OD1" <-> "OD2" Residue "G PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 643": "NH1" <-> "NH2" Residue "G GLU 668": "OE1" <-> "OE2" Residue "G ARG 670": "NH1" <-> "NH2" Residue "G TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 611": "OE1" <-> "OE2" Residue "H GLU 611": "OE1" <-> "OE2" Residue "H ARG 670": "NH1" <-> "NH2" Residue "H TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "I ASP 112": "OD1" <-> "OD2" Residue "I ARG 141": "NH1" <-> "NH2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 506": "OD1" <-> "OD2" Residue "I GLU 611": "OE1" <-> "OE2" Residue "I GLU 611": "OE1" <-> "OE2" Residue "I ARG 643": "NH1" <-> "NH2" Residue "I ARG 670": "NH1" <-> "NH2" Residue "I TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J GLU 104": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ASP 112": "OD1" <-> "OD2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 206": "NH1" <-> "NH2" Residue "J TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 263": "NH1" <-> "NH2" Residue "J TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J ASP 506": "OD1" <-> "OD2" Residue "J PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 608": "NH1" <-> "NH2" Residue "J GLU 668": "OE1" <-> "OE2" Residue "J ARG 670": "NH1" <-> "NH2" Residue "J TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56994 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "D" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "E" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "I" Number of atoms: 5703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 5832 Chain: "J" Number of atoms: 5697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5697 Classifications: {'peptide': 711} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 33, 'TRANS': 673} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 32.30, per 1000 atoms: 0.57 Number of scatterers: 56994 At special positions: 0 Unit cell: (197.784, 192.96, 104.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 370 16.00 P 10 15.00 O 10648 8.00 N 9500 7.00 C 36466 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: 15.75 Conformation dependent library (CDL) restraints added in 10.2 seconds 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 301 helices and 60 sheets defined 42.1% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.40 Creating SS restraints... Processing helix chain 'A' and resid 13 through 29 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 59 through 73 removed outlier: 5.887A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLU A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 110 through 128 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 195 through 208 removed outlier: 4.047A pdb=" N ILE A 204 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 231 removed outlier: 3.518A pdb=" N LYS A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 315 through 321 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 365 through 368 removed outlier: 4.281A pdb=" N LEU A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 418 through 445 Processing helix chain 'A' and resid 511 through 520 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 586 through 600 Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 667 through 684 removed outlier: 3.561A pdb=" N ARG A 670 " --> pdb=" O GLU A 667 " (cutoff:3.500A) Proline residue: A 671 - end of helix removed outlier: 3.949A pdb=" N GLY A 683 " --> pdb=" O CYS A 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 28 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 59 through 73 removed outlier: 6.093A pdb=" N LEU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 110 through 128 Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.563A pdb=" N LYS B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 160' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 195 through 208 Processing helix chain 'B' and resid 219 through 231 Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 315 through 321 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 365 through 368 removed outlier: 4.266A pdb=" N LEU B 368 " --> pdb=" O THR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 368' Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 418 through 445 Processing helix chain 'B' and resid 511 through 520 Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 566 through 569 No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 586 through 600 Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.630A pdb=" N PHE B 610 " --> pdb=" O MET B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 628 Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.634A pdb=" N ARG B 670 " --> pdb=" O GLU B 667 " (cutoff:3.500A) Proline residue: B 671 - end of helix removed outlier: 3.987A pdb=" N GLY B 683 " --> pdb=" O CYS B 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 28 Proline residue: C 18 - end of helix Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 59 through 71 removed outlier: 6.063A pdb=" N LEU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 110 through 128 Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.520A pdb=" N LYS C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 282 through 291 Processing helix chain 'C' and resid 315 through 321 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 365 through 368 removed outlier: 4.329A pdb=" N LEU C 368 " --> pdb=" O THR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 386 through 394 Processing helix chain 'C' and resid 403 through 415 removed outlier: 3.648A pdb=" N ALA C 413 " --> pdb=" O THR C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 445 Processing helix chain 'C' and resid 511 through 520 Processing helix chain 'C' and resid 543 through 561 Processing helix chain 'C' and resid 566 through 569 No H-bonds generated for 'chain 'C' and resid 566 through 569' Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 586 through 600 Processing helix chain 'C' and resid 602 through 611 Processing helix chain 'C' and resid 620 through 628 Processing helix chain 'C' and resid 637 through 639 No H-bonds generated for 'chain 'C' and resid 637 through 639' Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'D' and resid 13 through 28 Proline residue: D 18 - end of helix Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 59 through 73 removed outlier: 5.865A pdb=" N LEU D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU D 69 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 110 through 128 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'D' and resid 173 through 177 Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 195 through 208 Processing helix chain 'D' and resid 219 through 231 removed outlier: 3.584A pdb=" N LYS D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 277 through 280 Processing helix chain 'D' and resid 282 through 291 Processing helix chain 'D' and resid 315 through 321 Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 341 through 343 No H-bonds generated for 'chain 'D' and resid 341 through 343' Processing helix chain 'D' and resid 365 through 368 removed outlier: 4.260A pdb=" N LEU D 368 " --> pdb=" O THR D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 403 through 415 removed outlier: 3.650A pdb=" N ALA D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 445 Processing helix chain 'D' and resid 511 through 521 removed outlier: 3.533A pdb=" N HIS D 521 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 561 Processing helix chain 'D' and resid 566 through 569 No H-bonds generated for 'chain 'D' and resid 566 through 569' Processing helix chain 'D' and resid 571 through 576 Processing helix chain 'D' and resid 586 through 600 Processing helix chain 'D' and resid 602 through 610 Processing helix chain 'D' and resid 620 through 629 Processing helix chain 'D' and resid 638 through 640 No H-bonds generated for 'chain 'D' and resid 638 through 640' Processing helix chain 'D' and resid 670 through 682 removed outlier: 3.671A pdb=" N LEU D 676 " --> pdb=" O VAL D 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 28 Proline residue: E 18 - end of helix Processing helix chain 'E' and resid 39 through 48 Processing helix chain 'E' and resid 59 through 73 removed outlier: 6.011A pdb=" N LEU E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLU E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 110 through 128 Processing helix chain 'E' and resid 131 through 142 Processing helix chain 'E' and resid 162 through 171 Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 219 through 231 removed outlier: 3.635A pdb=" N LYS E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 277 through 280 Processing helix chain 'E' and resid 282 through 291 Processing helix chain 'E' and resid 315 through 321 Processing helix chain 'E' and resid 341 through 343 No H-bonds generated for 'chain 'E' and resid 341 through 343' Processing helix chain 'E' and resid 365 through 368 removed outlier: 4.215A pdb=" N LEU E 368 " --> pdb=" O THR E 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 368' Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.728A pdb=" N HIS E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 415 removed outlier: 3.712A pdb=" N ALA E 413 " --> pdb=" O THR E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 445 Processing helix chain 'E' and resid 511 through 520 Processing helix chain 'E' and resid 543 through 561 Processing helix chain 'E' and resid 566 through 569 No H-bonds generated for 'chain 'E' and resid 566 through 569' Processing helix chain 'E' and resid 571 through 576 Processing helix chain 'E' and resid 586 through 600 Processing helix chain 'E' and resid 602 through 610 Processing helix chain 'E' and resid 620 through 628 Processing helix chain 'E' and resid 637 through 639 No H-bonds generated for 'chain 'E' and resid 637 through 639' Processing helix chain 'E' and resid 670 through 682 Processing helix chain 'F' and resid 13 through 29 Proline residue: F 18 - end of helix Processing helix chain 'F' and resid 39 through 48 Processing helix chain 'F' and resid 59 through 73 removed outlier: 5.882A pdb=" N LEU F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 110 through 128 Processing helix chain 'F' and resid 131 through 142 Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 162 through 177 Proline residue: F 173 - end of helix removed outlier: 3.640A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'F' and resid 195 through 208 removed outlier: 4.043A pdb=" N ILE F 204 " --> pdb=" O GLU F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.527A pdb=" N LYS F 225 " --> pdb=" O SER F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 254 Processing helix chain 'F' and resid 277 through 280 Processing helix chain 'F' and resid 282 through 290 Processing helix chain 'F' and resid 315 through 321 Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 341 through 343 No H-bonds generated for 'chain 'F' and resid 341 through 343' Processing helix chain 'F' and resid 365 through 368 removed outlier: 4.277A pdb=" N LEU F 368 " --> pdb=" O THR F 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 365 through 368' Processing helix chain 'F' and resid 386 through 394 Processing helix chain 'F' and resid 403 through 415 Processing helix chain 'F' and resid 418 through 445 Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'F' and resid 543 through 561 Processing helix chain 'F' and resid 566 through 569 No H-bonds generated for 'chain 'F' and resid 566 through 569' Processing helix chain 'F' and resid 571 through 576 Processing helix chain 'F' and resid 586 through 600 Processing helix chain 'F' and resid 602 through 609 Processing helix chain 'F' and resid 620 through 628 Processing helix chain 'F' and resid 637 through 639 No H-bonds generated for 'chain 'F' and resid 637 through 639' Processing helix chain 'F' and resid 667 through 684 removed outlier: 3.574A pdb=" N ARG F 670 " --> pdb=" O GLU F 667 " (cutoff:3.500A) Proline residue: F 671 - end of helix removed outlier: 3.978A pdb=" N GLY F 683 " --> pdb=" O CYS F 680 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 684 " --> pdb=" O GLU F 681 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 28 Proline residue: G 18 - end of helix Processing helix chain 'G' and resid 39 through 48 Processing helix chain 'G' and resid 59 through 73 removed outlier: 6.094A pdb=" N LEU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 93 No H-bonds generated for 'chain 'G' and resid 91 through 93' Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 131 through 142 Processing helix chain 'G' and resid 156 through 159 No H-bonds generated for 'chain 'G' and resid 156 through 159' Processing helix chain 'G' and resid 162 through 171 Processing helix chain 'G' and resid 173 through 177 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 195 through 208 Processing helix chain 'G' and resid 219 through 231 removed outlier: 3.510A pdb=" N LYS G 225 " --> pdb=" O SER G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 254 Processing helix chain 'G' and resid 277 through 280 Processing helix chain 'G' and resid 282 through 291 Processing helix chain 'G' and resid 315 through 321 Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 341 through 343 No H-bonds generated for 'chain 'G' and resid 341 through 343' Processing helix chain 'G' and resid 365 through 368 removed outlier: 4.260A pdb=" N LEU G 368 " --> pdb=" O THR G 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 365 through 368' Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 403 through 415 Processing helix chain 'G' and resid 418 through 445 Processing helix chain 'G' and resid 511 through 520 Processing helix chain 'G' and resid 543 through 561 Processing helix chain 'G' and resid 566 through 569 No H-bonds generated for 'chain 'G' and resid 566 through 569' Processing helix chain 'G' and resid 571 through 576 Processing helix chain 'G' and resid 586 through 600 Processing helix chain 'G' and resid 602 through 610 removed outlier: 3.646A pdb=" N PHE G 610 " --> pdb=" O MET G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 620 through 628 Processing helix chain 'G' and resid 637 through 639 No H-bonds generated for 'chain 'G' and resid 637 through 639' Processing helix chain 'G' and resid 667 through 684 removed outlier: 3.639A pdb=" N ARG G 670 " --> pdb=" O GLU G 667 " (cutoff:3.500A) Proline residue: G 671 - end of helix removed outlier: 3.988A pdb=" N GLY G 683 " --> pdb=" O CYS G 680 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 28 Proline residue: H 18 - end of helix Processing helix chain 'H' and resid 39 through 48 Processing helix chain 'H' and resid 59 through 73 removed outlier: 6.063A pdb=" N LEU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLU H 68 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU H 69 " --> pdb=" O GLU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 110 through 128 Processing helix chain 'H' and resid 131 through 142 Processing helix chain 'H' and resid 158 through 160 No H-bonds generated for 'chain 'H' and resid 158 through 160' Processing helix chain 'H' and resid 162 through 171 Processing helix chain 'H' and resid 173 through 177 Processing helix chain 'H' and resid 185 through 187 No H-bonds generated for 'chain 'H' and resid 185 through 187' Processing helix chain 'H' and resid 195 through 208 Processing helix chain 'H' and resid 219 through 231 removed outlier: 3.568A pdb=" N LYS H 225 " --> pdb=" O SER H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 254 Processing helix chain 'H' and resid 277 through 280 Processing helix chain 'H' and resid 282 through 291 Processing helix chain 'H' and resid 315 through 321 Processing helix chain 'H' and resid 341 through 343 No H-bonds generated for 'chain 'H' and resid 341 through 343' Processing helix chain 'H' and resid 365 through 368 removed outlier: 4.301A pdb=" N LEU H 368 " --> pdb=" O THR H 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 365 through 368' Processing helix chain 'H' and resid 386 through 394 Processing helix chain 'H' and resid 403 through 415 removed outlier: 3.645A pdb=" N ALA H 413 " --> pdb=" O THR H 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 445 Processing helix chain 'H' and resid 511 through 520 Processing helix chain 'H' and resid 543 through 561 Processing helix chain 'H' and resid 566 through 569 No H-bonds generated for 'chain 'H' and resid 566 through 569' Processing helix chain 'H' and resid 571 through 576 Processing helix chain 'H' and resid 586 through 600 Processing helix chain 'H' and resid 602 through 610 Processing helix chain 'H' and resid 620 through 628 Processing helix chain 'H' and resid 637 through 639 No H-bonds generated for 'chain 'H' and resid 637 through 639' Processing helix chain 'H' and resid 670 through 682 Processing helix chain 'I' and resid 13 through 28 Proline residue: I 18 - end of helix Processing helix chain 'I' and resid 39 through 48 Processing helix chain 'I' and resid 59 through 73 removed outlier: 5.837A pdb=" N LEU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU I 68 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU I 69 " --> pdb=" O GLU I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 110 through 128 Processing helix chain 'I' and resid 131 through 142 Processing helix chain 'I' and resid 162 through 171 Processing helix chain 'I' and resid 173 through 177 Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing helix chain 'I' and resid 195 through 208 Processing helix chain 'I' and resid 219 through 231 removed outlier: 3.593A pdb=" N LYS I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 253 Processing helix chain 'I' and resid 277 through 280 Processing helix chain 'I' and resid 282 through 291 Processing helix chain 'I' and resid 315 through 321 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 341 through 343 No H-bonds generated for 'chain 'I' and resid 341 through 343' Processing helix chain 'I' and resid 365 through 368 removed outlier: 4.256A pdb=" N LEU I 368 " --> pdb=" O THR I 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 365 through 368' Processing helix chain 'I' and resid 386 through 394 Processing helix chain 'I' and resid 403 through 415 removed outlier: 3.651A pdb=" N ALA I 413 " --> pdb=" O THR I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 445 Processing helix chain 'I' and resid 511 through 521 removed outlier: 3.537A pdb=" N HIS I 521 " --> pdb=" O TYR I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 543 through 561 Processing helix chain 'I' and resid 566 through 569 No H-bonds generated for 'chain 'I' and resid 566 through 569' Processing helix chain 'I' and resid 571 through 576 Processing helix chain 'I' and resid 586 through 600 Processing helix chain 'I' and resid 602 through 610 Processing helix chain 'I' and resid 620 through 629 Processing helix chain 'I' and resid 637 through 639 No H-bonds generated for 'chain 'I' and resid 637 through 639' Processing helix chain 'I' and resid 670 through 682 removed outlier: 3.694A pdb=" N LEU I 676 " --> pdb=" O VAL I 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 28 Proline residue: J 18 - end of helix Processing helix chain 'J' and resid 39 through 48 Processing helix chain 'J' and resid 59 through 71 removed outlier: 6.053A pdb=" N LEU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 93 No H-bonds generated for 'chain 'J' and resid 91 through 93' Processing helix chain 'J' and resid 110 through 128 Processing helix chain 'J' and resid 131 through 142 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 173 through 177 Processing helix chain 'J' and resid 185 through 187 No H-bonds generated for 'chain 'J' and resid 185 through 187' Processing helix chain 'J' and resid 195 through 208 Processing helix chain 'J' and resid 219 through 231 removed outlier: 3.627A pdb=" N LYS J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 254 Processing helix chain 'J' and resid 277 through 280 Processing helix chain 'J' and resid 282 through 291 Processing helix chain 'J' and resid 315 through 321 Processing helix chain 'J' and resid 341 through 343 No H-bonds generated for 'chain 'J' and resid 341 through 343' Processing helix chain 'J' and resid 365 through 368 removed outlier: 4.240A pdb=" N LEU J 368 " --> pdb=" O THR J 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 365 through 368' Processing helix chain 'J' and resid 386 through 394 Processing helix chain 'J' and resid 403 through 415 removed outlier: 3.714A pdb=" N ALA J 413 " --> pdb=" O THR J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 445 Processing helix chain 'J' and resid 511 through 520 Processing helix chain 'J' and resid 543 through 561 Processing helix chain 'J' and resid 566 through 569 No H-bonds generated for 'chain 'J' and resid 566 through 569' Processing helix chain 'J' and resid 571 through 576 Processing helix chain 'J' and resid 586 through 600 Processing helix chain 'J' and resid 602 through 610 Processing helix chain 'J' and resid 620 through 628 Processing helix chain 'J' and resid 637 through 639 No H-bonds generated for 'chain 'J' and resid 637 through 639' Processing helix chain 'J' and resid 670 through 682 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.201A pdb=" N ALA A 5 " --> pdb=" O CYS A 53 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 55 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 7 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE A 57 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN A 99 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 81 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER A 101 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA A 83 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 103 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 212 through 216 removed outlier: 6.226A pdb=" N ALA A 301 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ASP A 330 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 303 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS A 300 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 258 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 240 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 260 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= D, first strand: chain 'A' and resid 490 through 494 Processing sheet with id= E, first strand: chain 'A' and resid 632 through 636 Processing sheet with id= F, first strand: chain 'A' and resid 650 through 652 removed outlier: 4.513A pdb=" N ASP A 692 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.082A pdb=" N ALA B 5 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL B 55 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 7 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE B 57 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLN B 99 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA B 81 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER B 101 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 83 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 103 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.261A pdb=" N ALA B 301 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP B 330 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 303 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS B 300 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 304 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR B 258 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE B 240 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE B 260 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 311 through 313 Processing sheet with id= J, first strand: chain 'B' and resid 490 through 494 removed outlier: 4.001A pdb=" N LYS B 527 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 632 through 636 Processing sheet with id= L, first strand: chain 'B' and resid 650 through 652 removed outlier: 4.505A pdb=" N ASP B 692 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.422A pdb=" N ASP C 58 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN C 99 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA C 81 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER C 101 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 212 through 216 removed outlier: 6.268A pdb=" N ALA C 301 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP C 330 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 303 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N HIS C 300 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 304 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR C 258 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 240 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE C 260 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 311 through 313 Processing sheet with id= P, first strand: chain 'C' and resid 490 through 494 Processing sheet with id= Q, first strand: chain 'C' and resid 632 through 636 Processing sheet with id= R, first strand: chain 'C' and resid 650 through 652 removed outlier: 4.477A pdb=" N ASP C 692 " --> pdb=" O TYR C 652 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 32 through 34 removed outlier: 4.362A pdb=" N ASP D 58 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN D 99 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA D 81 " --> pdb=" O GLN D 99 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N SER D 101 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 212 through 216 removed outlier: 6.217A pdb=" N ALA D 301 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP D 330 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE D 303 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS D 300 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR D 258 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 240 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ILE D 260 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 311 through 313 Processing sheet with id= V, first strand: chain 'D' and resid 490 through 494 Processing sheet with id= W, first strand: chain 'D' and resid 632 through 636 Processing sheet with id= X, first strand: chain 'D' and resid 650 through 652 removed outlier: 4.584A pdb=" N ASP D 692 " --> pdb=" O TYR D 652 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 32 through 34 removed outlier: 7.145A pdb=" N ALA E 5 " --> pdb=" O CYS E 53 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL E 55 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU E 7 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N PHE E 57 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN E 99 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA E 81 " --> pdb=" O GLN E 99 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER E 101 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 212 through 216 removed outlier: 6.259A pdb=" N ALA E 301 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP E 330 " --> pdb=" O ALA E 301 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE E 303 " --> pdb=" O ASP E 330 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS E 300 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR E 258 " --> pdb=" O ILE E 238 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE E 240 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE E 260 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 311 through 313 Processing sheet with id= AB, first strand: chain 'E' and resid 490 through 494 Processing sheet with id= AC, first strand: chain 'E' and resid 632 through 636 Processing sheet with id= AD, first strand: chain 'E' and resid 650 through 652 removed outlier: 4.542A pdb=" N ASP E 692 " --> pdb=" O TYR E 652 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 32 through 34 removed outlier: 7.198A pdb=" N ALA F 5 " --> pdb=" O CYS F 53 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL F 55 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU F 7 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE F 57 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN F 99 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA F 81 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER F 101 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA F 83 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE F 103 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 212 through 216 removed outlier: 6.227A pdb=" N ALA F 301 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP F 330 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE F 303 " --> pdb=" O ASP F 330 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS F 300 " --> pdb=" O THR F 237 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR F 304 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR F 258 " --> pdb=" O ILE F 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE F 240 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE F 260 " --> pdb=" O ILE F 240 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 311 through 313 Processing sheet with id= AH, first strand: chain 'F' and resid 490 through 494 Processing sheet with id= AI, first strand: chain 'F' and resid 632 through 636 Processing sheet with id= AJ, first strand: chain 'F' and resid 650 through 652 removed outlier: 4.451A pdb=" N ASP F 692 " --> pdb=" O TYR F 652 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 32 through 34 removed outlier: 7.084A pdb=" N ALA G 5 " --> pdb=" O CYS G 53 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL G 55 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU G 7 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE G 57 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN G 99 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA G 81 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER G 101 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA G 83 " --> pdb=" O SER G 101 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE G 103 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 212 through 216 removed outlier: 6.262A pdb=" N ALA G 301 " --> pdb=" O HIS G 328 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASP G 330 " --> pdb=" O ALA G 301 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE G 303 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS G 300 " --> pdb=" O THR G 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR G 304 " --> pdb=" O ASP G 241 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 258 " --> pdb=" O ILE G 238 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE G 240 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE G 260 " --> pdb=" O ILE G 240 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 311 through 313 Processing sheet with id= AN, first strand: chain 'G' and resid 490 through 494 removed outlier: 4.000A pdb=" N LYS G 527 " --> pdb=" O LEU G 534 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 632 through 636 Processing sheet with id= AP, first strand: chain 'G' and resid 650 through 652 removed outlier: 4.500A pdb=" N ASP G 692 " --> pdb=" O TYR G 652 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.422A pdb=" N ASP H 58 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN H 99 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA H 81 " --> pdb=" O GLN H 99 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER H 101 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 212 through 216 removed outlier: 6.252A pdb=" N ALA H 301 " --> pdb=" O HIS H 328 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP H 330 " --> pdb=" O ALA H 301 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE H 303 " --> pdb=" O ASP H 330 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS H 300 " --> pdb=" O THR H 237 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR H 304 " --> pdb=" O ASP H 241 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR H 258 " --> pdb=" O ILE H 238 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE H 240 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE H 260 " --> pdb=" O ILE H 240 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 311 through 313 Processing sheet with id= AT, first strand: chain 'H' and resid 490 through 494 Processing sheet with id= AU, first strand: chain 'H' and resid 632 through 636 Processing sheet with id= AV, first strand: chain 'H' and resid 650 through 652 removed outlier: 4.473A pdb=" N ASP H 692 " --> pdb=" O TYR H 652 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 32 through 34 removed outlier: 7.138A pdb=" N ALA I 5 " --> pdb=" O CYS I 53 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL I 55 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU I 7 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE I 57 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN I 99 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA I 81 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER I 101 " --> pdb=" O ALA I 81 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 212 through 216 removed outlier: 6.212A pdb=" N ALA I 301 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP I 330 " --> pdb=" O ALA I 301 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE I 303 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS I 300 " --> pdb=" O THR I 237 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR I 258 " --> pdb=" O ILE I 238 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE I 240 " --> pdb=" O THR I 258 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE I 260 " --> pdb=" O ILE I 240 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 311 through 313 Processing sheet with id= AZ, first strand: chain 'I' and resid 490 through 494 Processing sheet with id= BA, first strand: chain 'I' and resid 632 through 636 Processing sheet with id= BB, first strand: chain 'I' and resid 650 through 652 removed outlier: 4.542A pdb=" N ASP I 692 " --> pdb=" O TYR I 652 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'J' and resid 32 through 34 removed outlier: 7.147A pdb=" N ALA J 5 " --> pdb=" O CYS J 53 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL J 55 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU J 7 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE J 57 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN J 99 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA J 81 " --> pdb=" O GLN J 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER J 101 " --> pdb=" O ALA J 81 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'J' and resid 212 through 216 removed outlier: 6.257A pdb=" N ALA J 301 " --> pdb=" O HIS J 328 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP J 330 " --> pdb=" O ALA J 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE J 303 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS J 300 " --> pdb=" O THR J 237 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR J 258 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE J 240 " --> pdb=" O THR J 258 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE J 260 " --> pdb=" O ILE J 240 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'J' and resid 311 through 313 Processing sheet with id= BF, first strand: chain 'J' and resid 490 through 494 Processing sheet with id= BG, first strand: chain 'J' and resid 632 through 636 Processing sheet with id= BH, first strand: chain 'J' and resid 650 through 652 removed outlier: 4.560A pdb=" N ASP J 692 " --> pdb=" O TYR J 652 " (cutoff:3.500A) 2183 hydrogen bonds defined for protein. 5969 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: 18.72 Time building geometry restraints manager: 17.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16077 1.33 - 1.45: 10428 1.45 - 1.57: 31233 1.57 - 1.69: 10 1.69 - 1.81: 670 Bond restraints: 58418 Sorted by residual: bond pdb=" OP4 LLP I 367 " pdb=" P LLP I 367 " ideal model delta sigma weight residual 1.730 1.530 0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" OP4 LLP D 367 " pdb=" P LLP D 367 " ideal model delta sigma weight residual 1.730 1.531 0.199 2.00e-02 2.50e+03 9.95e+01 bond pdb=" OP4 LLP B 367 " pdb=" P LLP B 367 " ideal model delta sigma weight residual 1.730 1.532 0.198 2.00e-02 2.50e+03 9.78e+01 bond pdb=" OP4 LLP C 367 " pdb=" P LLP C 367 " ideal model delta sigma weight residual 1.730 1.532 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" OP4 LLP G 367 " pdb=" P LLP G 367 " ideal model delta sigma weight residual 1.730 1.533 0.197 2.00e-02 2.50e+03 9.69e+01 ... (remaining 58413 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.86: 1323 104.86 - 112.56: 29638 112.56 - 120.27: 24680 120.27 - 127.98: 23036 127.98 - 135.69: 537 Bond angle restraints: 79214 Sorted by residual: angle pdb=" C CYS E 148 " pdb=" N THR E 149 " pdb=" CA THR E 149 " ideal model delta sigma weight residual 122.48 135.69 -13.21 1.77e+00 3.19e-01 5.57e+01 angle pdb=" C CYS J 148 " pdb=" N THR J 149 " pdb=" CA THR J 149 " ideal model delta sigma weight residual 122.48 135.52 -13.04 1.77e+00 3.19e-01 5.43e+01 angle pdb=" N ASN A 8 " pdb=" CA ASN A 8 " pdb=" C ASN A 8 " ideal model delta sigma weight residual 107.73 118.99 -11.26 1.61e+00 3.86e-01 4.89e+01 angle pdb=" C CYS H 148 " pdb=" N THR H 149 " pdb=" CA THR H 149 " ideal model delta sigma weight residual 122.48 134.76 -12.28 1.77e+00 3.19e-01 4.81e+01 angle pdb=" N ASN D 8 " pdb=" CA ASN D 8 " pdb=" C ASN D 8 " ideal model delta sigma weight residual 108.07 118.81 -10.74 1.59e+00 3.96e-01 4.56e+01 ... (remaining 79209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 34461 32.96 - 65.91: 477 65.91 - 98.87: 50 98.87 - 131.82: 8 131.82 - 164.78: 2 Dihedral angle restraints: 34998 sinusoidal: 14202 harmonic: 20796 Sorted by residual: dihedral pdb=" CA ASN J 8 " pdb=" C ASN J 8 " pdb=" N HIS J 9 " pdb=" CA HIS J 9 " ideal model delta harmonic sigma weight residual 180.00 140.51 39.49 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA LEU I 7 " pdb=" C LEU I 7 " pdb=" N ASN I 8 " pdb=" CA ASN I 8 " ideal model delta harmonic sigma weight residual 180.00 140.70 39.30 0 5.00e+00 4.00e-02 6.18e+01 dihedral pdb=" CA ASN E 8 " pdb=" C ASN E 8 " pdb=" N HIS E 9 " pdb=" CA HIS E 9 " ideal model delta harmonic sigma weight residual 180.00 141.83 38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 34995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5961 0.050 - 0.100: 2167 0.100 - 0.150: 513 0.150 - 0.200: 31 0.200 - 0.250: 2 Chirality restraints: 8674 Sorted by residual: chirality pdb=" CB THR I 492 " pdb=" CA THR I 492 " pdb=" OG1 THR I 492 " pdb=" CG2 THR I 492 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB THR D 492 " pdb=" CA THR D 492 " pdb=" OG1 THR D 492 " pdb=" CG2 THR D 492 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA ASN A 8 " pdb=" N ASN A 8 " pdb=" C ASN A 8 " pdb=" CB ASN A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 ... (remaining 8671 not shown) Planarity restraints: 10168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP G 367 " 0.197 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" NZ LLP G 367 " -0.495 2.00e-02 2.50e+03 pdb=" C4 LLP G 367 " -0.095 2.00e-02 2.50e+03 pdb=" C4' LLP G 367 " 0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 367 " -0.197 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" NZ LLP B 367 " 0.494 2.00e-02 2.50e+03 pdb=" C4 LLP B 367 " 0.095 2.00e-02 2.50e+03 pdb=" C4' LLP B 367 " -0.392 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP H 367 " 0.204 2.00e-02 2.50e+03 3.33e-01 1.11e+03 pdb=" NZ LLP H 367 " -0.497 2.00e-02 2.50e+03 pdb=" C4 LLP H 367 " -0.088 2.00e-02 2.50e+03 pdb=" C4' LLP H 367 " 0.382 2.00e-02 2.50e+03 ... (remaining 10165 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12168 2.78 - 3.31: 51344 3.31 - 3.84: 101858 3.84 - 4.37: 125294 4.37 - 4.90: 209663 Nonbonded interactions: 500327 Sorted by model distance: nonbonded pdb=" O MET I 215 " pdb=" OH TYR I 393 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR F 574 " pdb=" OE1 GLU F 582 " model vdw 2.250 2.440 nonbonded pdb=" O MET D 215 " pdb=" OH TYR D 393 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR A 574 " pdb=" OE1 GLU A 582 " model vdw 2.258 2.440 nonbonded pdb=" O MET G 215 " pdb=" OH TYR G 393 " model vdw 2.263 2.440 ... (remaining 500322 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' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'B' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'C' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'D' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'E' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'F' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'G' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'H' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'I' and (resid 1 through 610 or resid 612 through 711)) selection = (chain 'J' and (resid 1 through 610 or resid 612 through 711)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.040 Extract box with map and model: 5.850 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 125.140 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.200 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:8.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 0.200 58418 Z= 0.564 Angle : 0.825 13.209 79214 Z= 0.458 Chirality : 0.052 0.250 8674 Planarity : 0.012 0.334 10168 Dihedral : 12.215 164.780 21650 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.10), residues: 7064 helix: -0.08 (0.09), residues: 2980 sheet: -0.10 (0.16), residues: 1070 loop : -0.21 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 333 HIS 0.018 0.002 HIS D 599 PHE 0.071 0.003 PHE C 82 TYR 0.035 0.003 TYR H 531 ARG 0.016 0.001 ARG I 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 4.929 Fit side-chains revert: symmetry clash REVERT: A 664 MET cc_start: 0.8571 (ttm) cc_final: 0.8219 (ttp) REVERT: B 569 MET cc_start: 0.8877 (ttt) cc_final: 0.8169 (ttp) REVERT: C 122 ASP cc_start: 0.8175 (m-30) cc_final: 0.7925 (m-30) REVERT: D 122 ASP cc_start: 0.8162 (m-30) cc_final: 0.7881 (m-30) REVERT: E 122 ASP cc_start: 0.8132 (m-30) cc_final: 0.7861 (m-30) REVERT: E 664 MET cc_start: 0.8587 (ttm) cc_final: 0.8278 (ttm) REVERT: G 569 MET cc_start: 0.8877 (ttt) cc_final: 0.8166 (ttp) REVERT: G 618 MET cc_start: 0.8866 (ptp) cc_final: 0.8511 (ptp) REVERT: G 631 MET cc_start: 0.7932 (mmm) cc_final: 0.7526 (mmm) REVERT: H 122 ASP cc_start: 0.8181 (m-30) cc_final: 0.7933 (m-30) REVERT: I 122 ASP cc_start: 0.8170 (m-30) cc_final: 0.7901 (m-30) REVERT: I 660 MET cc_start: 0.9041 (mmt) cc_final: 0.8621 (mmm) REVERT: J 39 ARG cc_start: 0.8527 (tmm-80) cc_final: 0.8284 (tmm-80) REVERT: J 122 ASP cc_start: 0.8138 (m-30) cc_final: 0.7880 (m-30) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 1.6217 time to fit residues: 1297.1221 Evaluate side-chains 538 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 4.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 599 optimal weight: 5.9990 chunk 538 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 287 optimal weight: 2.9990 chunk 556 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 338 optimal weight: 0.9990 chunk 414 optimal weight: 7.9990 chunk 644 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN B 9 HIS C 385 ASN C 591 GLN D 9 HIS D 250 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 647 ASN E 76 ASN F 115 ASN F 281 GLN G 9 HIS H 385 ASN H 591 GLN I 250 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 58418 Z= 0.149 Angle : 0.467 7.628 79214 Z= 0.245 Chirality : 0.041 0.147 8674 Planarity : 0.005 0.054 10168 Dihedral : 8.372 149.721 7868 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.66 % Allowed : 4.85 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.10), residues: 7064 helix: 0.90 (0.09), residues: 2900 sheet: -0.13 (0.15), residues: 1170 loop : 0.02 (0.12), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 454 HIS 0.009 0.001 HIS G 9 PHE 0.020 0.001 PHE C 82 TYR 0.014 0.001 TYR C 531 ARG 0.006 0.000 ARG I 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 604 time to evaluate : 5.125 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8632 (ttm) cc_final: 0.8405 (ttp) REVERT: B 569 MET cc_start: 0.8846 (ttt) cc_final: 0.7984 (ttp) REVERT: C 122 ASP cc_start: 0.8149 (m-30) cc_final: 0.7911 (m-30) REVERT: C 637 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8851 (tm) REVERT: C 668 GLU cc_start: 0.7660 (mp0) cc_final: 0.7260 (mp0) REVERT: D 122 ASP cc_start: 0.8143 (m-30) cc_final: 0.7855 (m-30) REVERT: D 246 LYS cc_start: 0.7743 (ttpp) cc_final: 0.7388 (tptm) REVERT: D 660 MET cc_start: 0.9162 (tpp) cc_final: 0.8874 (mpp) REVERT: E 1 MET cc_start: 0.8263 (tpp) cc_final: 0.8051 (tpp) REVERT: E 122 ASP cc_start: 0.8186 (m-30) cc_final: 0.7948 (m-30) REVERT: E 387 GLU cc_start: 0.7905 (mp0) cc_final: 0.7700 (mp0) REVERT: E 599 HIS cc_start: 0.8347 (t70) cc_final: 0.8107 (t-170) REVERT: E 664 MET cc_start: 0.8426 (ttm) cc_final: 0.8201 (ttm) REVERT: F 668 GLU cc_start: 0.7538 (mp0) cc_final: 0.7320 (mp0) REVERT: G 1 MET cc_start: 0.8635 (ttm) cc_final: 0.8410 (ttp) REVERT: G 73 MET cc_start: 0.8717 (mtm) cc_final: 0.8500 (mtm) REVERT: G 569 MET cc_start: 0.8844 (ttt) cc_final: 0.7957 (ttp) REVERT: G 618 MET cc_start: 0.8934 (ptp) cc_final: 0.8594 (ptp) REVERT: G 631 MET cc_start: 0.7863 (mmm) cc_final: 0.7456 (mmm) REVERT: H 122 ASP cc_start: 0.8152 (m-30) cc_final: 0.7916 (m-30) REVERT: H 668 GLU cc_start: 0.7641 (mp0) cc_final: 0.7329 (mp0) REVERT: I 122 ASP cc_start: 0.8133 (m-30) cc_final: 0.7843 (m-30) REVERT: I 145 TYR cc_start: 0.8469 (m-80) cc_final: 0.8256 (m-80) REVERT: I 246 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7537 (tptm) REVERT: J 1 MET cc_start: 0.8266 (tpp) cc_final: 0.8051 (tpp) REVERT: J 119 GLN cc_start: 0.8412 (mt0) cc_final: 0.8173 (mt0) REVERT: J 122 ASP cc_start: 0.8132 (m-30) cc_final: 0.7873 (m-30) outliers start: 38 outliers final: 16 residues processed: 619 average time/residue: 1.5064 time to fit residues: 1165.0865 Evaluate side-chains 556 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 539 time to evaluate : 4.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 358 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 536 optimal weight: 9.9990 chunk 439 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 645 optimal weight: 2.9990 chunk 697 optimal weight: 3.9990 chunk 575 optimal weight: 7.9990 chunk 640 optimal weight: 0.9990 chunk 220 optimal weight: 0.7980 chunk 518 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 282 HIS B 645 ASN C 591 GLN C 599 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 HIS G 645 ASN H 250 HIS H 591 GLN H 599 HIS J 591 GLN J 599 HIS ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 58418 Z= 0.152 Angle : 0.454 7.768 79214 Z= 0.236 Chirality : 0.041 0.130 8674 Planarity : 0.004 0.050 10168 Dihedral : 7.955 151.650 7868 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.77 % Allowed : 6.50 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 7064 helix: 1.17 (0.10), residues: 2940 sheet: -0.12 (0.15), residues: 1170 loop : 0.10 (0.12), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.009 0.001 HIS C 599 PHE 0.018 0.001 PHE C 82 TYR 0.013 0.001 TYR J 139 ARG 0.006 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 573 time to evaluate : 5.021 Fit side-chains REVERT: B 122 ASP cc_start: 0.7927 (m-30) cc_final: 0.7661 (m-30) REVERT: B 569 MET cc_start: 0.8846 (ttt) cc_final: 0.8047 (ttp) REVERT: C 122 ASP cc_start: 0.8148 (m-30) cc_final: 0.7925 (m-30) REVERT: C 637 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8914 (tm) REVERT: D 122 ASP cc_start: 0.8151 (m-30) cc_final: 0.7869 (m-30) REVERT: D 410 GLU cc_start: 0.7533 (tt0) cc_final: 0.7274 (tt0) REVERT: D 660 MET cc_start: 0.9170 (tpp) cc_final: 0.8849 (mpp) REVERT: E 122 ASP cc_start: 0.8191 (m-30) cc_final: 0.7937 (m-30) REVERT: E 153 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: E 387 GLU cc_start: 0.7857 (mp0) cc_final: 0.7644 (mp0) REVERT: E 664 MET cc_start: 0.8546 (ttm) cc_final: 0.8341 (ttm) REVERT: G 73 MET cc_start: 0.8701 (mtm) cc_final: 0.8490 (mtm) REVERT: G 569 MET cc_start: 0.8881 (ttt) cc_final: 0.8098 (ttp) REVERT: G 618 MET cc_start: 0.8953 (ptp) cc_final: 0.8475 (ptp) REVERT: G 631 MET cc_start: 0.7833 (mmm) cc_final: 0.7430 (mmm) REVERT: H 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7928 (m-30) REVERT: H 246 LYS cc_start: 0.7640 (tptt) cc_final: 0.7406 (mmtt) REVERT: H 668 GLU cc_start: 0.7639 (mp0) cc_final: 0.7359 (mp0) REVERT: I 122 ASP cc_start: 0.8157 (m-30) cc_final: 0.7856 (m-30) REVERT: I 246 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7573 (tptm) REVERT: J 119 GLN cc_start: 0.8416 (mt0) cc_final: 0.8180 (mt0) REVERT: J 122 ASP cc_start: 0.8137 (m-30) cc_final: 0.7876 (m-30) REVERT: J 153 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7730 (mtt) outliers start: 45 outliers final: 16 residues processed: 593 average time/residue: 1.5321 time to fit residues: 1136.3347 Evaluate side-chains 561 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 542 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 638 optimal weight: 9.9990 chunk 485 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 648 optimal weight: 0.8980 chunk 686 optimal weight: 0.4980 chunk 338 optimal weight: 0.6980 chunk 614 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 694 HIS B 694 HIS ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 HIS C 694 HIS D 174 ASN D 599 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 591 GLN E 599 HIS ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 HIS F 591 GLN F 694 HIS ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 599 HIS I 9 HIS I 599 HIS J 9 HIS J 599 HIS ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 694 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58418 Z= 0.199 Angle : 0.471 7.489 79214 Z= 0.245 Chirality : 0.042 0.150 8674 Planarity : 0.004 0.050 10168 Dihedral : 7.992 153.335 7868 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.02 % Allowed : 7.54 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 0.75 (0.10), residues: 7064 helix: 1.18 (0.10), residues: 2970 sheet: -0.15 (0.15), residues: 1170 loop : 0.24 (0.12), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 454 HIS 0.010 0.001 HIS C 599 PHE 0.024 0.002 PHE C 82 TYR 0.014 0.002 TYR I 139 ARG 0.006 0.000 ARG E 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 550 time to evaluate : 4.942 Fit side-chains revert: symmetry clash REVERT: B 65 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: B 122 ASP cc_start: 0.7943 (m-30) cc_final: 0.7689 (m-30) REVERT: B 153 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7405 (mtm) REVERT: B 468 ARG cc_start: 0.7396 (mtp85) cc_final: 0.7093 (mtp85) REVERT: B 569 MET cc_start: 0.8842 (ttt) cc_final: 0.8084 (ttp) REVERT: C 122 ASP cc_start: 0.8159 (m-30) cc_final: 0.7924 (m-30) REVERT: C 668 GLU cc_start: 0.7622 (mp0) cc_final: 0.7227 (mp0) REVERT: D 122 ASP cc_start: 0.8161 (m-30) cc_final: 0.7876 (m-30) REVERT: D 246 LYS cc_start: 0.7917 (ttmm) cc_final: 0.7604 (tptm) REVERT: D 410 GLU cc_start: 0.7537 (tt0) cc_final: 0.7272 (tt0) REVERT: E 39 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8223 (tmm-80) REVERT: E 122 ASP cc_start: 0.8211 (m-30) cc_final: 0.7958 (m-30) REVERT: E 153 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: E 387 GLU cc_start: 0.7913 (mp0) cc_final: 0.7699 (mp0) REVERT: E 489 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8967 (pt) REVERT: F 668 GLU cc_start: 0.7553 (mp0) cc_final: 0.7317 (mp0) REVERT: G 65 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: G 72 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8535 (mtpt) REVERT: G 73 MET cc_start: 0.8707 (mtm) cc_final: 0.8457 (mtm) REVERT: G 153 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: G 248 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.8999 (mm) REVERT: G 569 MET cc_start: 0.8842 (ttt) cc_final: 0.8071 (ttp) REVERT: G 618 MET cc_start: 0.8904 (ptp) cc_final: 0.8540 (ptp) REVERT: G 631 MET cc_start: 0.7872 (mmm) cc_final: 0.7453 (mmm) REVERT: H 122 ASP cc_start: 0.8162 (m-30) cc_final: 0.7938 (m-30) REVERT: H 272 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8690 (mp) REVERT: I 122 ASP cc_start: 0.8166 (m-30) cc_final: 0.7865 (m-30) REVERT: I 246 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7644 (tptm) REVERT: J 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7895 (m-30) REVERT: J 153 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7658 (mtt) REVERT: J 489 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8977 (pt) outliers start: 60 outliers final: 26 residues processed: 582 average time/residue: 1.5108 time to fit residues: 1104.2678 Evaluate side-chains 568 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 530 time to evaluate : 4.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 254 MET Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 638 ASP Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 571 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 9 optimal weight: 0.0270 chunk 510 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 585 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 615 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 385 ASN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 591 GLN E 599 HIS ** E 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 HIS ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 ASN H 385 ASN H 599 HIS H 694 HIS I 9 HIS I 174 ASN I 599 HIS J 9 HIS J 599 HIS ** J 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 58418 Z= 0.340 Angle : 0.545 7.645 79214 Z= 0.284 Chirality : 0.045 0.183 8674 Planarity : 0.005 0.049 10168 Dihedral : 8.296 154.178 7868 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.40 % Allowed : 7.79 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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 (0.10), residues: 7064 helix: 0.98 (0.09), residues: 2950 sheet: -0.22 (0.15), residues: 1170 loop : 0.18 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 454 HIS 0.011 0.001 HIS C 599 PHE 0.036 0.002 PHE C 82 TYR 0.020 0.002 TYR C 531 ARG 0.005 0.001 ARG G 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 532 time to evaluate : 4.966 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7380 (mtm) REVERT: B 65 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: B 153 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7277 (mtm) REVERT: B 468 ARG cc_start: 0.7443 (mtp85) cc_final: 0.7153 (mtp85) REVERT: C 122 ASP cc_start: 0.8173 (m-30) cc_final: 0.7937 (m-30) REVERT: C 668 GLU cc_start: 0.7619 (mp0) cc_final: 0.7296 (mp0) REVERT: D 122 ASP cc_start: 0.8181 (m-30) cc_final: 0.7886 (m-30) REVERT: D 246 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7678 (tptm) REVERT: D 410 GLU cc_start: 0.7628 (tt0) cc_final: 0.7388 (tt0) REVERT: E 39 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8203 (tmm-80) REVERT: E 122 ASP cc_start: 0.8236 (m-30) cc_final: 0.7985 (m-30) REVERT: E 489 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8999 (pt) REVERT: F 153 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7347 (mtm) REVERT: F 668 GLU cc_start: 0.7556 (mp0) cc_final: 0.7335 (mp0) REVERT: G 65 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: G 72 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8544 (mtpt) REVERT: G 73 MET cc_start: 0.8767 (mtm) cc_final: 0.8522 (mtm) REVERT: G 153 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7289 (mtm) REVERT: G 248 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.8945 (mm) REVERT: H 122 ASP cc_start: 0.8179 (m-30) cc_final: 0.7939 (m-30) REVERT: H 272 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8679 (mp) REVERT: H 668 GLU cc_start: 0.7744 (mp0) cc_final: 0.7400 (mp0) REVERT: I 122 ASP cc_start: 0.8200 (m-30) cc_final: 0.7897 (m-30) REVERT: J 97 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7863 (ttt90) REVERT: J 122 ASP cc_start: 0.8174 (m-30) cc_final: 0.7908 (m-30) REVERT: J 489 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9007 (pt) outliers start: 84 outliers final: 38 residues processed: 573 average time/residue: 1.4912 time to fit residues: 1076.5918 Evaluate side-chains 578 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 527 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 498 MET Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 153 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 65 GLU Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 638 ASP Chi-restraints excluded: chain J residue 97 ARG Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 230 optimal weight: 0.9990 chunk 618 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 402 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 686 optimal weight: 1.9990 chunk 570 optimal weight: 0.7980 chunk 318 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 227 optimal weight: 0.1980 chunk 360 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 385 ASN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS ** D 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 599 HIS E 645 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 ASN H 385 ASN H 599 HIS I 9 HIS I 599 HIS J 9 HIS J 76 ASN J 599 HIS J 645 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 58418 Z= 0.119 Angle : 0.430 8.171 79214 Z= 0.223 Chirality : 0.040 0.132 8674 Planarity : 0.004 0.051 10168 Dihedral : 7.704 149.904 7868 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.14 % Allowed : 8.46 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 1.02 (0.10), residues: 7064 helix: 1.55 (0.10), residues: 2900 sheet: -0.15 (0.15), residues: 1150 loop : 0.31 (0.12), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.011 0.001 HIS D 599 PHE 0.012 0.001 PHE C 82 TYR 0.011 0.001 TYR D 686 ARG 0.007 0.000 ARG J 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 573 time to evaluate : 5.128 Fit side-chains revert: symmetry clash REVERT: B 122 ASP cc_start: 0.7998 (m-30) cc_final: 0.7744 (m-30) REVERT: B 153 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7392 (mtm) REVERT: B 569 MET cc_start: 0.8711 (ttt) cc_final: 0.7980 (mtp) REVERT: C 122 ASP cc_start: 0.8147 (m-30) cc_final: 0.7915 (m-30) REVERT: C 637 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8925 (tm) REVERT: C 668 GLU cc_start: 0.7637 (mp0) cc_final: 0.7328 (mp0) REVERT: D 122 ASP cc_start: 0.8145 (m-30) cc_final: 0.7864 (m-30) REVERT: D 410 GLU cc_start: 0.7539 (tt0) cc_final: 0.7269 (tt0) REVERT: E 39 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: E 122 ASP cc_start: 0.8206 (m-30) cc_final: 0.7964 (m-30) REVERT: E 153 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7290 (mtm) REVERT: E 489 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8952 (pt) REVERT: E 668 GLU cc_start: 0.7679 (mp0) cc_final: 0.7383 (mp0) REVERT: G 73 MET cc_start: 0.8685 (mtm) cc_final: 0.8480 (mtm) REVERT: G 122 ASP cc_start: 0.8000 (m-30) cc_final: 0.7767 (m-30) REVERT: G 248 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8951 (mm) REVERT: G 569 MET cc_start: 0.8707 (ttt) cc_final: 0.8105 (ttp) REVERT: G 618 MET cc_start: 0.8894 (ptm) cc_final: 0.8552 (ptp) REVERT: H 122 ASP cc_start: 0.8153 (m-30) cc_final: 0.7934 (m-30) REVERT: H 637 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8813 (tm) REVERT: H 668 GLU cc_start: 0.7640 (mp0) cc_final: 0.7300 (mp0) REVERT: I 122 ASP cc_start: 0.8155 (m-30) cc_final: 0.7854 (m-30) REVERT: I 246 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7591 (tptm) REVERT: J 122 ASP cc_start: 0.8213 (m-30) cc_final: 0.7975 (m-30) REVERT: J 153 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: J 387 GLU cc_start: 0.7869 (mp0) cc_final: 0.7570 (mp0) REVERT: J 489 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8941 (pt) REVERT: J 498 MET cc_start: 0.8801 (mtm) cc_final: 0.8558 (mmm) REVERT: J 668 GLU cc_start: 0.7650 (mp0) cc_final: 0.7381 (mp0) outliers start: 68 outliers final: 24 residues processed: 614 average time/residue: 1.4821 time to fit residues: 1152.8006 Evaluate side-chains 579 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 546 time to evaluate : 4.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 662 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 501 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 578 optimal weight: 0.7980 chunk 383 optimal weight: 10.0000 chunk 684 optimal weight: 7.9990 chunk 428 optimal weight: 0.0770 chunk 417 optimal weight: 8.9990 chunk 315 optimal weight: 7.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 599 HIS D 645 ASN E 599 HIS F 591 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 599 HIS I 9 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58418 Z= 0.186 Angle : 0.463 8.432 79214 Z= 0.239 Chirality : 0.041 0.138 8674 Planarity : 0.004 0.050 10168 Dihedral : 7.835 152.378 7868 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.24 % Allowed : 8.67 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 1.03 (0.10), residues: 7064 helix: 1.54 (0.10), residues: 2890 sheet: -0.16 (0.15), residues: 1150 loop : 0.33 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 454 HIS 0.012 0.001 HIS I 599 PHE 0.019 0.001 PHE C 82 TYR 0.013 0.001 TYR D 686 ARG 0.008 0.000 ARG G 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 546 time to evaluate : 5.046 Fit side-chains revert: symmetry clash REVERT: B 122 ASP cc_start: 0.8010 (m-30) cc_final: 0.7770 (m-30) REVERT: B 153 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7400 (mtm) REVERT: C 122 ASP cc_start: 0.8160 (m-30) cc_final: 0.7933 (m-30) REVERT: D 122 ASP cc_start: 0.8159 (m-30) cc_final: 0.7875 (m-30) REVERT: D 410 GLU cc_start: 0.7559 (tt0) cc_final: 0.7247 (tt0) REVERT: E 39 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8216 (tmm-80) REVERT: E 122 ASP cc_start: 0.8221 (m-30) cc_final: 0.7970 (m-30) REVERT: E 153 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: E 489 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8974 (pt) REVERT: G 73 MET cc_start: 0.8706 (mtm) cc_final: 0.8460 (mtm) REVERT: G 122 ASP cc_start: 0.8021 (m-30) cc_final: 0.7792 (m-30) REVERT: G 153 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7410 (mtm) REVERT: G 248 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9048 (mm) REVERT: G 618 MET cc_start: 0.8860 (ptm) cc_final: 0.8647 (ptp) REVERT: G 631 MET cc_start: 0.7985 (mmm) cc_final: 0.7528 (mmm) REVERT: H 122 ASP cc_start: 0.8164 (m-30) cc_final: 0.7932 (m-30) REVERT: H 668 GLU cc_start: 0.7610 (mp0) cc_final: 0.7304 (mp0) REVERT: I 122 ASP cc_start: 0.8168 (m-30) cc_final: 0.7866 (m-30) REVERT: I 246 LYS cc_start: 0.7860 (ttpt) cc_final: 0.7631 (tptm) REVERT: J 122 ASP cc_start: 0.8226 (m-30) cc_final: 0.7981 (m-30) REVERT: J 153 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7553 (mtt) REVERT: J 387 GLU cc_start: 0.7867 (mp0) cc_final: 0.7579 (mp0) REVERT: J 489 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8982 (pt) outliers start: 74 outliers final: 40 residues processed: 584 average time/residue: 1.5148 time to fit residues: 1115.8701 Evaluate side-chains 590 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 542 time to evaluate : 4.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 638 ASP Chi-restraints excluded: chain C residue 660 MET Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 638 ASP Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 489 ILE Chi-restraints excluded: chain J residue 498 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 423 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 408 optimal weight: 8.9990 chunk 206 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 0.0570 chunk 435 optimal weight: 0.9980 chunk 466 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 537 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS E 599 HIS F 591 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 599 HIS I 9 HIS I 599 HIS J 591 GLN J 599 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 58418 Z= 0.109 Angle : 0.419 8.108 79214 Z= 0.215 Chirality : 0.040 0.131 8674 Planarity : 0.004 0.051 10168 Dihedral : 7.570 149.930 7868 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.00 % Allowed : 9.16 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 1.24 (0.10), residues: 7064 helix: 1.80 (0.10), residues: 2890 sheet: -0.11 (0.16), residues: 1150 loop : 0.37 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 473 HIS 0.012 0.001 HIS D 599 PHE 0.011 0.001 PHE J 624 TYR 0.010 0.001 TYR D 686 ARG 0.009 0.000 ARG G 468 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 580 time to evaluate : 6.293 Fit side-chains revert: symmetry clash REVERT: A 265 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 122 ASP cc_start: 0.7985 (m-30) cc_final: 0.7725 (m-30) REVERT: B 569 MET cc_start: 0.8667 (ttt) cc_final: 0.8024 (mtp) REVERT: C 122 ASP cc_start: 0.8143 (m-30) cc_final: 0.7925 (m-30) REVERT: C 637 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8876 (tm) REVERT: C 668 GLU cc_start: 0.7675 (mp0) cc_final: 0.7311 (mp0) REVERT: D 122 ASP cc_start: 0.8140 (m-30) cc_final: 0.7858 (m-30) REVERT: D 377 MET cc_start: 0.8434 (mtt) cc_final: 0.7802 (mtt) REVERT: D 410 GLU cc_start: 0.7443 (tt0) cc_final: 0.7190 (tt0) REVERT: D 660 MET cc_start: 0.8973 (tpp) cc_final: 0.8738 (mmm) REVERT: E 122 ASP cc_start: 0.8207 (m-30) cc_final: 0.7964 (m-30) REVERT: E 153 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7642 (mtt) REVERT: E 254 MET cc_start: 0.8073 (mtp) cc_final: 0.7869 (mtp) REVERT: E 387 GLU cc_start: 0.7888 (mp0) cc_final: 0.7647 (mp0) REVERT: E 489 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8923 (pt) REVERT: E 668 GLU cc_start: 0.7683 (mp0) cc_final: 0.7386 (mp0) REVERT: G 122 ASP cc_start: 0.7994 (m-30) cc_final: 0.7744 (m-30) REVERT: G 569 MET cc_start: 0.8711 (ttt) cc_final: 0.8193 (mtp) REVERT: G 618 MET cc_start: 0.8876 (ptm) cc_final: 0.8588 (ptp) REVERT: G 631 MET cc_start: 0.7936 (mmm) cc_final: 0.7473 (mmm) REVERT: H 122 ASP cc_start: 0.8147 (m-30) cc_final: 0.7923 (m-30) REVERT: H 668 GLU cc_start: 0.7596 (mp0) cc_final: 0.7281 (mp0) REVERT: I 122 ASP cc_start: 0.8147 (m-30) cc_final: 0.7853 (m-30) REVERT: I 377 MET cc_start: 0.8450 (mtt) cc_final: 0.7816 (mtt) REVERT: I 410 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: J 122 ASP cc_start: 0.8211 (m-30) cc_final: 0.7970 (m-30) REVERT: J 153 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: J 387 GLU cc_start: 0.7833 (mp0) cc_final: 0.7604 (mp0) REVERT: J 489 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8930 (pt) REVERT: J 668 GLU cc_start: 0.7679 (mp0) cc_final: 0.7345 (mp0) outliers start: 59 outliers final: 22 residues processed: 615 average time/residue: 1.4869 time to fit residues: 1147.4015 Evaluate side-chains 580 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 551 time to evaluate : 4.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain I residue 410 GLU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 358 VAL Chi-restraints excluded: chain J residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 622 optimal weight: 2.9990 chunk 655 optimal weight: 4.9990 chunk 598 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 500 optimal weight: 0.0970 chunk 195 optimal weight: 7.9990 chunk 576 optimal weight: 9.9990 chunk 603 optimal weight: 9.9990 chunk 635 optimal weight: 0.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 599 HIS E 599 HIS ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 599 HIS I 9 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 58418 Z= 0.297 Angle : 0.528 9.182 79214 Z= 0.272 Chirality : 0.044 0.178 8674 Planarity : 0.005 0.049 10168 Dihedral : 8.040 153.683 7868 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.08 % Allowed : 9.54 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 0.87 (0.10), residues: 7064 helix: 1.31 (0.09), residues: 2950 sheet: -0.18 (0.15), residues: 1170 loop : 0.31 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 454 HIS 0.012 0.001 HIS D 599 PHE 0.034 0.002 PHE C 82 TYR 0.018 0.002 TYR I 80 ARG 0.009 0.001 ARG B 468 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 535 time to evaluate : 5.027 Fit side-chains revert: symmetry clash REVERT: A 265 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 153 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7406 (mtm) REVERT: B 569 MET cc_start: 0.8661 (ttt) cc_final: 0.8130 (mtp) REVERT: C 122 ASP cc_start: 0.8173 (m-30) cc_final: 0.7927 (m-30) REVERT: C 668 GLU cc_start: 0.7674 (mp0) cc_final: 0.7286 (mp0) REVERT: D 122 ASP cc_start: 0.8178 (m-30) cc_final: 0.7894 (m-30) REVERT: E 39 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8188 (tmm-80) REVERT: E 122 ASP cc_start: 0.8132 (m-30) cc_final: 0.7862 (m-30) REVERT: E 153 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7688 (mtt) REVERT: E 254 MET cc_start: 0.8094 (mtp) cc_final: 0.7883 (mtp) REVERT: E 489 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8990 (pt) REVERT: E 668 GLU cc_start: 0.7646 (mp0) cc_final: 0.7375 (mp0) REVERT: G 153 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7410 (mtm) REVERT: G 631 MET cc_start: 0.7985 (mmm) cc_final: 0.7499 (mmm) REVERT: H 122 ASP cc_start: 0.8177 (m-30) cc_final: 0.7944 (m-30) REVERT: H 272 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8669 (mp) REVERT: H 668 GLU cc_start: 0.7572 (mp0) cc_final: 0.7289 (mp0) REVERT: I 122 ASP cc_start: 0.8174 (m-30) cc_final: 0.7859 (m-30) REVERT: J 122 ASP cc_start: 0.8118 (m-30) cc_final: 0.7854 (m-30) REVERT: J 153 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7653 (mtt) REVERT: J 489 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8997 (pt) REVERT: J 668 GLU cc_start: 0.7677 (mp0) cc_final: 0.7384 (mp0) outliers start: 64 outliers final: 32 residues processed: 573 average time/residue: 1.5210 time to fit residues: 1093.8808 Evaluate side-chains 564 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 523 time to evaluate : 4.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain E residue 39 ARG Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 664 MET Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 461 THR Chi-restraints excluded: chain G residue 572 SER Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 638 ASP Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 489 ILE Chi-restraints excluded: chain J residue 498 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 418 optimal weight: 9.9990 chunk 674 optimal weight: 10.0000 chunk 411 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 468 optimal weight: 4.9990 chunk 707 optimal weight: 0.4980 chunk 651 optimal weight: 0.8980 chunk 563 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 chunk 435 optimal weight: 0.0060 chunk 345 optimal weight: 9.9990 overall best weight: 1.0896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS E 599 HIS ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 599 HIS I 9 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 58418 Z= 0.143 Angle : 0.450 7.836 79214 Z= 0.232 Chirality : 0.041 0.132 8674 Planarity : 0.004 0.050 10168 Dihedral : 7.774 150.396 7868 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.90 % Allowed : 9.80 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 7064 helix: 1.60 (0.10), residues: 2900 sheet: -0.16 (0.15), residues: 1150 loop : 0.40 (0.12), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 454 HIS 0.013 0.001 HIS D 599 PHE 0.016 0.001 PHE C 82 TYR 0.013 0.001 TYR D 686 ARG 0.009 0.000 ARG G 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14128 Ramachandran restraints generated. 7064 Oldfield, 0 Emsley, 7064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 537 time to evaluate : 5.800 Fit side-chains REVERT: A 265 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8031 (p) REVERT: B 122 ASP cc_start: 0.8006 (m-30) cc_final: 0.7763 (m-30) REVERT: B 569 MET cc_start: 0.8658 (ttt) cc_final: 0.8140 (mtp) REVERT: C 122 ASP cc_start: 0.8154 (m-30) cc_final: 0.7928 (m-30) REVERT: C 637 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8966 (tm) REVERT: C 668 GLU cc_start: 0.7671 (mp0) cc_final: 0.7285 (mp0) REVERT: D 122 ASP cc_start: 0.8155 (m-30) cc_final: 0.7864 (m-30) REVERT: D 246 LYS cc_start: 0.7150 (tptm) cc_final: 0.6853 (mppt) REVERT: E 122 ASP cc_start: 0.8221 (m-30) cc_final: 0.7973 (m-30) REVERT: E 153 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7526 (mtm) REVERT: E 254 MET cc_start: 0.8098 (mtp) cc_final: 0.7891 (mtp) REVERT: E 489 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8971 (pt) REVERT: E 668 GLU cc_start: 0.7670 (mp0) cc_final: 0.7388 (mp0) REVERT: F 395 MET cc_start: 0.8739 (mtp) cc_final: 0.8462 (ttm) REVERT: F 410 GLU cc_start: 0.7642 (tt0) cc_final: 0.7298 (tm-30) REVERT: G 122 ASP cc_start: 0.8012 (m-30) cc_final: 0.7785 (m-30) REVERT: G 569 MET cc_start: 0.8498 (ttt) cc_final: 0.8052 (mtp) REVERT: G 631 MET cc_start: 0.7982 (mmm) cc_final: 0.7526 (mmm) REVERT: H 122 ASP cc_start: 0.8160 (m-30) cc_final: 0.7934 (m-30) REVERT: H 272 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8661 (mp) REVERT: H 668 GLU cc_start: 0.7592 (mp0) cc_final: 0.7289 (mp0) REVERT: I 122 ASP cc_start: 0.8163 (m-30) cc_final: 0.7858 (m-30) REVERT: J 122 ASP cc_start: 0.8162 (m-30) cc_final: 0.7905 (m-30) REVERT: J 153 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7540 (mtm) REVERT: J 387 GLU cc_start: 0.7883 (mp0) cc_final: 0.7579 (mp0) REVERT: J 489 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8983 (pt) REVERT: J 668 GLU cc_start: 0.7662 (mp0) cc_final: 0.7359 (mp0) outliers start: 53 outliers final: 33 residues processed: 570 average time/residue: 1.4925 time to fit residues: 1071.4047 Evaluate side-chains 573 residues out of total 6196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 533 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 572 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 572 SER Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 503 THR Chi-restraints excluded: chain F residue 637 LEU Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain G residue 410 GLU Chi-restraints excluded: chain G residue 638 ASP Chi-restraints excluded: chain G residue 682 ILE Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 637 LEU Chi-restraints excluded: chain H residue 638 ASP Chi-restraints excluded: chain I residue 536 LEU Chi-restraints excluded: chain I residue 637 LEU Chi-restraints excluded: chain I residue 638 ASP Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 153 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 334 VAL Chi-restraints excluded: chain J residue 489 ILE Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 710 random chunks: chunk 447 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 172 optimal weight: 8.9990 chunk 519 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 564 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 chunk 579 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN C 385 ASN C 599 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 HIS ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 HIS ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 599 HIS I 9 HIS I 599 HIS J 599 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.081450 restraints weight = 113551.511| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.85 r_work: 0.2801 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 58418 Z= 0.355 Angle : 0.558 9.916 79214 Z= 0.287 Chirality : 0.045 0.190 8674 Planarity : 0.005 0.053 10168 Dihedral : 8.142 154.377 7868 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.13 % Allowed : 9.67 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.15 % 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: 0.72 (0.10), residues: 7064 helix: 1.13 (0.09), residues: 2950 sheet: -0.23 (0.15), residues: 1170 loop : 0.28 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 454 HIS 0.013 0.001 HIS D 599 PHE 0.036 0.002 PHE C 82 TYR 0.018 0.002 TYR I 139 ARG 0.009 0.001 ARG G 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16653.23 seconds wall clock time: 291 minutes 59.55 seconds (17519.55 seconds total)