Starting phenix.real_space_refine on Sat Mar 7 08:28:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fep_31559/03_2026/7fep_31559.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.006 sd= 0.269 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 S 98 5.16 5 C 13356 2.51 5 N 3528 2.21 5 O 4046 1.98 5 H 19353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40381 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2815 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "C" Number of atoms: 2821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2821 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "D" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "E" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2849 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "F" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "G" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2831 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "I" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "J" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "K" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2840 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "L" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2822 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "M" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2822 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "N" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2827 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "H" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2826 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT O 1 " pdbres="PHE O 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT P 1 " pdbres="PHE P 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Q 1 " pdbres="PHE Q 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT R 1 " pdbres="PHE R 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT S 1 " pdbres="PHE S 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT T 1 " pdbres="PHE T 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT U 1 " pdbres="PHE U 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT V 1 " pdbres="PHE V 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT W 1 " pdbres="PHE W 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT X 1 " pdbres="PHE X 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Y 1 " pdbres="PHE Y 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT Z 1 " pdbres="PHE Z 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT a 1 " pdbres="PHE a 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "b" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'OTT': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="OTT b 1 " pdbres="PHE b 2 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'OTT:plan-1': 1, 'MAA:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.33, per 1000 atoms: 0.18 Number of scatterers: 40381 At special positions: 0 Unit cell: (122.08, 118.72, 128.8, 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 98 16.00 O 4046 8.00 N 3528 7.00 C 13356 6.00 H 19353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 63 sheets defined 47.2% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 83 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.754A pdb=" N ILE B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.824A pdb=" N LEU C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 24' Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 83 " --> pdb=" O THR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.824A pdb=" N LEU D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 24' Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 36 through 54 removed outlier: 3.589A pdb=" N ALA D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA D 104 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 24' Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER E 42 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 83 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE E 137 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 154 " --> pdb=" O ASN E 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.754A pdb=" N ILE E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.829A pdb=" N GLU E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU F 23 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 24 " --> pdb=" O TYR F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 24' Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 36 through 54 removed outlier: 3.589A pdb=" N ALA F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER F 42 " --> pdb=" O ASN F 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 83 " --> pdb=" O THR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA F 104 " --> pdb=" O ALA F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 158 removed outlier: 3.724A pdb=" N GLU F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE F 137 " --> pdb=" O THR F 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.754A pdb=" N ILE F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.829A pdb=" N GLU F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.824A pdb=" N LEU G 23 " --> pdb=" O ILE G 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 24 " --> pdb=" O TYR G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 19 through 24' Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 48 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN G 81 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 158 removed outlier: 3.724A pdb=" N GLU G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE G 137 " --> pdb=" O THR G 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 138 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 154 " --> pdb=" O ASN G 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 24 removed outlier: 3.824A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 19 through 24' Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA I 40 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER I 42 " --> pdb=" O ASN I 38 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN I 81 " --> pdb=" O TYR I 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE I 83 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU I 136 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE I 137 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA I 138 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU I 143 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN I 150 " --> pdb=" O ARG I 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 154 " --> pdb=" O ASN I 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU I 155 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 removed outlier: 3.754A pdb=" N ILE I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU I 181 " --> pdb=" O GLU I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU J 23 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU J 24 " --> pdb=" O TYR J 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 19 through 24' Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 48 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN J 81 " --> pdb=" O TYR J 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE J 83 " --> pdb=" O THR J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU J 136 " --> pdb=" O ALA J 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA J 138 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU J 143 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU J 144 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN J 150 " --> pdb=" O ARG J 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS J 151 " --> pdb=" O ASP J 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 152 " --> pdb=" O LYS J 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA J 154 " --> pdb=" O ASN J 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU J 155 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR J 168 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU J 181 " --> pdb=" O GLU J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU K 24 " --> pdb=" O TYR K 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 19 through 24' Processing helix chain 'K' and resid 25 through 27 No H-bonds generated for 'chain 'K' and resid 25 through 27' Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN K 81 " --> pdb=" O TYR K 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE K 83 " --> pdb=" O THR K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU K 136 " --> pdb=" O ALA K 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 140 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 143 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU K 144 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN K 150 " --> pdb=" O ARG K 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS K 151 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL K 152 " --> pdb=" O LYS K 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA K 154 " --> pdb=" O ASN K 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU K 155 " --> pdb=" O LYS K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 183 removed outlier: 3.827A pdb=" N GLU K 181 " --> pdb=" O GLU K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU L 24 " --> pdb=" O TYR L 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 19 through 24' Processing helix chain 'L' and resid 25 through 27 No H-bonds generated for 'chain 'L' and resid 25 through 27' Processing helix chain 'L' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA L 40 " --> pdb=" O ASP L 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER L 42 " --> pdb=" O ASN L 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA L 52 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE L 83 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 138 " --> pdb=" O GLU L 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU L 143 " --> pdb=" O ALA L 139 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL L 152 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA L 154 " --> pdb=" O ASN L 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU L 155 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE L 164 " --> pdb=" O PRO L 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR L 168 " --> pdb=" O ILE L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 183 removed outlier: 3.829A pdb=" N GLU L 181 " --> pdb=" O GLU L 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU M 23 " --> pdb=" O ILE M 19 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU M 24 " --> pdb=" O TYR M 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 19 through 24' Processing helix chain 'M' and resid 25 through 27 No H-bonds generated for 'chain 'M' and resid 25 through 27' Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.589A pdb=" N ALA M 40 " --> pdb=" O ASP M 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER M 42 " --> pdb=" O ASN M 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU M 53 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 83 removed outlier: 3.793A pdb=" N THR M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE M 83 " --> pdb=" O THR M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU M 136 " --> pdb=" O ALA M 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA M 138 " --> pdb=" O GLU M 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 140 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU M 144 " --> pdb=" O LYS M 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN M 150 " --> pdb=" O ARG M 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL M 152 " --> pdb=" O LYS M 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA M 154 " --> pdb=" O ASN M 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU M 155 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE M 164 " --> pdb=" O PRO M 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR M 168 " --> pdb=" O ILE M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.824A pdb=" N LEU N 23 " --> pdb=" O ILE N 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU N 24 " --> pdb=" O TYR N 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 19 through 24' Processing helix chain 'N' and resid 25 through 27 No H-bonds generated for 'chain 'N' and resid 25 through 27' Processing helix chain 'N' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA N 40 " --> pdb=" O ASP N 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER N 42 " --> pdb=" O ASN N 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER N 45 " --> pdb=" O ASN N 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR N 79 " --> pdb=" O ALA N 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN N 81 " --> pdb=" O TYR N 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE N 83 " --> pdb=" O THR N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 104 removed outlier: 3.540A pdb=" N ALA N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 158 removed outlier: 3.725A pdb=" N GLU N 136 " --> pdb=" O ALA N 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA N 138 " --> pdb=" O GLU N 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN N 150 " --> pdb=" O ARG N 146 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS N 151 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA N 154 " --> pdb=" O ASN N 150 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU N 155 " --> pdb=" O LYS N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE N 164 " --> pdb=" O PRO N 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR N 168 " --> pdb=" O ILE N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 183 removed outlier: 3.828A pdb=" N GLU N 181 " --> pdb=" O GLU N 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.823A pdb=" N LEU H 23 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 24' Processing helix chain 'H' and resid 25 through 27 No H-bonds generated for 'chain 'H' and resid 25 through 27' Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.590A pdb=" N ALA H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER H 42 " --> pdb=" O ASN H 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 52 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 83 removed outlier: 3.792A pdb=" N THR H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN H 81 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 83 " --> pdb=" O THR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 104 removed outlier: 3.539A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 158 removed outlier: 3.724A pdb=" N GLU H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA H 154 " --> pdb=" O ASN H 150 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.755A pdb=" N ILE H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR H 168 " --> pdb=" O ILE H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 183 removed outlier: 3.827A pdb=" N GLU H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER A 65 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET A 94 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE A 59 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE A 90 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR A 112 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 89 " --> pdb=" O TYR A 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.568A pdb=" N ILE A 121 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 172 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 125 through 131 removed outlier: 4.085A pdb=" N GLY H 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 130 " --> pdb=" O GLY H 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B 65 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET B 94 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE B 59 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE B 90 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR B 112 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 89 " --> pdb=" O TYR B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE B 121 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 172 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 131 removed outlier: 4.018A pdb=" N GLY N 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 130 " --> pdb=" O GLY N 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 65 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET C 94 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE C 59 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE C 90 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR C 112 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR C 89 " --> pdb=" O TYR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE C 121 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 172 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 125 through 131 removed outlier: 3.924A pdb=" N GLY M 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY C 130 " --> pdb=" O GLY M 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 8 Processing sheet with id=AB8, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER D 65 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET D 94 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE D 59 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE D 90 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR D 112 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR D 89 " --> pdb=" O TYR D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE D 121 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN D 172 " --> pdb=" O ILE D 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 125 through 131 removed outlier: 3.899A pdb=" N GLY L 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AC4, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER E 65 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET E 94 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE E 59 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE E 90 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR E 112 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR E 89 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE E 121 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 172 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 125 through 131 removed outlier: 4.041A pdb=" N GLY K 130 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY E 130 " --> pdb=" O GLY K 126 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 5 through 8 Processing sheet with id=AC9, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER F 65 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET F 94 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE F 59 " --> pdb=" O SER F 88 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE F 90 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR F 112 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR F 89 " --> pdb=" O TYR F 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE F 121 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 172 " --> pdb=" O ILE F 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 125 through 131 removed outlier: 3.723A pdb=" N GLY J 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY F 130 " --> pdb=" O GLY J 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AD5, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.527A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER G 65 " --> pdb=" O ILE G 92 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET G 94 " --> pdb=" O SER G 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.527A pdb=" N ILE G 59 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE G 90 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR G 112 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR G 89 " --> pdb=" O TYR G 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE G 121 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN G 172 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 125 through 131 removed outlier: 3.909A pdb=" N GLY I 130 " --> pdb=" O GLY G 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY G 130 " --> pdb=" O GLY I 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 5 through 8 Processing sheet with id=AE1, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER I 65 " --> pdb=" O ILE I 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET I 94 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR I 89 " --> pdb=" O TYR I 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE I 121 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN I 172 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 5 through 8 Processing sheet with id=AE5, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER J 65 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET J 94 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR J 112 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR J 89 " --> pdb=" O TYR J 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE J 121 " --> pdb=" O ASN J 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN J 172 " --> pdb=" O ILE J 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AE9, first strand: chain 'K' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER K 65 " --> pdb=" O ILE K 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET K 94 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR K 89 " --> pdb=" O TYR K 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'K' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE K 121 " --> pdb=" O ASN K 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN K 172 " --> pdb=" O ILE K 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AF4, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER L 65 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET L 94 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR L 89 " --> pdb=" O TYR L 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.570A pdb=" N ILE L 121 " --> pdb=" O ASN L 172 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN L 172 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AF8, first strand: chain 'M' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER M 65 " --> pdb=" O ILE M 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET M 94 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 59 through 60 removed outlier: 6.528A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR M 89 " --> pdb=" O TYR M 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'M' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE M 121 " --> pdb=" O ASN M 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN M 172 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AG3, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER N 65 " --> pdb=" O ILE N 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET N 94 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR N 89 " --> pdb=" O TYR N 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE N 121 " --> pdb=" O ASN N 172 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN N 172 " --> pdb=" O ILE N 121 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 8 Processing sheet with id=AG7, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER H 65 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET H 94 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.529A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N TYR H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR H 89 " --> pdb=" O TYR H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.569A pdb=" N ILE H 121 " --> pdb=" O ASN H 172 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 172 " --> pdb=" O ILE H 121 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.66 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 19328 1.00 - 1.20: 25 1.20 - 1.40: 7966 1.40 - 1.60: 13104 1.60 - 1.80: 210 Bond restraints: 40633 Sorted by residual: bond pdb=" C ALA W 6 " pdb=" N MP8 W 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.76e+01 bond pdb=" C ALA T 6 " pdb=" N MP8 T 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.72e+01 bond pdb=" C ALA X 6 " pdb=" N MP8 X 7 " ideal model delta sigma weight residual 1.329 1.467 -0.138 1.40e-02 5.10e+03 9.68e+01 bond pdb=" C ALA Y 6 " pdb=" N MP8 Y 7 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.40e-02 5.10e+03 9.64e+01 bond pdb=" C ALA O 6 " pdb=" N MP8 O 7 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.40e-02 5.10e+03 9.63e+01 ... (remaining 40628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.54: 71378 12.54 - 25.08: 103 25.08 - 37.62: 716 37.62 - 50.17: 398 50.17 - 62.71: 228 Bond angle restraints: 72823 Sorted by residual: angle pdb=" CA GLY E 13 " pdb=" N GLY E 13 " pdb=" H GLY E 13 " ideal model delta sigma weight residual 113.82 51.11 62.71 3.00e+00 1.11e-01 4.37e+02 angle pdb=" C THR G 168 " pdb=" N ASP G 169 " pdb=" H ASP G 169 " ideal model delta sigma weight residual 124.38 61.68 62.70 3.00e+00 1.11e-01 4.37e+02 angle pdb=" CA ILE K 43 " pdb=" N ILE K 43 " pdb=" H ILE K 43 " ideal model delta sigma weight residual 114.62 53.77 60.85 3.00e+00 1.11e-01 4.11e+02 angle pdb=" CA LEU G 144 " pdb=" N LEU G 144 " pdb=" H LEU G 144 " ideal model delta sigma weight residual 114.71 53.97 60.74 3.00e+00 1.11e-01 4.10e+02 angle pdb=" CA GLU E 14 " pdb=" N GLU E 14 " pdb=" H GLU E 14 " ideal model delta sigma weight residual 113.46 53.05 60.41 3.00e+00 1.11e-01 4.05e+02 ... (remaining 72818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 16167 15.54 - 31.09: 1985 31.09 - 46.63: 615 46.63 - 62.17: 356 62.17 - 77.72: 2 Dihedral angle restraints: 19125 sinusoidal: 10617 harmonic: 8508 Sorted by residual: dihedral pdb=" CA ASP B 169 " pdb=" C ASP B 169 " pdb=" N ARG B 170 " pdb=" CA ARG B 170 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ARG A 170 " pdb=" CA ARG A 170 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP L 169 " pdb=" C ASP L 169 " pdb=" N ARG L 170 " pdb=" CA ARG L 170 " ideal model delta harmonic sigma weight residual -180.00 -153.20 -26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 19122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2148 0.084 - 0.169: 858 0.169 - 0.253: 201 0.253 - 0.338: 111 0.338 - 0.422: 42 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CG LEU B 144 " pdb=" CB LEU B 144 " pdb=" CD1 LEU B 144 " pdb=" CD2 LEU B 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CG LEU M 144 " pdb=" CB LEU M 144 " pdb=" CD1 LEU M 144 " pdb=" CD2 LEU M 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CG LEU E 144 " pdb=" CB LEU E 144 " pdb=" CD1 LEU E 144 " pdb=" CD2 LEU E 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3357 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 13 " 0.022 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" N GLU E 14 " -0.009 2.00e-02 2.50e+03 pdb=" CA GLU E 14 " 0.024 2.00e-02 2.50e+03 pdb=" H GLU E 14 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 168 " -0.020 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" N ASP F 169 " 0.011 2.00e-02 2.50e+03 pdb=" CA ASP F 169 " -0.020 2.00e-02 2.50e+03 pdb=" H ASP F 169 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 168 " 0.019 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" N ASP G 169 " -0.008 2.00e-02 2.50e+03 pdb=" CA ASP G 169 " 0.017 2.00e-02 2.50e+03 pdb=" H ASP G 169 " -0.028 2.00e-02 2.50e+03 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 1498 2.01 - 2.66: 52977 2.66 - 3.31: 99413 3.31 - 3.95: 129078 3.95 - 4.60: 210660 Nonbonded interactions: 493626 Sorted by model distance: nonbonded pdb=" H ASP G 169 " pdb=" HA ASP G 169 " model vdw 1.367 1.816 nonbonded pdb=" H LEU J 61 " pdb=" HA LEU J 61 " model vdw 1.456 1.816 nonbonded pdb=" H ILE K 188 " pdb=" HA ILE K 188 " model vdw 1.457 1.816 nonbonded pdb=" H MET F 120 " pdb=" HA MET F 120 " model vdw 1.460 1.816 nonbonded pdb=" H LEU K 61 " pdb=" HA LEU K 61 " model vdw 1.461 1.816 ... (remaining 493621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH )) or resid 18 or (resid 19 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 thr \ ough 58 or (resid 59 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1 or name H or name HA )) or resid 60 through 190)) \ selection = (chain 'B' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'C' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 through 47 or (resid 48 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or n \ ame HE1 or name HE2 or name HZ )) or resid 50 through 190)) selection = (chain 'D' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'E' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O )) or (resid 14 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 15 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1 or name NH2)) or (resid 16 and (name N or name CA or name C or name \ O or name CB )) or (resid 17 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or resid 18 or (resid 19 and (name N or name CA or name C or name O or na \ me CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 o \ r (resid 48 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name H \ E2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or name CA or n \ ame C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name \ HA )) or resid 60 through 190)) selection = (chain 'F' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'G' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or resid 17 through 18 or (resid 19 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 throug \ h 47 or (resid 48 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or \ name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name H o \ r name HA )) or resid 60 through 190)) selection = (chain 'H' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 16 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 17 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resi \ d 18 or (resid 19 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1 or name HA )) or resid 20 through 47 or (resid 48 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2)) or (resid 49 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA or \ name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ \ )) or resid 50 through 58 or (resid 59 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA )) or resi \ d 60 through 190)) selection = (chain 'L' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or resid 18 or (resid 19 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or re \ sid 20 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1 or name H or name HA )) or resid 60 through 190)) selection = (chain 'M' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ or name OH )) or resid 18 or (resid 19 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or re \ sid 20 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or \ name HE1 or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1 or name H or name HA )) or resid 60 through 190)) selection = (chain 'N' and (resid 2 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or (resid 17 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z or name OH )) or resid 18 or (resid 19 and (name N or name CA or name C or nam \ e O or name CB or name CG1 or name CG2 or name CD1 or name HA )) or resid 20 thr \ ough 47 or (resid 48 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2)) or (resid 49 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 \ or name HE2 or name HZ )) or resid 50 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 or name \ H or name HA )) or resid 60 through 190)) } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.660 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: 0.220 Extract box with map and model: 0.530 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 37.130 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 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:1.470 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 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 : 0.015 0.138 21308 Z= 0.740 Angle : 1.256 9.103 28658 Z= 0.661 Chirality : 0.110 0.422 3360 Planarity : 0.005 0.037 3724 Dihedral : 14.371 61.454 8092 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.57 % Favored : 89.89 % Rotamer: Outliers : 2.53 % Allowed : 1.90 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.30 (0.11), residues: 2632 helix: -3.60 (0.10), residues: 1106 sheet: -3.00 (0.20), residues: 434 loop : -3.47 (0.13), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 12 TYR 0.020 0.002 TYR M 17 PHE 0.006 0.001 PHE A 49 HIS 0.003 0.002 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.01509 (21280) covalent geometry : angle 1.25625 (28658) hydrogen bonds : bond 0.19199 ( 588) hydrogen bonds : angle 7.48339 ( 1638) Misc. bond : bond 0.03662 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 612 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 556 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.6959 (ttmm) cc_final: 0.6641 (tttt) REVERT: A 108 LYS cc_start: 0.8324 (tptm) cc_final: 0.7795 (tppt) REVERT: A 169 ASP cc_start: 0.7652 (t70) cc_final: 0.7349 (t0) REVERT: A 181 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 186 ASP cc_start: 0.7979 (m-30) cc_final: 0.7675 (m-30) REVERT: B 8 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6172 (tt0) REVERT: B 84 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6820 (tttt) REVERT: B 108 LYS cc_start: 0.8606 (tptm) cc_final: 0.8254 (tppt) REVERT: B 118 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6811 (mm-30) REVERT: C 84 LYS cc_start: 0.7426 (ttmm) cc_final: 0.7188 (mtpt) REVERT: C 89 THR cc_start: 0.7688 (p) cc_final: 0.7415 (p) REVERT: C 108 LYS cc_start: 0.8453 (tptm) cc_final: 0.7991 (tppt) REVERT: C 118 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7042 (mm-30) REVERT: C 151 LYS cc_start: 0.7542 (tppp) cc_final: 0.7317 (mttt) REVERT: C 165 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7473 (mt-10) REVERT: D 84 LYS cc_start: 0.7248 (ttmm) cc_final: 0.6939 (tttt) REVERT: D 107 GLU cc_start: 0.5819 (tp30) cc_final: 0.5591 (tp30) REVERT: D 108 LYS cc_start: 0.8328 (tptm) cc_final: 0.7566 (tppt) REVERT: E 84 LYS cc_start: 0.6818 (ttmm) cc_final: 0.6571 (tttt) REVERT: E 108 LYS cc_start: 0.8262 (tptm) cc_final: 0.7716 (tppt) REVERT: E 116 ASN cc_start: 0.6863 (p0) cc_final: 0.5524 (p0) REVERT: F 8 GLU cc_start: 0.6820 (tm-30) cc_final: 0.6493 (tt0) REVERT: F 84 LYS cc_start: 0.7105 (ttmm) cc_final: 0.6762 (tttt) REVERT: F 108 LYS cc_start: 0.8314 (tptm) cc_final: 0.7744 (tppt) REVERT: F 156 ARG cc_start: 0.6337 (mmt180) cc_final: 0.6080 (mmt180) REVERT: F 186 ASP cc_start: 0.7670 (m-30) cc_final: 0.7161 (m-30) REVERT: G 8 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6315 (tt0) REVERT: G 37 ASP cc_start: 0.6567 (OUTLIER) cc_final: 0.6203 (m-30) REVERT: G 118 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6988 (mm-30) REVERT: I 84 LYS cc_start: 0.7254 (ttmm) cc_final: 0.6977 (tttt) REVERT: I 108 LYS cc_start: 0.8428 (tptm) cc_final: 0.7822 (tppt) REVERT: I 186 ASP cc_start: 0.7645 (m-30) cc_final: 0.7223 (m-30) REVERT: J 6 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6923 (m) REVERT: J 108 LYS cc_start: 0.8344 (tptm) cc_final: 0.7912 (tppt) REVERT: J 110 LYS cc_start: 0.6017 (mttp) cc_final: 0.5762 (mtmm) REVERT: J 129 GLN cc_start: 0.8533 (tt0) cc_final: 0.8276 (tt0) REVERT: K 8 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6612 (tt0) REVERT: K 84 LYS cc_start: 0.7139 (ttmm) cc_final: 0.6852 (ttpt) REVERT: K 108 LYS cc_start: 0.8359 (tptm) cc_final: 0.7889 (tppt) REVERT: K 116 ASN cc_start: 0.6908 (p0) cc_final: 0.5715 (p0) REVERT: K 172 ASN cc_start: 0.6632 (t0) cc_final: 0.6380 (t0) REVERT: K 186 ASP cc_start: 0.8165 (m-30) cc_final: 0.7756 (m-30) REVERT: L 8 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6918 (tt0) REVERT: L 84 LYS cc_start: 0.7369 (ttmm) cc_final: 0.7166 (tttt) REVERT: L 108 LYS cc_start: 0.8544 (tptm) cc_final: 0.7932 (tppt) REVERT: M 8 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6263 (tt0) REVERT: M 54 ASP cc_start: 0.6730 (t0) cc_final: 0.6301 (t0) REVERT: M 58 GLU cc_start: 0.6987 (tt0) cc_final: 0.6690 (tt0) REVERT: M 84 LYS cc_start: 0.7092 (ttmm) cc_final: 0.6770 (tttt) REVERT: N 108 LYS cc_start: 0.8533 (tptm) cc_final: 0.8167 (tppt) REVERT: N 165 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7795 (mt-10) REVERT: H 84 LYS cc_start: 0.7450 (ttmm) cc_final: 0.7223 (mtpt) REVERT: H 89 THR cc_start: 0.7646 (p) cc_final: 0.7379 (p) REVERT: H 108 LYS cc_start: 0.8340 (tptm) cc_final: 0.7955 (tppt) REVERT: H 165 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7233 (mt-10) outliers start: 56 outliers final: 4 residues processed: 598 average time/residue: 0.3707 time to fit residues: 327.6526 Evaluate side-chains 392 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 386 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain M residue 2 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114550 restraints weight = 65566.253| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.34 r_work: 0.3213 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21308 Z= 0.145 Angle : 1.404 21.956 28658 Z= 0.759 Chirality : 0.246 1.657 3360 Planarity : 0.004 0.045 3724 Dihedral : 5.560 33.614 2993 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.05 % Favored : 91.76 % Rotamer: Outliers : 1.40 % Allowed : 8.77 % Favored : 89.83 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.13), residues: 2632 helix: -2.44 (0.13), residues: 1092 sheet: -2.46 (0.22), residues: 434 loop : -2.64 (0.15), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 15 TYR 0.017 0.001 TYR K 17 PHE 0.006 0.001 PHE I 49 HIS 0.004 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00334 (21280) covalent geometry : angle 1.40413 (28658) hydrogen bonds : bond 0.05845 ( 588) hydrogen bonds : angle 5.25594 ( 1638) Misc. bond : bond 0.00033 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 416 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8819 (tptm) cc_final: 0.8515 (tppt) REVERT: B 108 LYS cc_start: 0.8989 (tptm) cc_final: 0.8509 (tppt) REVERT: C 108 LYS cc_start: 0.8930 (tptm) cc_final: 0.8626 (tppt) REVERT: C 165 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 167 ASP cc_start: 0.7029 (m-30) cc_final: 0.6814 (m-30) REVERT: D 108 LYS cc_start: 0.8821 (tptm) cc_final: 0.8442 (tppt) REVERT: E 108 LYS cc_start: 0.8870 (tptm) cc_final: 0.8628 (tppt) REVERT: F 108 LYS cc_start: 0.8765 (tptm) cc_final: 0.8461 (tppt) REVERT: F 186 ASP cc_start: 0.8746 (m-30) cc_final: 0.8512 (m-30) REVERT: G 151 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8451 (mttt) REVERT: I 89 THR cc_start: 0.8953 (p) cc_final: 0.8730 (p) REVERT: I 108 LYS cc_start: 0.8954 (tptm) cc_final: 0.8504 (tppt) REVERT: J 108 LYS cc_start: 0.8816 (tptm) cc_final: 0.8559 (tppt) REVERT: J 110 LYS cc_start: 0.8417 (mttp) cc_final: 0.8173 (mtmm) REVERT: J 120 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8083 (ttm) REVERT: K 98 MET cc_start: 0.7920 (mmt) cc_final: 0.7019 (mmt) REVERT: K 108 LYS cc_start: 0.8895 (tptm) cc_final: 0.8572 (tppt) REVERT: K 110 LYS cc_start: 0.8759 (mttm) cc_final: 0.8557 (mttm) REVERT: L 108 LYS cc_start: 0.8893 (tptm) cc_final: 0.8615 (tppt) REVERT: L 116 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7117 (p0) REVERT: M 74 MET cc_start: 0.7576 (mmm) cc_final: 0.7351 (mmm) REVERT: N 108 LYS cc_start: 0.9018 (tptm) cc_final: 0.8636 (tppt) REVERT: H 108 LYS cc_start: 0.8795 (tptm) cc_final: 0.8535 (tppt) REVERT: H 165 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7897 (mt-10) outliers start: 31 outliers final: 12 residues processed: 422 average time/residue: 0.4095 time to fit residues: 249.3060 Evaluate side-chains 385 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 371 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 166 ARG Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 166 ARG Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain H residue 166 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108430 restraints weight = 67115.121| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.47 r_work: 0.3036 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21308 Z= 0.148 Angle : 1.396 22.313 28658 Z= 0.752 Chirality : 0.249 1.692 3360 Planarity : 0.004 0.039 3724 Dihedral : 5.244 26.513 2982 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.10 % Favored : 92.55 % Rotamer: Outliers : 1.31 % Allowed : 10.22 % Favored : 88.47 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.14), residues: 2632 helix: -1.83 (0.14), residues: 1176 sheet: -2.38 (0.27), residues: 294 loop : -2.25 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 15 TYR 0.013 0.001 TYR N 17 PHE 0.014 0.001 PHE T 2 HIS 0.003 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00353 (21280) covalent geometry : angle 1.39644 (28658) hydrogen bonds : bond 0.05849 ( 588) hydrogen bonds : angle 4.53690 ( 1638) Misc. bond : bond 0.00135 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 424 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 395 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8715 (tptm) cc_final: 0.8423 (tppt) REVERT: A 165 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 108 LYS cc_start: 0.8953 (tptm) cc_final: 0.8586 (tppt) REVERT: C 108 LYS cc_start: 0.8942 (tptm) cc_final: 0.8640 (tppt) REVERT: C 165 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 108 LYS cc_start: 0.8935 (tptm) cc_final: 0.8500 (tppt) REVERT: E 56 GLU cc_start: 0.8108 (pm20) cc_final: 0.7822 (pm20) REVERT: E 108 LYS cc_start: 0.8916 (tptm) cc_final: 0.8652 (tppt) REVERT: F 108 LYS cc_start: 0.8776 (tptm) cc_final: 0.8537 (tppt) REVERT: F 186 ASP cc_start: 0.8773 (m-30) cc_final: 0.8414 (m-30) REVERT: G 151 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8565 (mttt) REVERT: I 108 LYS cc_start: 0.8991 (tptm) cc_final: 0.8619 (tppt) REVERT: J 108 LYS cc_start: 0.8851 (tptm) cc_final: 0.8643 (tppt) REVERT: J 110 LYS cc_start: 0.8497 (mttp) cc_final: 0.8253 (mtmm) REVERT: K 108 LYS cc_start: 0.8780 (tptm) cc_final: 0.8482 (tppt) REVERT: L 98 MET cc_start: 0.7978 (mmt) cc_final: 0.7473 (mmt) REVERT: L 108 LYS cc_start: 0.8899 (tptm) cc_final: 0.8610 (tppt) REVERT: M 56 GLU cc_start: 0.8101 (pm20) cc_final: 0.7874 (pm20) REVERT: M 74 MET cc_start: 0.7816 (mmm) cc_final: 0.7430 (mmm) REVERT: N 108 LYS cc_start: 0.8983 (tptm) cc_final: 0.8614 (tppt) REVERT: H 108 LYS cc_start: 0.8843 (tptm) cc_final: 0.8558 (tppt) REVERT: H 165 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7973 (mt-10) outliers start: 29 outliers final: 13 residues processed: 404 average time/residue: 0.4104 time to fit residues: 239.6223 Evaluate side-chains 396 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 383 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain U residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 52 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 232 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106599 restraints weight = 67859.529| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.48 r_work: 0.3059 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21308 Z= 0.146 Angle : 1.404 22.720 28658 Z= 0.757 Chirality : 0.254 1.721 3360 Planarity : 0.004 0.036 3724 Dihedral : 5.127 27.018 2982 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.76 % Rotamer: Outliers : 1.31 % Allowed : 10.80 % Favored : 87.88 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.15), residues: 2632 helix: -1.15 (0.15), residues: 1078 sheet: -1.33 (0.20), residues: 588 loop : -2.02 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 156 TYR 0.012 0.001 TYR B 17 PHE 0.009 0.001 PHE Q 2 HIS 0.003 0.001 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00353 (21280) covalent geometry : angle 1.40380 (28658) hydrogen bonds : bond 0.05546 ( 588) hydrogen bonds : angle 4.40528 ( 1638) Misc. bond : bond 0.00125 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 424 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 395 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLU cc_start: 0.8033 (tp30) cc_final: 0.7831 (tp30) REVERT: A 108 LYS cc_start: 0.8709 (tptm) cc_final: 0.8361 (tppt) REVERT: A 165 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8273 (mt-10) REVERT: B 108 LYS cc_start: 0.8934 (tptm) cc_final: 0.8561 (tppt) REVERT: C 108 LYS cc_start: 0.8951 (tptm) cc_final: 0.8617 (tppt) REVERT: C 116 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 165 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8120 (mt-10) REVERT: D 108 LYS cc_start: 0.8954 (tptm) cc_final: 0.8567 (tppt) REVERT: E 56 GLU cc_start: 0.8066 (pm20) cc_final: 0.7804 (pm20) REVERT: E 108 LYS cc_start: 0.8905 (tptm) cc_final: 0.8640 (tppt) REVERT: F 186 ASP cc_start: 0.8775 (m-30) cc_final: 0.8435 (m-30) REVERT: G 56 GLU cc_start: 0.8356 (pm20) cc_final: 0.8072 (pm20) REVERT: G 151 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8502 (mttt) REVERT: I 108 LYS cc_start: 0.9007 (tptm) cc_final: 0.8618 (tppt) REVERT: J 108 LYS cc_start: 0.8886 (tptm) cc_final: 0.8667 (tppt) REVERT: K 108 LYS cc_start: 0.8809 (tptm) cc_final: 0.8520 (tppt) REVERT: L 108 LYS cc_start: 0.8919 (tptm) cc_final: 0.8631 (tppt) REVERT: M 56 GLU cc_start: 0.8156 (pm20) cc_final: 0.7889 (pm20) REVERT: M 74 MET cc_start: 0.7806 (mmm) cc_final: 0.7433 (mmm) REVERT: N 108 LYS cc_start: 0.8977 (tptm) cc_final: 0.8546 (tppt) REVERT: H 108 LYS cc_start: 0.8849 (tptm) cc_final: 0.8555 (tppt) REVERT: H 165 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8030 (mt-10) outliers start: 29 outliers final: 13 residues processed: 402 average time/residue: 0.4020 time to fit residues: 231.3940 Evaluate side-chains 399 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 385 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109067 restraints weight = 67603.587| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.51 r_work: 0.3118 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21308 Z= 0.124 Angle : 1.396 23.400 28658 Z= 0.754 Chirality : 0.254 1.714 3360 Planarity : 0.003 0.035 3724 Dihedral : 4.666 24.588 2982 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.76 % Favored : 93.12 % Rotamer: Outliers : 0.68 % Allowed : 11.75 % Favored : 87.57 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.16), residues: 2632 helix: -0.75 (0.15), residues: 1106 sheet: -1.11 (0.20), residues: 588 loop : -1.77 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.009 0.001 TYR K 17 PHE 0.005 0.001 PHE Z 2 HIS 0.003 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00304 (21280) covalent geometry : angle 1.39587 (28658) hydrogen bonds : bond 0.04336 ( 588) hydrogen bonds : angle 3.98240 ( 1638) Misc. bond : bond 0.00076 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 403 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 388 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8689 (tptm) cc_final: 0.8437 (tppt) REVERT: B 108 LYS cc_start: 0.8894 (tptm) cc_final: 0.8518 (tppt) REVERT: B 151 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8503 (ttmt) REVERT: C 108 LYS cc_start: 0.8934 (tptm) cc_final: 0.8601 (tppt) REVERT: C 116 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7723 (p0) REVERT: D 108 LYS cc_start: 0.8949 (tptm) cc_final: 0.8536 (tppt) REVERT: E 56 GLU cc_start: 0.8033 (pm20) cc_final: 0.7677 (pm20) REVERT: E 108 LYS cc_start: 0.8805 (tptm) cc_final: 0.8580 (tppt) REVERT: F 186 ASP cc_start: 0.8800 (m-30) cc_final: 0.8387 (m-30) REVERT: G 56 GLU cc_start: 0.8271 (pm20) cc_final: 0.7923 (pm20) REVERT: G 151 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8446 (mttt) REVERT: I 108 LYS cc_start: 0.8977 (tptm) cc_final: 0.8520 (tppt) REVERT: J 108 LYS cc_start: 0.8877 (tptm) cc_final: 0.8645 (tppt) REVERT: K 108 LYS cc_start: 0.8733 (tptm) cc_final: 0.8380 (tppt) REVERT: K 167 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7287 (t0) REVERT: L 108 LYS cc_start: 0.8881 (tptm) cc_final: 0.8552 (tppt) REVERT: M 56 GLU cc_start: 0.8132 (pm20) cc_final: 0.7812 (pm20) REVERT: M 74 MET cc_start: 0.7707 (mmm) cc_final: 0.7351 (mmm) REVERT: N 98 MET cc_start: 0.8450 (mmt) cc_final: 0.7841 (mmt) REVERT: N 108 LYS cc_start: 0.8950 (tptm) cc_final: 0.8452 (tppt) REVERT: H 108 LYS cc_start: 0.8824 (tptm) cc_final: 0.8514 (tppt) outliers start: 15 outliers final: 10 residues processed: 395 average time/residue: 0.3908 time to fit residues: 224.6386 Evaluate side-chains 385 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 373 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 167 ASP Chi-restraints excluded: chain L residue 30 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 61 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.098016 restraints weight = 69783.406| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.50 r_work: 0.2952 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21308 Z= 0.224 Angle : 1.428 22.472 28658 Z= 0.768 Chirality : 0.253 1.786 3360 Planarity : 0.004 0.040 3724 Dihedral : 5.851 54.762 2982 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.85 % Favored : 90.62 % Rotamer: Outliers : 0.95 % Allowed : 12.48 % Favored : 86.57 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.15), residues: 2632 helix: -0.78 (0.15), residues: 1078 sheet: -1.37 (0.23), residues: 462 loop : -1.71 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 27 TYR 0.015 0.001 TYR G 17 PHE 0.014 0.001 PHE Z 2 HIS 0.002 0.000 HIS N 122 Details of bonding type rmsd covalent geometry : bond 0.00548 (21280) covalent geometry : angle 1.42767 (28658) hydrogen bonds : bond 0.07130 ( 588) hydrogen bonds : angle 4.50494 ( 1638) Misc. bond : bond 0.00141 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 386 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8860 (tptm) cc_final: 0.8532 (tppt) REVERT: A 167 ASP cc_start: 0.8032 (m-30) cc_final: 0.7808 (m-30) REVERT: B 98 MET cc_start: 0.8393 (mmt) cc_final: 0.8069 (tpt) REVERT: B 108 LYS cc_start: 0.8932 (tptm) cc_final: 0.8513 (tppt) REVERT: C 108 LYS cc_start: 0.8936 (tptm) cc_final: 0.8618 (tppt) REVERT: C 116 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7790 (p0) REVERT: D 108 LYS cc_start: 0.8955 (tptm) cc_final: 0.8536 (tppt) REVERT: E 108 LYS cc_start: 0.8830 (tptm) cc_final: 0.8617 (tppt) REVERT: F 186 ASP cc_start: 0.8783 (m-30) cc_final: 0.8446 (m-30) REVERT: G 56 GLU cc_start: 0.8362 (pm20) cc_final: 0.8014 (pm20) REVERT: G 151 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8548 (mttt) REVERT: I 108 LYS cc_start: 0.8949 (tptm) cc_final: 0.8508 (tppt) REVERT: I 177 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7885 (tm-30) REVERT: K 108 LYS cc_start: 0.8792 (tptm) cc_final: 0.8439 (tppt) REVERT: L 108 LYS cc_start: 0.8882 (tptm) cc_final: 0.8583 (tppt) REVERT: N 108 LYS cc_start: 0.8991 (tptm) cc_final: 0.8530 (tppt) REVERT: H 58 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: H 108 LYS cc_start: 0.8869 (tptm) cc_final: 0.8577 (tppt) outliers start: 21 outliers final: 17 residues processed: 393 average time/residue: 0.4110 time to fit residues: 229.8100 Evaluate side-chains 377 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 358 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain N residue 3 ILE Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 26 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100568 restraints weight = 68068.861| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.62 r_work: 0.2998 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21308 Z= 0.184 Angle : 1.415 22.669 28658 Z= 0.763 Chirality : 0.253 1.741 3360 Planarity : 0.004 0.036 3724 Dihedral : 5.560 46.493 2982 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.14 % Favored : 92.44 % Rotamer: Outliers : 1.18 % Allowed : 12.61 % Favored : 86.21 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 2632 helix: -0.74 (0.15), residues: 1078 sheet: -1.36 (0.24), residues: 434 loop : -1.73 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.012 0.001 TYR G 17 PHE 0.011 0.001 PHE Z 2 HIS 0.002 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00446 (21280) covalent geometry : angle 1.41518 (28658) hydrogen bonds : bond 0.06191 ( 588) hydrogen bonds : angle 4.36644 ( 1638) Misc. bond : bond 0.00120 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 384 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 358 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8835 (tptm) cc_final: 0.8463 (tppt) REVERT: A 167 ASP cc_start: 0.8033 (m-30) cc_final: 0.7828 (m-30) REVERT: B 8 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: B 98 MET cc_start: 0.8227 (mmt) cc_final: 0.7912 (tpt) REVERT: B 108 LYS cc_start: 0.8934 (tptm) cc_final: 0.8446 (tppt) REVERT: C 8 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: C 108 LYS cc_start: 0.8957 (tptm) cc_final: 0.8573 (tppt) REVERT: C 116 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7931 (p0) REVERT: D 8 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6856 (tt0) REVERT: D 108 LYS cc_start: 0.8968 (tptm) cc_final: 0.8473 (tppt) REVERT: E 108 LYS cc_start: 0.8838 (tptm) cc_final: 0.8585 (tppt) REVERT: F 8 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: F 186 ASP cc_start: 0.8826 (m-30) cc_final: 0.8487 (m-30) REVERT: G 8 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7570 (tt0) REVERT: G 151 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8484 (mttt) REVERT: I 108 LYS cc_start: 0.8955 (tptm) cc_final: 0.8439 (tppt) REVERT: I 177 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7856 (tm-30) REVERT: K 8 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: L 8 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: L 108 LYS cc_start: 0.8875 (tptm) cc_final: 0.8535 (tppt) REVERT: M 74 MET cc_start: 0.7733 (mmm) cc_final: 0.7422 (mmm) REVERT: N 108 LYS cc_start: 0.8970 (tptm) cc_final: 0.8462 (tppt) REVERT: H 8 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: H 58 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: H 108 LYS cc_start: 0.8913 (tptm) cc_final: 0.8557 (tppt) outliers start: 26 outliers final: 14 residues processed: 377 average time/residue: 0.3893 time to fit residues: 213.6777 Evaluate side-chains 376 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 352 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 110 LYS Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 56 GLU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 204 optimal weight: 0.0030 chunk 19 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 230 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102965 restraints weight = 67800.058| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.55 r_work: 0.2836 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21308 Z= 0.141 Angle : 1.404 23.288 28658 Z= 0.758 Chirality : 0.254 1.712 3360 Planarity : 0.004 0.034 3724 Dihedral : 5.084 34.123 2982 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.32 % Favored : 91.49 % Rotamer: Outliers : 0.95 % Allowed : 13.20 % Favored : 85.85 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2632 helix: -0.51 (0.16), residues: 1078 sheet: -1.23 (0.24), residues: 434 loop : -1.57 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.010 0.001 TYR E 17 PHE 0.007 0.001 PHE Z 2 HIS 0.002 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00342 (21280) covalent geometry : angle 1.40426 (28658) hydrogen bonds : bond 0.05216 ( 588) hydrogen bonds : angle 4.15885 ( 1638) Misc. bond : bond 0.00087 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 354 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 108 LYS cc_start: 0.8803 (tptm) cc_final: 0.8382 (tppt) REVERT: B 8 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6752 (tt0) REVERT: B 98 MET cc_start: 0.7989 (mmt) cc_final: 0.7761 (tpt) REVERT: B 108 LYS cc_start: 0.8871 (tptm) cc_final: 0.8350 (tppt) REVERT: C 8 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: C 108 LYS cc_start: 0.8931 (tptm) cc_final: 0.8523 (tppt) REVERT: C 116 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7814 (p0) REVERT: D 108 LYS cc_start: 0.8961 (tptm) cc_final: 0.8403 (tppt) REVERT: E 108 LYS cc_start: 0.8788 (tptm) cc_final: 0.8456 (tppt) REVERT: F 186 ASP cc_start: 0.8817 (m-30) cc_final: 0.8448 (m-30) REVERT: G 151 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8368 (mttt) REVERT: I 8 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6705 (tt0) REVERT: I 20 TYR cc_start: 0.8737 (m-80) cc_final: 0.8358 (m-10) REVERT: I 108 LYS cc_start: 0.8831 (tptm) cc_final: 0.8365 (tppt) REVERT: I 177 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7777 (tm-30) REVERT: L 108 LYS cc_start: 0.8882 (tptm) cc_final: 0.8503 (tppt) REVERT: M 8 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: M 74 MET cc_start: 0.7523 (mmm) cc_final: 0.7190 (mmm) REVERT: N 8 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6697 (tt0) REVERT: N 78 ASP cc_start: 0.8413 (m-30) cc_final: 0.8179 (m-30) REVERT: N 108 LYS cc_start: 0.8817 (tptm) cc_final: 0.8349 (tppt) REVERT: H 8 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6737 (tt0) REVERT: H 58 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: H 108 LYS cc_start: 0.8895 (tptm) cc_final: 0.8490 (tppt) outliers start: 21 outliers final: 11 residues processed: 368 average time/residue: 0.4222 time to fit residues: 225.8483 Evaluate side-chains 365 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 345 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 124 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101824 restraints weight = 68113.000| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.51 r_work: 0.3020 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21308 Z= 0.164 Angle : 1.410 23.105 28658 Z= 0.760 Chirality : 0.254 1.737 3360 Planarity : 0.004 0.034 3724 Dihedral : 5.334 42.512 2982 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.90 % Favored : 91.83 % Rotamer: Outliers : 1.18 % Allowed : 13.02 % Favored : 85.80 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.16), residues: 2632 helix: -0.45 (0.16), residues: 1078 sheet: -1.18 (0.25), residues: 434 loop : -1.61 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 146 TYR 0.011 0.001 TYR G 17 PHE 0.009 0.001 PHE b 2 HIS 0.002 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00398 (21280) covalent geometry : angle 1.41002 (28658) hydrogen bonds : bond 0.05761 ( 588) hydrogen bonds : angle 4.22787 ( 1638) Misc. bond : bond 0.00102 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 347 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 108 LYS cc_start: 0.8809 (tptm) cc_final: 0.8450 (tppt) REVERT: B 8 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.6930 (tt0) REVERT: B 108 LYS cc_start: 0.8887 (tptm) cc_final: 0.8447 (tppt) REVERT: C 8 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7013 (tt0) REVERT: C 108 LYS cc_start: 0.8857 (tptm) cc_final: 0.8573 (tppt) REVERT: C 116 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7973 (p0) REVERT: D 8 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: D 108 LYS cc_start: 0.8867 (tptm) cc_final: 0.8490 (tppt) REVERT: E 108 LYS cc_start: 0.8790 (tptm) cc_final: 0.8559 (tppt) REVERT: F 8 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: F 186 ASP cc_start: 0.8812 (m-30) cc_final: 0.8492 (m-30) REVERT: G 8 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: G 151 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8487 (mttt) REVERT: I 8 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: I 20 TYR cc_start: 0.8828 (m-80) cc_final: 0.8475 (m-10) REVERT: I 108 LYS cc_start: 0.8860 (tptm) cc_final: 0.8450 (tppt) REVERT: I 177 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7936 (tm-30) REVERT: J 8 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7017 (tt0) REVERT: J 20 TYR cc_start: 0.8859 (m-80) cc_final: 0.8611 (m-80) REVERT: J 177 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7692 (tm-30) REVERT: K 8 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: L 8 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7061 (tt0) REVERT: L 108 LYS cc_start: 0.8882 (tptm) cc_final: 0.8585 (tppt) REVERT: N 8 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: N 78 ASP cc_start: 0.8314 (m-30) cc_final: 0.8064 (m-30) REVERT: N 108 LYS cc_start: 0.8846 (tptm) cc_final: 0.8462 (tppt) REVERT: H 8 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: H 58 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: H 108 LYS cc_start: 0.8859 (tptm) cc_final: 0.8541 (tppt) outliers start: 26 outliers final: 11 residues processed: 368 average time/residue: 0.3986 time to fit residues: 214.4564 Evaluate side-chains 370 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 345 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 196 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.099981 restraints weight = 68145.373| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.49 r_work: 0.2956 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21308 Z= 0.201 Angle : 1.424 22.742 28658 Z= 0.767 Chirality : 0.253 1.754 3360 Planarity : 0.004 0.035 3724 Dihedral : 5.768 53.354 2982 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.16 % Favored : 90.31 % Rotamer: Outliers : 1.13 % Allowed : 13.16 % Favored : 85.71 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.16), residues: 2632 helix: -0.60 (0.16), residues: 1078 sheet: -1.24 (0.25), residues: 434 loop : -1.70 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 146 TYR 0.013 0.001 TYR G 17 PHE 0.011 0.001 PHE Z 2 HIS 0.002 0.000 HIS N 122 Details of bonding type rmsd covalent geometry : bond 0.00491 (21280) covalent geometry : angle 1.42408 (28658) hydrogen bonds : bond 0.06577 ( 588) hydrogen bonds : angle 4.43710 ( 1638) Misc. bond : bond 0.00126 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5264 Ramachandran restraints generated. 2632 Oldfield, 0 Emsley, 2632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 19 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue ALA 16 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 350 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.8824 (tptm) cc_final: 0.8442 (tppt) REVERT: B 8 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: B 108 LYS cc_start: 0.8817 (tptm) cc_final: 0.8482 (tppt) REVERT: C 8 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: C 108 LYS cc_start: 0.8887 (tptm) cc_final: 0.8560 (tppt) REVERT: C 116 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8027 (p0) REVERT: D 108 LYS cc_start: 0.8872 (tptm) cc_final: 0.8462 (tppt) REVERT: E 108 LYS cc_start: 0.8840 (tptm) cc_final: 0.8581 (tppt) REVERT: F 8 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: F 186 ASP cc_start: 0.8828 (m-30) cc_final: 0.8514 (m-30) REVERT: G 8 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: G 146 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8047 (ttp-170) REVERT: G 151 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8491 (mttt) REVERT: I 8 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: I 20 TYR cc_start: 0.8845 (m-80) cc_final: 0.8498 (m-10) REVERT: I 108 LYS cc_start: 0.8860 (tptm) cc_final: 0.8431 (tppt) REVERT: I 177 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7963 (tm-30) REVERT: J 8 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: J 20 TYR cc_start: 0.8886 (m-80) cc_final: 0.8660 (m-80) REVERT: J 177 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7744 (tm-30) REVERT: L 8 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: L 108 LYS cc_start: 0.8909 (tptm) cc_final: 0.8563 (tppt) REVERT: N 78 ASP cc_start: 0.8326 (m-30) cc_final: 0.8043 (m-30) REVERT: N 108 LYS cc_start: 0.8880 (tptm) cc_final: 0.8461 (tppt) REVERT: H 8 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: H 58 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: H 108 LYS cc_start: 0.8858 (tptm) cc_final: 0.8572 (tppt) outliers start: 25 outliers final: 15 residues processed: 370 average time/residue: 0.3999 time to fit residues: 216.3822 Evaluate side-chains 372 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 116 ASN Chi-restraints excluded: chain J residue 120 MET Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain L residue 8 GLU Chi-restraints excluded: chain L residue 30 MET Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102239 restraints weight = 68040.258| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.65 r_work: 0.3060 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21308 Z= 0.141 Angle : 1.408 23.326 28658 Z= 0.760 Chirality : 0.254 1.708 3360 Planarity : 0.004 0.032 3724 Dihedral : 5.140 37.110 2982 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.88 % Favored : 92.86 % Rotamer: Outliers : 1.22 % Allowed : 13.11 % Favored : 85.67 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 1.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2632 helix: -0.45 (0.16), residues: 1092 sheet: -1.12 (0.25), residues: 434 loop : -1.52 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 146 TYR 0.009 0.001 TYR G 17 PHE 0.007 0.001 PHE b 2 HIS 0.002 0.000 HIS J 122 Details of bonding type rmsd covalent geometry : bond 0.00343 (21280) covalent geometry : angle 1.40760 (28658) hydrogen bonds : bond 0.05218 ( 588) hydrogen bonds : angle 4.20209 ( 1638) Misc. bond : bond 0.00084 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9216.60 seconds wall clock time: 156 minutes 45.90 seconds (9405.90 seconds total)