Starting phenix.real_space_refine (version: dev) on Sun Dec 18 20:41:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999.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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/12_2022/6ezj_3999_updated.pdb" } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 33600 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "H" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "J" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "K" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "L" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "O" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "P" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "Q" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "S" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "T" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "U" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "V" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "X" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 18.48, per 1000 atoms: 0.55 Number of scatterers: 33600 At special positions: 0 Unit cell: (125.775, 125.775, 125.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 48 24.99 S 48 16.00 P 24 15.00 O 6168 8.00 N 6336 7.00 C 20976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.00 Conformation dependent library (CDL) restraints added in 5.1 seconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 48 sheets defined 30.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 74 through 90 removed outlier: 3.588A pdb=" N ASP A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.727A pdb=" N ALA C 180 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 54 No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.786A pdb=" N THR D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 54 No H-bonds generated for 'chain 'E' and resid 51 through 54' Processing helix chain 'E' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.786A pdb=" N THR E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA E 180 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 54 No H-bonds generated for 'chain 'F' and resid 51 through 54' Processing helix chain 'F' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 54 No H-bonds generated for 'chain 'G' and resid 51 through 54' Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP G 78 " --> pdb=" O HIS G 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 154 removed outlier: 3.788A pdb=" N THR G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA G 180 " --> pdb=" O PHE G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS H 47 " --> pdb=" O PRO H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 54 No H-bonds generated for 'chain 'H' and resid 51 through 54' Processing helix chain 'H' and resid 74 through 90 removed outlier: 3.586A pdb=" N ASP H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 154 removed outlier: 3.788A pdb=" N THR H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA H 180 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS I 47 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 54 No H-bonds generated for 'chain 'I' and resid 51 through 54' Processing helix chain 'I' and resid 74 through 90 removed outlier: 3.586A pdb=" N ASP I 78 " --> pdb=" O HIS I 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA I 180 " --> pdb=" O PHE I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS J 47 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 54 No H-bonds generated for 'chain 'J' and resid 51 through 54' Processing helix chain 'J' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP J 78 " --> pdb=" O HIS J 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 84 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA J 180 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS K 47 " --> pdb=" O PRO K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA K 180 " --> pdb=" O PHE K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 54 No H-bonds generated for 'chain 'L' and resid 51 through 54' Processing helix chain 'L' and resid 74 through 90 removed outlier: 3.588A pdb=" N ASP L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL L 79 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 154 removed outlier: 3.788A pdb=" N THR L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA L 180 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS M 47 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 54 No H-bonds generated for 'chain 'M' and resid 51 through 54' Processing helix chain 'M' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP M 78 " --> pdb=" O HIS M 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY M 84 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA M 180 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS N 47 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 54 No H-bonds generated for 'chain 'N' and resid 51 through 54' Processing helix chain 'N' and resid 74 through 90 removed outlier: 3.588A pdb=" N ASP N 78 " --> pdb=" O HIS N 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA N 180 " --> pdb=" O PHE N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS O 47 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 54 No H-bonds generated for 'chain 'O' and resid 51 through 54' Processing helix chain 'O' and resid 74 through 90 removed outlier: 3.588A pdb=" N ASP O 78 " --> pdb=" O HIS O 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY O 84 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA O 180 " --> pdb=" O PHE O 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS P 47 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 54 No H-bonds generated for 'chain 'P' and resid 51 through 54' Processing helix chain 'P' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP P 78 " --> pdb=" O HIS P 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL P 79 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 54 No H-bonds generated for 'chain 'Q' and resid 51 through 54' Processing helix chain 'Q' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP Q 78 " --> pdb=" O HIS Q 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL Q 79 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR Q 153 " --> pdb=" O SER Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA Q 180 " --> pdb=" O PHE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS R 47 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP R 78 " --> pdb=" O HIS R 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA R 180 " --> pdb=" O PHE R 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 54 No H-bonds generated for 'chain 'S' and resid 51 through 54' Processing helix chain 'S' and resid 74 through 90 removed outlier: 3.588A pdb=" N ASP S 78 " --> pdb=" O HIS S 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL S 79 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY S 84 " --> pdb=" O ALA S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR S 153 " --> pdb=" O SER S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA S 180 " --> pdb=" O PHE S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS T 47 " --> pdb=" O PRO T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 54 No H-bonds generated for 'chain 'T' and resid 51 through 54' Processing helix chain 'T' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL T 79 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR T 153 " --> pdb=" O SER T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA T 180 " --> pdb=" O PHE T 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS U 47 " --> pdb=" O PRO U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 54 No H-bonds generated for 'chain 'U' and resid 51 through 54' Processing helix chain 'U' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP U 78 " --> pdb=" O HIS U 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 154 removed outlier: 3.786A pdb=" N THR U 153 " --> pdb=" O SER U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA U 180 " --> pdb=" O PHE U 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS V 47 " --> pdb=" O PRO V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 54 No H-bonds generated for 'chain 'V' and resid 51 through 54' Processing helix chain 'V' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP V 78 " --> pdb=" O HIS V 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL V 79 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY V 84 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR V 153 " --> pdb=" O SER V 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA V 180 " --> pdb=" O PHE V 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS W 47 " --> pdb=" O PRO W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 54 No H-bonds generated for 'chain 'W' and resid 51 through 54' Processing helix chain 'W' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP W 78 " --> pdb=" O HIS W 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR W 153 " --> pdb=" O SER W 149 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA W 180 " --> pdb=" O PHE W 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS X 47 " --> pdb=" O PRO X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 54 No H-bonds generated for 'chain 'X' and resid 51 through 54' Processing helix chain 'X' and resid 74 through 90 removed outlier: 3.587A pdb=" N ASP X 78 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL X 79 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY X 84 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 154 removed outlier: 3.787A pdb=" N THR X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA X 180 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP A 37 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 62 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 64 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE A 112 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 164 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS A 113 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN A 162 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER A 115 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE A 160 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 123 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A 160 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY A 125 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN A 162 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP B 37 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 62 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 64 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE B 112 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 164 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS B 113 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN B 162 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 115 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE B 160 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 123 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE B 160 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 125 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN B 162 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP C 37 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 62 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 64 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE C 112 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 164 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS C 113 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN C 162 " --> pdb=" O HIS C 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER C 115 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE C 160 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 123 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE C 160 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY C 125 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN C 162 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP D 37 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 62 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 64 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE D 112 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 164 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS D 113 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN D 162 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER D 115 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE D 160 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR D 123 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 160 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY D 125 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN D 162 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP E 37 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 62 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 64 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE E 112 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA E 164 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS E 113 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN E 162 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER E 115 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 160 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 123 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE E 160 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY E 125 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN E 162 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP F 37 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 62 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 64 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE F 112 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA F 164 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 113 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN F 162 " --> pdb=" O HIS F 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER F 115 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 160 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR F 123 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE F 160 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY F 125 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN F 162 " --> pdb=" O GLY F 125 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP G 37 " --> pdb=" O VAL G 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 62 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 64 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE G 112 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 164 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS G 113 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN G 162 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER G 115 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE G 160 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR G 123 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE G 160 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY G 125 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN G 162 " --> pdb=" O GLY G 125 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP H 37 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 62 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 64 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE H 112 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA H 164 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS H 113 " --> pdb=" O GLN H 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN H 162 " --> pdb=" O HIS H 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER H 115 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE H 160 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR H 123 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE H 160 " --> pdb=" O TYR H 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY H 125 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN H 162 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP I 37 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 62 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 64 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 101 through 106 removed outlier: 3.829A pdb=" N ILE I 112 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA I 164 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS I 113 " --> pdb=" O GLN I 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN I 162 " --> pdb=" O HIS I 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER I 115 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE I 160 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 123 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE I 160 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY I 125 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN I 162 " --> pdb=" O GLY I 125 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP J 37 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 62 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA J 64 " --> pdb=" O SER J 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE J 112 " --> pdb=" O ALA J 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA J 164 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS J 113 " --> pdb=" O GLN J 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN J 162 " --> pdb=" O HIS J 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER J 115 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE J 160 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR J 123 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE J 160 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY J 125 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN J 162 " --> pdb=" O GLY J 125 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP K 37 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL K 62 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA K 64 " --> pdb=" O SER K 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE K 112 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA K 164 " --> pdb=" O LEU K 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS K 113 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN K 162 " --> pdb=" O HIS K 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER K 115 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE K 160 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR K 123 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE K 160 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY K 125 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN K 162 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP L 37 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 62 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA L 64 " --> pdb=" O SER L 39 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE L 112 " --> pdb=" O ALA L 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA L 164 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS L 113 " --> pdb=" O GLN L 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN L 162 " --> pdb=" O HIS L 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER L 115 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE L 160 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR L 123 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE L 160 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY L 125 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN L 162 " --> pdb=" O GLY L 125 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP M 37 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL M 62 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA M 64 " --> pdb=" O SER M 39 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE M 112 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA M 164 " --> pdb=" O LEU M 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS M 113 " --> pdb=" O GLN M 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN M 162 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER M 115 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE M 160 " --> pdb=" O SER M 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR M 123 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE M 160 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY M 125 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN M 162 " --> pdb=" O GLY M 125 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP N 37 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL N 62 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 64 " --> pdb=" O SER N 39 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 101 through 106 removed outlier: 3.829A pdb=" N ILE N 112 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA N 164 " --> pdb=" O LEU N 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS N 113 " --> pdb=" O GLN N 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN N 162 " --> pdb=" O HIS N 113 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER N 115 " --> pdb=" O ILE N 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE N 160 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR N 123 " --> pdb=" O LEU N 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE N 160 " --> pdb=" O TYR N 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY N 125 " --> pdb=" O ILE N 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN N 162 " --> pdb=" O GLY N 125 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP O 37 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL O 62 " --> pdb=" O ASP O 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA O 64 " --> pdb=" O SER O 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE O 112 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA O 164 " --> pdb=" O LEU O 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS O 113 " --> pdb=" O GLN O 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN O 162 " --> pdb=" O HIS O 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER O 115 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE O 160 " --> pdb=" O SER O 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR O 123 " --> pdb=" O LEU O 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE O 160 " --> pdb=" O TYR O 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY O 125 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN O 162 " --> pdb=" O GLY O 125 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP P 37 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 62 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA P 64 " --> pdb=" O SER P 39 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'P' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE P 112 " --> pdb=" O ALA P 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA P 164 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS P 113 " --> pdb=" O GLN P 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN P 162 " --> pdb=" O HIS P 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER P 115 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE P 160 " --> pdb=" O SER P 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR P 123 " --> pdb=" O LEU P 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE P 160 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY P 125 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN P 162 " --> pdb=" O GLY P 125 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Q' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP Q 37 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL Q 62 " --> pdb=" O ASP Q 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 64 " --> pdb=" O SER Q 39 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Q' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE Q 112 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA Q 164 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS Q 113 " --> pdb=" O GLN Q 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN Q 162 " --> pdb=" O HIS Q 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER Q 115 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE Q 160 " --> pdb=" O SER Q 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR Q 123 " --> pdb=" O LEU Q 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE Q 160 " --> pdb=" O TYR Q 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY Q 125 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN Q 162 " --> pdb=" O GLY Q 125 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'R' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP R 37 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL R 62 " --> pdb=" O ASP R 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA R 64 " --> pdb=" O SER R 39 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'R' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE R 112 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA R 164 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS R 113 " --> pdb=" O GLN R 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN R 162 " --> pdb=" O HIS R 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER R 115 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE R 160 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR R 123 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE R 160 " --> pdb=" O TYR R 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY R 125 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN R 162 " --> pdb=" O GLY R 125 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP S 37 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL S 62 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA S 64 " --> pdb=" O SER S 39 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE S 112 " --> pdb=" O ALA S 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA S 164 " --> pdb=" O LEU S 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS S 113 " --> pdb=" O GLN S 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN S 162 " --> pdb=" O HIS S 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER S 115 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE S 160 " --> pdb=" O SER S 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR S 123 " --> pdb=" O LEU S 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE S 160 " --> pdb=" O TYR S 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY S 125 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN S 162 " --> pdb=" O GLY S 125 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP T 37 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL T 62 " --> pdb=" O ASP T 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA T 64 " --> pdb=" O SER T 39 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE T 112 " --> pdb=" O ALA T 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA T 164 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS T 113 " --> pdb=" O GLN T 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN T 162 " --> pdb=" O HIS T 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER T 115 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE T 160 " --> pdb=" O SER T 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR T 123 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE T 160 " --> pdb=" O TYR T 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY T 125 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN T 162 " --> pdb=" O GLY T 125 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP U 37 " --> pdb=" O VAL U 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL U 62 " --> pdb=" O ASP U 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA U 64 " --> pdb=" O SER U 39 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'U' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE U 112 " --> pdb=" O ALA U 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA U 164 " --> pdb=" O LEU U 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS U 113 " --> pdb=" O GLN U 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN U 162 " --> pdb=" O HIS U 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER U 115 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE U 160 " --> pdb=" O SER U 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR U 123 " --> pdb=" O LEU U 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE U 160 " --> pdb=" O TYR U 123 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY U 125 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN U 162 " --> pdb=" O GLY U 125 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'V' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP V 37 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL V 62 " --> pdb=" O ASP V 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA V 64 " --> pdb=" O SER V 39 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'V' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE V 112 " --> pdb=" O ALA V 105 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA V 164 " --> pdb=" O LEU V 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS V 113 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN V 162 " --> pdb=" O HIS V 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER V 115 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE V 160 " --> pdb=" O SER V 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR V 123 " --> pdb=" O LEU V 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE V 160 " --> pdb=" O TYR V 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY V 125 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN V 162 " --> pdb=" O GLY V 125 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP W 37 " --> pdb=" O VAL W 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL W 62 " --> pdb=" O ASP W 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA W 64 " --> pdb=" O SER W 39 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE W 112 " --> pdb=" O ALA W 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA W 164 " --> pdb=" O LEU W 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS W 113 " --> pdb=" O GLN W 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN W 162 " --> pdb=" O HIS W 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER W 115 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE W 160 " --> pdb=" O SER W 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR W 123 " --> pdb=" O LEU W 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE W 160 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY W 125 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN W 162 " --> pdb=" O GLY W 125 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'X' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP X 37 " --> pdb=" O VAL X 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL X 62 " --> pdb=" O ASP X 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA X 64 " --> pdb=" O SER X 39 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'X' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE X 112 " --> pdb=" O ALA X 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA X 164 " --> pdb=" O LEU X 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS X 113 " --> pdb=" O GLN X 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN X 162 " --> pdb=" O HIS X 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER X 115 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE X 160 " --> pdb=" O SER X 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR X 123 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE X 160 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY X 125 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN X 162 " --> pdb=" O GLY X 125 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3384 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: 12.16 Time building geometry restraints manager: 14.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11541 1.34 - 1.46: 6395 1.46 - 1.58: 16144 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 34200 Sorted by residual: bond pdb=" N1 5LD U 303 " pdb=" N2 5LD U 303 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" N1 5LD N 303 " pdb=" N2 5LD N 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" N1 5LD V 303 " pdb=" N2 5LD V 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" N1 5LD Q 303 " pdb=" N2 5LD Q 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N1 5LD X 303 " pdb=" N2 5LD X 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.26: 816 106.26 - 112.97: 19024 112.97 - 119.67: 9513 119.67 - 126.38: 16607 126.38 - 133.08: 480 Bond angle restraints: 46440 Sorted by residual: angle pdb=" C ASP V 108 " pdb=" N GLU V 109 " pdb=" CA GLU V 109 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP R 108 " pdb=" N GLU R 109 " pdb=" CA GLU R 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP U 108 " pdb=" N GLU U 109 " pdb=" CA GLU U 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP Q 108 " pdb=" N GLU Q 109 " pdb=" CA GLU Q 109 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP B 108 " pdb=" N GLU B 109 " pdb=" CA GLU B 109 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 ... (remaining 46435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 18596 15.23 - 30.45: 1036 30.45 - 45.68: 240 45.68 - 60.91: 0 60.91 - 76.13: 24 Dihedral angle restraints: 19896 sinusoidal: 7344 harmonic: 12552 Sorted by residual: dihedral pdb=" CA PRO K 106 " pdb=" C PRO K 106 " pdb=" N LEU K 107 " pdb=" CA LEU K 107 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO G 106 " pdb=" C PRO G 106 " pdb=" N LEU G 107 " pdb=" CA LEU G 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO E 106 " pdb=" C PRO E 106 " pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 19893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3644 0.047 - 0.094: 1264 0.094 - 0.142: 354 0.142 - 0.189: 138 0.189 - 0.236: 24 Chirality restraints: 5424 Sorted by residual: chirality pdb=" C7 5LD L 303 " pdb=" C6 5LD L 303 " pdb=" C8 5LD L 303 " pdb=" O13 5LD L 303 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD M 402 " pdb=" C6 5LD M 402 " pdb=" C8 5LD M 402 " pdb=" O13 5LD M 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD O 402 " pdb=" C6 5LD O 402 " pdb=" C8 5LD O 402 " pdb=" O13 5LD O 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5421 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP N 108 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP N 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP N 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU N 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 108 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ASP Q 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP Q 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU Q 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 108 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C ASP I 108 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP I 108 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 846 2.67 - 3.23: 28357 3.23 - 3.78: 51930 3.78 - 4.34: 71786 4.34 - 4.90: 118843 Nonbonded interactions: 271762 Sorted by model distance: nonbonded pdb=" NE2 HIS C 73 " pdb="MN MN C 403 " model vdw 2.111 2.400 nonbonded pdb=" NE2 HIS R 73 " pdb="MN MN R 301 " model vdw 2.114 2.400 nonbonded pdb=" NE2 HIS B 73 " pdb="MN MN B 403 " model vdw 2.118 2.400 nonbonded pdb=" NE2 HIS Q 73 " pdb="MN MN Q 301 " model vdw 2.119 2.400 nonbonded pdb=" NE2 HIS L 73 " pdb="MN MN L 301 " model vdw 2.120 2.400 ... (remaining 271757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 195 or resid 401)) selection = (chain 'B' and (resid 11 through 195 or resid 401)) selection = (chain 'C' and (resid 11 through 195 or resid 401)) selection = (chain 'D' and (resid 11 through 195 or resid 401)) selection = (chain 'E' and (resid 11 through 195 or resid 401)) selection = (chain 'F' and (resid 11 through 195 or resid 401)) selection = (chain 'G' and (resid 11 through 195 or resid 401)) selection = (chain 'H' and (resid 11 through 195 or resid 301)) selection = (chain 'I' and (resid 11 through 195 or resid 401)) selection = (chain 'J' and (resid 11 through 195 or resid 401)) selection = (chain 'K' and (resid 11 through 195 or resid 401)) selection = (chain 'L' and (resid 11 through 195 or resid 301)) selection = (chain 'M' and (resid 11 through 195 or resid 401)) selection = (chain 'N' and (resid 11 through 195 or resid 301)) selection = (chain 'O' and (resid 11 through 195 or resid 401)) selection = (chain 'P' and (resid 11 through 195 or resid 301)) selection = (chain 'Q' and (resid 11 through 195 or resid 301)) selection = (chain 'R' and (resid 11 through 195 or resid 301)) selection = (chain 'S' and (resid 11 through 195 or resid 301)) selection = (chain 'T' and (resid 11 through 195 or resid 301)) selection = (chain 'U' and (resid 11 through 195 or resid 301)) selection = (chain 'V' and (resid 11 through 195 or resid 301)) selection = (chain 'W' and (resid 11 through 195 or resid 301)) selection = (chain 'X' and (resid 11 through 195 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 48 7.51 5 P 24 5.49 5 S 48 5.16 5 C 20976 2.51 5 N 6336 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.870 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.300 Process input model: 83.920 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.007 0.057 34200 Z= 0.446 Angle : 1.124 8.754 46440 Z= 0.605 Chirality : 0.057 0.236 5424 Planarity : 0.007 0.051 6024 Dihedral : 10.822 76.133 11832 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.09), residues: 4392 helix: -4.65 (0.04), residues: 1536 sheet: -0.55 (0.13), residues: 1248 loop : -4.12 (0.10), residues: 1608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 882 time to evaluate : 4.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 882 average time/residue: 0.5408 time to fit residues: 710.3364 Evaluate side-chains 625 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 40.0000 chunk 392 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 185 GLN C 185 GLN D 185 GLN E 185 GLN F 185 GLN G 185 GLN H 185 GLN I 185 GLN J 185 GLN K 185 GLN L 185 GLN M 185 GLN N 185 GLN O 185 GLN P 185 GLN Q 185 GLN R 185 GLN S 185 GLN T 185 GLN U 185 GLN W 185 GLN X 185 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 34200 Z= 0.368 Angle : 0.800 7.258 46440 Z= 0.420 Chirality : 0.049 0.138 5424 Planarity : 0.008 0.048 6024 Dihedral : 7.637 53.870 4824 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.11), residues: 4392 helix: -2.82 (0.08), residues: 1584 sheet: -0.65 (0.14), residues: 1440 loop : -3.69 (0.14), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 653 time to evaluate : 3.990 Fit side-chains outliers start: 115 outliers final: 88 residues processed: 734 average time/residue: 0.5315 time to fit residues: 591.3665 Evaluate side-chains 643 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 555 time to evaluate : 4.029 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.2945 time to fit residues: 54.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 40.0000 chunk 121 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 267 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 393 optimal weight: 3.9990 chunk 424 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 chunk 389 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 133 GLN D 133 GLN F 133 GLN K 76 ASN N 133 GLN O 133 GLN T 133 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 34200 Z= 0.295 Angle : 0.731 7.739 46440 Z= 0.384 Chirality : 0.048 0.127 5424 Planarity : 0.006 0.037 6024 Dihedral : 7.540 59.955 4824 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer Outliers : 3.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.12), residues: 4392 helix: -1.40 (0.11), residues: 1560 sheet: -0.73 (0.14), residues: 1464 loop : -3.77 (0.13), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 611 time to evaluate : 3.882 Fit side-chains outliers start: 132 outliers final: 70 residues processed: 698 average time/residue: 0.5025 time to fit residues: 542.9748 Evaluate side-chains 643 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 573 time to evaluate : 3.876 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.2892 time to fit residues: 43.7540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 417 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 373 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN C 76 ASN D 76 ASN E 76 ASN F 76 ASN G 76 ASN H 76 ASN H 133 GLN I 76 ASN J 76 ASN J 133 GLN L 76 ASN L 133 GLN M 76 ASN M 133 GLN N 76 ASN O 76 ASN P 76 ASN P 133 GLN Q 76 ASN Q 133 GLN R 76 ASN S 76 ASN T 76 ASN U 76 ASN W 76 ASN X 76 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 34200 Z= 0.236 Angle : 0.669 7.340 46440 Z= 0.351 Chirality : 0.047 0.193 5424 Planarity : 0.005 0.040 6024 Dihedral : 7.170 58.117 4824 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4392 helix: -0.66 (0.12), residues: 1560 sheet: -0.87 (0.14), residues: 1488 loop : -3.64 (0.13), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 581 time to evaluate : 4.255 Fit side-chains outliers start: 112 outliers final: 57 residues processed: 643 average time/residue: 0.5050 time to fit residues: 504.3316 Evaluate side-chains 598 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 541 time to evaluate : 3.769 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.2948 time to fit residues: 36.9127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 288 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 213 optimal weight: 9.9990 chunk 374 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN N 61 HIS V 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 34200 Z= 0.469 Angle : 0.893 8.183 46440 Z= 0.462 Chirality : 0.056 0.241 5424 Planarity : 0.008 0.058 6024 Dihedral : 7.427 54.924 4824 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.12), residues: 4392 helix: -0.69 (0.12), residues: 1560 sheet: -0.74 (0.14), residues: 1488 loop : -3.72 (0.13), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 502 time to evaluate : 3.772 Fit side-chains outliers start: 87 outliers final: 42 residues processed: 571 average time/residue: 0.5272 time to fit residues: 460.9633 Evaluate side-chains 523 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 481 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2944 time to fit residues: 28.9474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 9.9990 chunk 376 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 245 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 417 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 219 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 ASN C 76 ASN D 76 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 76 ASN K 76 ASN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN M 76 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 76 ASN Q 76 ASN ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN S 76 ASN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN V 76 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN X 61 HIS X 76 ASN X 133 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 34200 Z= 0.163 Angle : 0.649 9.412 46440 Z= 0.345 Chirality : 0.045 0.197 5424 Planarity : 0.005 0.050 6024 Dihedral : 6.251 52.712 4824 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.12), residues: 4392 helix: 0.25 (0.13), residues: 1560 sheet: -0.93 (0.13), residues: 1512 loop : -3.51 (0.13), residues: 1320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 654 time to evaluate : 3.792 Fit side-chains outliers start: 76 outliers final: 63 residues processed: 684 average time/residue: 0.4904 time to fit residues: 522.2021 Evaluate side-chains 651 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 588 time to evaluate : 3.681 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.2897 time to fit residues: 39.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 chunk 233 optimal weight: 20.0000 chunk 416 optimal weight: 40.0000 chunk 260 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 76 ASN B 76 ASN B 185 GLN C 185 GLN E 185 GLN F 76 ASN F 185 GLN G 185 GLN H 76 ASN H 185 GLN I 185 GLN J 185 GLN K 76 ASN K 185 GLN L 76 ASN M 76 ASN M 185 GLN N 185 GLN O 76 ASN Q 185 GLN R 185 GLN S 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 185 GLN X 76 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 34200 Z= 0.488 Angle : 0.923 11.227 46440 Z= 0.473 Chirality : 0.057 0.299 5424 Planarity : 0.008 0.058 6024 Dihedral : 7.014 38.757 4824 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4392 helix: -0.28 (0.13), residues: 1560 sheet: -0.79 (0.13), residues: 1488 loop : -3.53 (0.14), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 530 time to evaluate : 4.021 Fit side-chains outliers start: 63 outliers final: 57 residues processed: 583 average time/residue: 0.5135 time to fit residues: 467.0275 Evaluate side-chains 568 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 511 time to evaluate : 3.874 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.3176 time to fit residues: 40.1854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 327 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN B 29 ASN C 61 HIS D 29 ASN D 76 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN F 29 ASN G 76 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 ASN I 76 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN M 29 ASN M 61 HIS N 76 ASN O 29 ASN P 76 ASN Q 29 ASN Q 76 ASN R 29 ASN R 76 ASN S 29 ASN T 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 ASN U 76 ASN V 29 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 34200 Z= 0.255 Angle : 0.731 9.821 46440 Z= 0.380 Chirality : 0.049 0.252 5424 Planarity : 0.006 0.041 6024 Dihedral : 6.418 31.032 4824 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.12), residues: 4392 helix: 0.08 (0.13), residues: 1560 sheet: -0.67 (0.14), residues: 1488 loop : -3.37 (0.14), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 542 time to evaluate : 3.828 Fit side-chains outliers start: 54 outliers final: 44 residues processed: 555 average time/residue: 0.4996 time to fit residues: 430.2161 Evaluate side-chains 562 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 518 time to evaluate : 3.744 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.2896 time to fit residues: 29.4081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 40.0000 chunk 398 optimal weight: 4.9990 chunk 363 optimal weight: 0.7980 chunk 388 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 386 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 34200 Z= 0.247 Angle : 0.713 9.570 46440 Z= 0.368 Chirality : 0.048 0.234 5424 Planarity : 0.005 0.036 6024 Dihedral : 6.219 30.983 4824 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 4392 helix: 0.38 (0.13), residues: 1560 sheet: -0.62 (0.14), residues: 1488 loop : -3.40 (0.14), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 533 time to evaluate : 3.739 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 561 average time/residue: 0.5095 time to fit residues: 445.8475 Evaluate side-chains 557 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 531 time to evaluate : 3.793 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2965 time to fit residues: 20.0084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 430 optimal weight: 0.8980 chunk 396 optimal weight: 40.0000 chunk 342 optimal weight: 40.0000 chunk 35 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 34200 Z= 0.306 Angle : 0.774 11.272 46440 Z= 0.398 Chirality : 0.050 0.266 5424 Planarity : 0.006 0.037 6024 Dihedral : 6.381 31.415 4824 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.77 % Favored : 90.07 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4392 helix: 0.28 (0.13), residues: 1560 sheet: -0.56 (0.14), residues: 1488 loop : -3.43 (0.14), residues: 1344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 534 time to evaluate : 3.616 Fit side-chains outliers start: 45 outliers final: 41 residues processed: 539 average time/residue: 0.5065 time to fit residues: 423.0910 Evaluate side-chains 553 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 512 time to evaluate : 3.834 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2969 time to fit residues: 28.7250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 30.0000 chunk 365 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 343 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.195278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.175629 restraints weight = 32991.392| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.20 r_work: 0.3822 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4188 r_free = 0.4188 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4173 r_free = 0.4173 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 34200 Z= 0.500 Angle : 0.932 11.257 46440 Z= 0.478 Chirality : 0.057 0.284 5424 Planarity : 0.008 0.055 6024 Dihedral : 7.039 34.329 4824 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.34 % Favored : 89.44 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.12), residues: 4392 helix: -0.23 (0.13), residues: 1560 sheet: -0.74 (0.13), residues: 1488 loop : -3.59 (0.13), residues: 1344 =============================================================================== Job complete usr+sys time: 8602.24 seconds wall clock time: 153 minutes 50.26 seconds (9230.26 seconds total)