Starting phenix.real_space_refine on Sat Dec 9 08:46:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eq9_31256/12_2023/7eq9_31256.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 39240 2.51 5 N 10740 2.21 5 O 12360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62520 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "E" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "J" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "K" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "L" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "N" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "O" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "P" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "Q" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "R" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "S" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "T" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "V" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "W" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "X" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "Y" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "Z" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "AA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "BA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "CA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "DA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "EA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "FA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "GA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "HA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "IA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "JA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "KA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "LA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "MA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "NA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "OA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "PA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "QA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "RA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "SA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "TA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "UA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "VA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "WA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "XA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "YA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "ZA" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "AB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "BB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "CB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "DB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "EB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "FB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "GB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "HB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Chain: "IB" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1042 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 23.33, per 1000 atoms: 0.37 Number of scatterers: 62520 At special positions: 0 Unit cell: (214.755, 214.755, 214.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 12360 8.00 N 10740 7.00 C 39240 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: 19.02 Conformation dependent library (CDL) restraints added in 8.0 seconds 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 120 sheets defined 47.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 75 through 116 Processing helix chain 'A' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 116 Processing helix chain 'B' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 116 Processing helix chain 'C' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 116 Processing helix chain 'D' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 116 Processing helix chain 'E' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 116 Processing helix chain 'F' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 116 Processing helix chain 'G' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 116 Processing helix chain 'H' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN H 132 " --> pdb=" O GLU H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 116 Processing helix chain 'I' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 116 Processing helix chain 'J' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN J 132 " --> pdb=" O GLU J 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 116 Processing helix chain 'K' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN K 132 " --> pdb=" O GLU K 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 116 Processing helix chain 'L' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 116 Processing helix chain 'M' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN M 132 " --> pdb=" O GLU M 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 116 Processing helix chain 'N' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 116 Processing helix chain 'O' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 116 Processing helix chain 'P' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN P 132 " --> pdb=" O GLU P 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 116 Processing helix chain 'Q' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN Q 132 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 116 Processing helix chain 'R' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 116 Processing helix chain 'S' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN S 132 " --> pdb=" O GLU S 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 116 Processing helix chain 'T' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN T 132 " --> pdb=" O GLU T 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 116 Processing helix chain 'V' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN V 132 " --> pdb=" O GLU V 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 116 Processing helix chain 'W' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN W 132 " --> pdb=" O GLU W 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 116 Processing helix chain 'X' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLN X 132 " --> pdb=" O GLU X 128 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 116 Processing helix chain 'Y' and resid 119 through 136 removed outlier: 4.289A pdb=" N GLN Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 116 Processing helix chain 'Z' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLN Z 132 " --> pdb=" O GLU Z 128 " (cutoff:3.500A) Processing helix chain 'AA' and resid 75 through 116 Processing helix chain 'AA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNAA 132 " --> pdb=" O GLUAA 128 " (cutoff:3.500A) Processing helix chain 'BA' and resid 75 through 116 Processing helix chain 'BA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNBA 132 " --> pdb=" O GLUBA 128 " (cutoff:3.500A) Processing helix chain 'CA' and resid 75 through 116 Processing helix chain 'CA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNCA 132 " --> pdb=" O GLUCA 128 " (cutoff:3.500A) Processing helix chain 'DA' and resid 75 through 116 Processing helix chain 'DA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNDA 132 " --> pdb=" O GLUDA 128 " (cutoff:3.500A) Processing helix chain 'EA' and resid 75 through 116 Processing helix chain 'EA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNEA 132 " --> pdb=" O GLUEA 128 " (cutoff:3.500A) Processing helix chain 'FA' and resid 75 through 116 Processing helix chain 'FA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNFA 132 " --> pdb=" O GLUFA 128 " (cutoff:3.500A) Processing helix chain 'GA' and resid 75 through 116 Processing helix chain 'GA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNGA 132 " --> pdb=" O GLUGA 128 " (cutoff:3.500A) Processing helix chain 'HA' and resid 75 through 116 Processing helix chain 'HA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNHA 132 " --> pdb=" O GLUHA 128 " (cutoff:3.500A) Processing helix chain 'IA' and resid 75 through 116 Processing helix chain 'IA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNIA 132 " --> pdb=" O GLUIA 128 " (cutoff:3.500A) Processing helix chain 'JA' and resid 75 through 116 Processing helix chain 'JA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNJA 132 " --> pdb=" O GLUJA 128 " (cutoff:3.500A) Processing helix chain 'KA' and resid 75 through 116 Processing helix chain 'KA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNKA 132 " --> pdb=" O GLUKA 128 " (cutoff:3.500A) Processing helix chain 'LA' and resid 75 through 116 Processing helix chain 'LA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNLA 132 " --> pdb=" O GLULA 128 " (cutoff:3.500A) Processing helix chain 'MA' and resid 75 through 116 Processing helix chain 'MA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNMA 132 " --> pdb=" O GLUMA 128 " (cutoff:3.500A) Processing helix chain 'NA' and resid 75 through 116 Processing helix chain 'NA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNNA 132 " --> pdb=" O GLUNA 128 " (cutoff:3.500A) Processing helix chain 'OA' and resid 75 through 116 Processing helix chain 'OA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNOA 132 " --> pdb=" O GLUOA 128 " (cutoff:3.500A) Processing helix chain 'PA' and resid 75 through 116 Processing helix chain 'PA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNPA 132 " --> pdb=" O GLUPA 128 " (cutoff:3.500A) Processing helix chain 'QA' and resid 75 through 116 Processing helix chain 'QA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNQA 132 " --> pdb=" O GLUQA 128 " (cutoff:3.500A) Processing helix chain 'RA' and resid 75 through 116 Processing helix chain 'RA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNRA 132 " --> pdb=" O GLURA 128 " (cutoff:3.500A) Processing helix chain 'SA' and resid 75 through 116 Processing helix chain 'SA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNSA 132 " --> pdb=" O GLUSA 128 " (cutoff:3.500A) Processing helix chain 'TA' and resid 75 through 116 Processing helix chain 'TA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNTA 132 " --> pdb=" O GLUTA 128 " (cutoff:3.500A) Processing helix chain 'UA' and resid 75 through 116 Processing helix chain 'UA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNUA 132 " --> pdb=" O GLUUA 128 " (cutoff:3.500A) Processing helix chain 'VA' and resid 75 through 116 Processing helix chain 'VA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNVA 132 " --> pdb=" O GLUVA 128 " (cutoff:3.500A) Processing helix chain 'WA' and resid 75 through 116 Processing helix chain 'WA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNWA 132 " --> pdb=" O GLUWA 128 " (cutoff:3.500A) Processing helix chain 'XA' and resid 75 through 116 Processing helix chain 'XA' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNXA 132 " --> pdb=" O GLUXA 128 " (cutoff:3.500A) Processing helix chain 'YA' and resid 75 through 116 Processing helix chain 'YA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNYA 132 " --> pdb=" O GLUYA 128 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 75 through 116 Processing helix chain 'ZA' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNZA 132 " --> pdb=" O GLUZA 128 " (cutoff:3.500A) Processing helix chain 'AB' and resid 75 through 116 Processing helix chain 'AB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNAB 132 " --> pdb=" O GLUAB 128 " (cutoff:3.500A) Processing helix chain 'BB' and resid 75 through 116 Processing helix chain 'BB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNBB 132 " --> pdb=" O GLUBB 128 " (cutoff:3.500A) Processing helix chain 'CB' and resid 75 through 116 Processing helix chain 'CB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNCB 132 " --> pdb=" O GLUCB 128 " (cutoff:3.500A) Processing helix chain 'DB' and resid 75 through 116 Processing helix chain 'DB' and resid 119 through 136 removed outlier: 4.287A pdb=" N GLNDB 132 " --> pdb=" O GLUDB 128 " (cutoff:3.500A) Processing helix chain 'EB' and resid 75 through 116 Processing helix chain 'EB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNEB 132 " --> pdb=" O GLUEB 128 " (cutoff:3.500A) Processing helix chain 'FB' and resid 75 through 116 Processing helix chain 'FB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNFB 132 " --> pdb=" O GLUFB 128 " (cutoff:3.500A) Processing helix chain 'GB' and resid 75 through 116 Processing helix chain 'GB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNGB 132 " --> pdb=" O GLUGB 128 " (cutoff:3.500A) Processing helix chain 'HB' and resid 75 through 116 Processing helix chain 'HB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNHB 132 " --> pdb=" O GLUHB 128 " (cutoff:3.500A) Processing helix chain 'IB' and resid 75 through 116 Processing helix chain 'IB' and resid 119 through 136 removed outlier: 4.288A pdb=" N GLNIB 132 " --> pdb=" O GLUIB 128 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA A 31 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 16 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 33 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP A 14 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 6 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 71 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG A 8 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA B 31 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 16 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 33 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP B 14 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 6 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 8 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA C 31 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 16 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL C 33 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP C 14 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 6 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE C 71 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG C 8 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA D 31 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE D 16 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL D 33 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP D 14 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 6 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 71 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG D 8 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 48 through 51 Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA E 31 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE E 16 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL E 33 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP E 14 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 6 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 71 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG E 8 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 48 through 51 Processing sheet with id=AB3, first strand: chain 'F' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA F 31 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE F 16 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL F 33 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP F 14 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE F 6 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE F 71 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG F 8 " --> pdb=" O ILE F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 51 Processing sheet with id=AB5, first strand: chain 'G' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA G 31 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE G 16 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL G 33 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP G 14 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G 6 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE G 71 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG G 8 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 48 through 51 Processing sheet with id=AB7, first strand: chain 'H' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA H 31 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE H 16 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL H 33 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP H 14 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE H 6 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE H 71 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG H 8 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 48 through 51 Processing sheet with id=AB9, first strand: chain 'I' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA I 31 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE I 16 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL I 33 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP I 14 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE I 6 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE I 71 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG I 8 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 48 through 51 Processing sheet with id=AC2, first strand: chain 'J' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA J 31 " --> pdb=" O ILE J 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE J 16 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL J 33 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP J 14 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE J 6 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE J 71 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG J 8 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 48 through 51 Processing sheet with id=AC4, first strand: chain 'K' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA K 31 " --> pdb=" O ILE K 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE K 16 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL K 33 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP K 14 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE K 6 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE K 71 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG K 8 " --> pdb=" O ILE K 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 48 through 51 Processing sheet with id=AC6, first strand: chain 'L' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA L 31 " --> pdb=" O ILE L 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE L 16 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL L 33 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP L 14 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE L 6 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE L 71 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG L 8 " --> pdb=" O ILE L 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 51 Processing sheet with id=AC8, first strand: chain 'M' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA M 31 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE M 16 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 33 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP M 14 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE M 6 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE M 71 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG M 8 " --> pdb=" O ILE M 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 48 through 51 Processing sheet with id=AD1, first strand: chain 'N' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA N 31 " --> pdb=" O ILE N 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE N 16 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL N 33 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP N 14 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE N 6 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG N 8 " --> pdb=" O ILE N 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 48 through 51 Processing sheet with id=AD3, first strand: chain 'O' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA O 31 " --> pdb=" O ILE O 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE O 16 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL O 33 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP O 14 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE O 6 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE O 71 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG O 8 " --> pdb=" O ILE O 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 48 through 51 Processing sheet with id=AD5, first strand: chain 'P' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA P 31 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE P 16 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL P 33 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP P 14 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE P 6 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE P 71 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG P 8 " --> pdb=" O ILE P 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 48 through 51 Processing sheet with id=AD7, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA Q 31 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE Q 16 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP Q 14 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE Q 6 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Q 71 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG Q 8 " --> pdb=" O ILE Q 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 48 through 51 Processing sheet with id=AD9, first strand: chain 'R' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA R 31 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE R 16 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL R 33 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP R 14 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE R 6 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE R 71 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG R 8 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 48 through 51 Processing sheet with id=AE2, first strand: chain 'S' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA S 31 " --> pdb=" O ILE S 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE S 16 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL S 33 " --> pdb=" O ASP S 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP S 14 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE S 6 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE S 71 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG S 8 " --> pdb=" O ILE S 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 48 through 51 Processing sheet with id=AE4, first strand: chain 'T' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA T 31 " --> pdb=" O ILE T 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE T 16 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL T 33 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP T 14 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE T 6 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE T 71 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG T 8 " --> pdb=" O ILE T 69 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 48 through 51 Processing sheet with id=AE6, first strand: chain 'V' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA V 31 " --> pdb=" O ILE V 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE V 16 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL V 33 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP V 14 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE V 6 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE V 71 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG V 8 " --> pdb=" O ILE V 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 48 through 51 Processing sheet with id=AE8, first strand: chain 'W' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA W 31 " --> pdb=" O ILE W 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE W 16 " --> pdb=" O ALA W 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL W 33 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP W 14 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE W 6 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE W 71 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG W 8 " --> pdb=" O ILE W 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 48 through 51 Processing sheet with id=AF1, first strand: chain 'X' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALA X 31 " --> pdb=" O ILE X 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE X 16 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL X 33 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP X 14 " --> pdb=" O VAL X 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE X 6 " --> pdb=" O ILE X 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE X 71 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG X 8 " --> pdb=" O ILE X 69 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 48 through 51 Processing sheet with id=AF3, first strand: chain 'Y' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA Y 31 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE Y 16 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Y 33 " --> pdb=" O ASP Y 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP Y 14 " --> pdb=" O VAL Y 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE Y 6 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Y 71 " --> pdb=" O ILE Y 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG Y 8 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 48 through 51 Processing sheet with id=AF5, first strand: chain 'Z' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALA Z 31 " --> pdb=" O ILE Z 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE Z 16 " --> pdb=" O ALA Z 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL Z 33 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP Z 14 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE Z 6 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE Z 71 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG Z 8 " --> pdb=" O ILE Z 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AA' and resid 48 through 51 Processing sheet with id=AF7, first strand: chain 'AA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAAA 31 " --> pdb=" O ILEAA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEAA 16 " --> pdb=" O ALAAA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALAA 33 " --> pdb=" O ASPAA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPAA 14 " --> pdb=" O VALAA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEAA 6 " --> pdb=" O ILEAA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEAA 71 " --> pdb=" O ILEAA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGAA 8 " --> pdb=" O ILEAA 69 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'BA' and resid 48 through 51 Processing sheet with id=AF9, first strand: chain 'BA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALABA 31 " --> pdb=" O ILEBA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEBA 16 " --> pdb=" O ALABA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALBA 33 " --> pdb=" O ASPBA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPBA 14 " --> pdb=" O VALBA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEBA 6 " --> pdb=" O ILEBA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEBA 71 " --> pdb=" O ILEBA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGBA 8 " --> pdb=" O ILEBA 69 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'CA' and resid 48 through 51 Processing sheet with id=AG2, first strand: chain 'CA' and resid 48 through 51 removed outlier: 4.346A pdb=" N ALACA 31 " --> pdb=" O ILECA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILECA 16 " --> pdb=" O ALACA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALCA 33 " --> pdb=" O ASPCA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPCA 14 " --> pdb=" O VALCA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILECA 6 " --> pdb=" O ILECA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILECA 71 " --> pdb=" O ILECA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGCA 8 " --> pdb=" O ILECA 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'DA' and resid 48 through 51 Processing sheet with id=AG4, first strand: chain 'DA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALADA 31 " --> pdb=" O ILEDA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEDA 16 " --> pdb=" O ALADA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALDA 33 " --> pdb=" O ASPDA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPDA 14 " --> pdb=" O VALDA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEDA 6 " --> pdb=" O ILEDA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEDA 71 " --> pdb=" O ILEDA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGDA 8 " --> pdb=" O ILEDA 69 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'EA' and resid 48 through 51 Processing sheet with id=AG6, first strand: chain 'EA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAEA 31 " --> pdb=" O ILEEA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEEA 16 " --> pdb=" O ALAEA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALEA 33 " --> pdb=" O ASPEA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPEA 14 " --> pdb=" O VALEA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEEA 6 " --> pdb=" O ILEEA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEEA 71 " --> pdb=" O ILEEA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGEA 8 " --> pdb=" O ILEEA 69 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'FA' and resid 48 through 51 Processing sheet with id=AG8, first strand: chain 'FA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAFA 31 " --> pdb=" O ILEFA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEFA 16 " --> pdb=" O ALAFA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALFA 33 " --> pdb=" O ASPFA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPFA 14 " --> pdb=" O VALFA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEFA 6 " --> pdb=" O ILEFA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEFA 71 " --> pdb=" O ILEFA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGFA 8 " --> pdb=" O ILEFA 69 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'GA' and resid 48 through 51 Processing sheet with id=AH1, first strand: chain 'GA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAGA 31 " --> pdb=" O ILEGA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEGA 16 " --> pdb=" O ALAGA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALGA 33 " --> pdb=" O ASPGA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPGA 14 " --> pdb=" O VALGA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEGA 6 " --> pdb=" O ILEGA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEGA 71 " --> pdb=" O ILEGA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGGA 8 " --> pdb=" O ILEGA 69 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'HA' and resid 48 through 51 Processing sheet with id=AH3, first strand: chain 'HA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAHA 31 " --> pdb=" O ILEHA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEHA 16 " --> pdb=" O ALAHA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALHA 33 " --> pdb=" O ASPHA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPHA 14 " --> pdb=" O VALHA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEHA 6 " --> pdb=" O ILEHA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEHA 71 " --> pdb=" O ILEHA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGHA 8 " --> pdb=" O ILEHA 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'IA' and resid 48 through 51 Processing sheet with id=AH5, first strand: chain 'IA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAIA 31 " --> pdb=" O ILEIA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEIA 16 " --> pdb=" O ALAIA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALIA 33 " --> pdb=" O ASPIA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPIA 14 " --> pdb=" O VALIA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEIA 6 " --> pdb=" O ILEIA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEIA 71 " --> pdb=" O ILEIA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIA 8 " --> pdb=" O ILEIA 69 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'JA' and resid 48 through 51 Processing sheet with id=AH7, first strand: chain 'JA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAJA 31 " --> pdb=" O ILEJA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEJA 16 " --> pdb=" O ALAJA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALJA 33 " --> pdb=" O ASPJA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPJA 14 " --> pdb=" O VALJA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEJA 6 " --> pdb=" O ILEJA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEJA 71 " --> pdb=" O ILEJA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGJA 8 " --> pdb=" O ILEJA 69 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'KA' and resid 48 through 51 Processing sheet with id=AH9, first strand: chain 'KA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAKA 31 " --> pdb=" O ILEKA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEKA 16 " --> pdb=" O ALAKA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALKA 33 " --> pdb=" O ASPKA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPKA 14 " --> pdb=" O VALKA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEKA 6 " --> pdb=" O ILEKA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEKA 71 " --> pdb=" O ILEKA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGKA 8 " --> pdb=" O ILEKA 69 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'LA' and resid 48 through 51 Processing sheet with id=AI2, first strand: chain 'LA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALALA 31 " --> pdb=" O ILELA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILELA 16 " --> pdb=" O ALALA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALLA 33 " --> pdb=" O ASPLA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPLA 14 " --> pdb=" O VALLA 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILELA 6 " --> pdb=" O ILELA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILELA 71 " --> pdb=" O ILELA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGLA 8 " --> pdb=" O ILELA 69 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'MA' and resid 48 through 51 Processing sheet with id=AI4, first strand: chain 'MA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAMA 31 " --> pdb=" O ILEMA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEMA 16 " --> pdb=" O ALAMA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALMA 33 " --> pdb=" O ASPMA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPMA 14 " --> pdb=" O VALMA 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEMA 6 " --> pdb=" O ILEMA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEMA 71 " --> pdb=" O ILEMA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGMA 8 " --> pdb=" O ILEMA 69 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'NA' and resid 48 through 51 Processing sheet with id=AI6, first strand: chain 'NA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALANA 31 " --> pdb=" O ILENA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILENA 16 " --> pdb=" O ALANA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALNA 33 " --> pdb=" O ASPNA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPNA 14 " --> pdb=" O VALNA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILENA 6 " --> pdb=" O ILENA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILENA 71 " --> pdb=" O ILENA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGNA 8 " --> pdb=" O ILENA 69 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'OA' and resid 48 through 51 Processing sheet with id=AI8, first strand: chain 'OA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAOA 31 " --> pdb=" O ILEOA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEOA 16 " --> pdb=" O ALAOA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALOA 33 " --> pdb=" O ASPOA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPOA 14 " --> pdb=" O VALOA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEOA 6 " --> pdb=" O ILEOA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEOA 71 " --> pdb=" O ILEOA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGOA 8 " --> pdb=" O ILEOA 69 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'PA' and resid 48 through 51 Processing sheet with id=AJ1, first strand: chain 'PA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAPA 31 " --> pdb=" O ILEPA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEPA 16 " --> pdb=" O ALAPA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALPA 33 " --> pdb=" O ASPPA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPPA 14 " --> pdb=" O VALPA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEPA 6 " --> pdb=" O ILEPA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEPA 71 " --> pdb=" O ILEPA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGPA 8 " --> pdb=" O ILEPA 69 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'QA' and resid 48 through 51 Processing sheet with id=AJ3, first strand: chain 'QA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAQA 31 " --> pdb=" O ILEQA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEQA 16 " --> pdb=" O ALAQA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALQA 33 " --> pdb=" O ASPQA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPQA 14 " --> pdb=" O VALQA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEQA 6 " --> pdb=" O ILEQA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEQA 71 " --> pdb=" O ILEQA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGQA 8 " --> pdb=" O ILEQA 69 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'RA' and resid 48 through 51 Processing sheet with id=AJ5, first strand: chain 'RA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALARA 31 " --> pdb=" O ILERA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILERA 16 " --> pdb=" O ALARA 31 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VALRA 33 " --> pdb=" O ASPRA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPRA 14 " --> pdb=" O VALRA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILERA 6 " --> pdb=" O ILERA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILERA 71 " --> pdb=" O ILERA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGRA 8 " --> pdb=" O ILERA 69 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'SA' and resid 48 through 51 Processing sheet with id=AJ7, first strand: chain 'SA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALASA 31 " --> pdb=" O ILESA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILESA 16 " --> pdb=" O ALASA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALSA 33 " --> pdb=" O ASPSA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPSA 14 " --> pdb=" O VALSA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILESA 6 " --> pdb=" O ILESA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILESA 71 " --> pdb=" O ILESA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGSA 8 " --> pdb=" O ILESA 69 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'TA' and resid 48 through 51 Processing sheet with id=AJ9, first strand: chain 'TA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALATA 31 " --> pdb=" O ILETA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILETA 16 " --> pdb=" O ALATA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALTA 33 " --> pdb=" O ASPTA 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPTA 14 " --> pdb=" O VALTA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILETA 6 " --> pdb=" O ILETA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILETA 71 " --> pdb=" O ILETA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGTA 8 " --> pdb=" O ILETA 69 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'UA' and resid 48 through 51 Processing sheet with id=AK2, first strand: chain 'UA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAUA 31 " --> pdb=" O ILEUA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEUA 16 " --> pdb=" O ALAUA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALUA 33 " --> pdb=" O ASPUA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPUA 14 " --> pdb=" O VALUA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEUA 6 " --> pdb=" O ILEUA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEUA 71 " --> pdb=" O ILEUA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGUA 8 " --> pdb=" O ILEUA 69 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'VA' and resid 48 through 51 Processing sheet with id=AK4, first strand: chain 'VA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAVA 31 " --> pdb=" O ILEVA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEVA 16 " --> pdb=" O ALAVA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALVA 33 " --> pdb=" O ASPVA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPVA 14 " --> pdb=" O VALVA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEVA 6 " --> pdb=" O ILEVA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEVA 71 " --> pdb=" O ILEVA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGVA 8 " --> pdb=" O ILEVA 69 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'WA' and resid 48 through 51 Processing sheet with id=AK6, first strand: chain 'WA' and resid 48 through 51 removed outlier: 4.346A pdb=" N ALAWA 31 " --> pdb=" O ILEWA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEWA 16 " --> pdb=" O ALAWA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALWA 33 " --> pdb=" O ASPWA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPWA 14 " --> pdb=" O VALWA 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEWA 6 " --> pdb=" O ILEWA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEWA 71 " --> pdb=" O ILEWA 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGWA 8 " --> pdb=" O ILEWA 69 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'XA' and resid 48 through 51 Processing sheet with id=AK8, first strand: chain 'XA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAXA 31 " --> pdb=" O ILEXA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEXA 16 " --> pdb=" O ALAXA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALXA 33 " --> pdb=" O ASPXA 14 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPXA 14 " --> pdb=" O VALXA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEXA 6 " --> pdb=" O ILEXA 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEXA 71 " --> pdb=" O ILEXA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGXA 8 " --> pdb=" O ILEXA 69 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'YA' and resid 48 through 51 Processing sheet with id=AL1, first strand: chain 'YA' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAYA 31 " --> pdb=" O ILEYA 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEYA 16 " --> pdb=" O ALAYA 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALYA 33 " --> pdb=" O ASPYA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPYA 14 " --> pdb=" O VALYA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEYA 6 " --> pdb=" O ILEYA 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEYA 71 " --> pdb=" O ILEYA 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGYA 8 " --> pdb=" O ILEYA 69 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'ZA' and resid 48 through 51 Processing sheet with id=AL3, first strand: chain 'ZA' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAZA 31 " --> pdb=" O ILEZA 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEZA 16 " --> pdb=" O ALAZA 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALZA 33 " --> pdb=" O ASPZA 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPZA 14 " --> pdb=" O VALZA 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEZA 6 " --> pdb=" O ILEZA 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEZA 71 " --> pdb=" O ILEZA 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGZA 8 " --> pdb=" O ILEZA 69 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'AB' and resid 48 through 51 Processing sheet with id=AL5, first strand: chain 'AB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAAB 31 " --> pdb=" O ILEAB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEAB 16 " --> pdb=" O ALAAB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALAB 33 " --> pdb=" O ASPAB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPAB 14 " --> pdb=" O VALAB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEAB 6 " --> pdb=" O ILEAB 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEAB 71 " --> pdb=" O ILEAB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGAB 8 " --> pdb=" O ILEAB 69 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'BB' and resid 48 through 51 Processing sheet with id=AL7, first strand: chain 'BB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALABB 31 " --> pdb=" O ILEBB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEBB 16 " --> pdb=" O ALABB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALBB 33 " --> pdb=" O ASPBB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPBB 14 " --> pdb=" O VALBB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEBB 6 " --> pdb=" O ILEBB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEBB 71 " --> pdb=" O ILEBB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGBB 8 " --> pdb=" O ILEBB 69 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'CB' and resid 48 through 51 Processing sheet with id=AL9, first strand: chain 'CB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALACB 31 " --> pdb=" O ILECB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILECB 16 " --> pdb=" O ALACB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALCB 33 " --> pdb=" O ASPCB 14 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASPCB 14 " --> pdb=" O VALCB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILECB 6 " --> pdb=" O ILECB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILECB 71 " --> pdb=" O ILECB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGCB 8 " --> pdb=" O ILECB 69 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'DB' and resid 48 through 51 Processing sheet with id=AM2, first strand: chain 'DB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALADB 31 " --> pdb=" O ILEDB 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEDB 16 " --> pdb=" O ALADB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALDB 33 " --> pdb=" O ASPDB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPDB 14 " --> pdb=" O VALDB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEDB 6 " --> pdb=" O ILEDB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEDB 71 " --> pdb=" O ILEDB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGDB 8 " --> pdb=" O ILEDB 69 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'EB' and resid 48 through 51 Processing sheet with id=AM4, first strand: chain 'EB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAEB 31 " --> pdb=" O ILEEB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEEB 16 " --> pdb=" O ALAEB 31 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALEB 33 " --> pdb=" O ASPEB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPEB 14 " --> pdb=" O VALEB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEEB 6 " --> pdb=" O ILEEB 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEEB 71 " --> pdb=" O ILEEB 6 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARGEB 8 " --> pdb=" O ILEEB 69 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'FB' and resid 48 through 51 Processing sheet with id=AM6, first strand: chain 'FB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAFB 31 " --> pdb=" O ILEFB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEFB 16 " --> pdb=" O ALAFB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALFB 33 " --> pdb=" O ASPFB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPFB 14 " --> pdb=" O VALFB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEFB 6 " --> pdb=" O ILEFB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEFB 71 " --> pdb=" O ILEFB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGFB 8 " --> pdb=" O ILEFB 69 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'GB' and resid 48 through 51 Processing sheet with id=AM8, first strand: chain 'GB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAGB 31 " --> pdb=" O ILEGB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEGB 16 " --> pdb=" O ALAGB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALGB 33 " --> pdb=" O ASPGB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPGB 14 " --> pdb=" O VALGB 33 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILEGB 6 " --> pdb=" O ILEGB 71 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILEGB 71 " --> pdb=" O ILEGB 6 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGGB 8 " --> pdb=" O ILEGB 69 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'HB' and resid 48 through 51 Processing sheet with id=AN1, first strand: chain 'HB' and resid 48 through 51 removed outlier: 4.345A pdb=" N ALAHB 31 " --> pdb=" O ILEHB 16 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILEHB 16 " --> pdb=" O ALAHB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALHB 33 " --> pdb=" O ASPHB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPHB 14 " --> pdb=" O VALHB 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEHB 6 " --> pdb=" O ILEHB 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILEHB 71 " --> pdb=" O ILEHB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGHB 8 " --> pdb=" O ILEHB 69 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'IB' and resid 48 through 51 Processing sheet with id=AN3, first strand: chain 'IB' and resid 48 through 51 removed outlier: 4.344A pdb=" N ALAIB 31 " --> pdb=" O ILEIB 16 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILEIB 16 " --> pdb=" O ALAIB 31 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VALIB 33 " --> pdb=" O ASPIB 14 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASPIB 14 " --> pdb=" O VALIB 33 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILEIB 6 " --> pdb=" O ILEIB 71 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILEIB 71 " --> pdb=" O ILEIB 6 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARGIB 8 " --> pdb=" O ILEIB 69 " (cutoff:3.500A) 4320 hydrogen bonds defined for protein. 12420 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: 24.09 Time building geometry restraints manager: 20.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21119 1.34 - 1.46: 9059 1.46 - 1.58: 32462 1.58 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 63000 Sorted by residual: bond pdb=" CB ARG T 136 " pdb=" CG ARG T 136 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" CB ARGFB 136 " pdb=" CG ARGFB 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.12e-01 bond pdb=" CB ARG Y 136 " pdb=" CG ARG Y 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.12e-01 bond pdb=" CB ARGHA 136 " pdb=" CG ARGHA 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.08e-01 bond pdb=" CB ARGCA 136 " pdb=" CG ARGCA 136 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 62995 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.82: 1194 106.82 - 113.62: 36981 113.62 - 120.41: 22125 120.41 - 127.21: 23987 127.21 - 134.00: 253 Bond angle restraints: 84540 Sorted by residual: angle pdb=" CB ARGMA 136 " pdb=" CG ARGMA 136 " pdb=" CD ARGMA 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.88e+00 angle pdb=" CB ARGFB 136 " pdb=" CG ARGFB 136 " pdb=" CD ARGFB 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARGIA 136 " pdb=" CG ARGIA 136 " pdb=" CD ARGIA 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARGHB 136 " pdb=" CG ARGHB 136 " pdb=" CD ARGHB 136 " ideal model delta sigma weight residual 111.30 115.83 -4.53 2.30e+00 1.89e-01 3.87e+00 angle pdb=" CB ARG H 136 " pdb=" CG ARG H 136 " pdb=" CD ARG H 136 " ideal model delta sigma weight residual 111.30 115.82 -4.52 2.30e+00 1.89e-01 3.86e+00 ... (remaining 84535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 36120 17.34 - 34.69: 3300 34.69 - 52.03: 600 52.03 - 69.37: 300 69.37 - 86.72: 240 Dihedral angle restraints: 40560 sinusoidal: 18060 harmonic: 22500 Sorted by residual: dihedral pdb=" CA ASP L 65 " pdb=" CB ASP L 65 " pdb=" CG ASP L 65 " pdb=" OD1 ASP L 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.48 55.48 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASPAB 65 " pdb=" CB ASPAB 65 " pdb=" CG ASPAB 65 " pdb=" OD1 ASPAB 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.47 55.47 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASPBB 65 " pdb=" CB ASPBB 65 " pdb=" CG ASPBB 65 " pdb=" OD1 ASPBB 65 " ideal model delta sinusoidal sigma weight residual -30.00 -85.47 55.47 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 40557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 6116 0.026 - 0.051: 2114 0.051 - 0.077: 1010 0.077 - 0.102: 245 0.102 - 0.128: 595 Chirality restraints: 10080 Sorted by residual: chirality pdb=" CA ILEIA 28 " pdb=" N ILEIA 28 " pdb=" C ILEIA 28 " pdb=" CB ILEIA 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILECA 28 " pdb=" N ILECA 28 " pdb=" C ILECA 28 " pdb=" CB ILECA 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE X 28 " pdb=" N ILE X 28 " pdb=" C ILE X 28 " pdb=" CB ILE X 28 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 10077 not shown) Planarity restraints: 10740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGJA 109 " 0.059 9.50e-02 1.11e+02 2.69e-02 6.18e-01 pdb=" NE ARGJA 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARGJA 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARGJA 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGJA 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 109 " 0.060 9.50e-02 1.11e+02 2.70e-02 6.16e-01 pdb=" NE ARG Y 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG Y 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 109 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDB 109 " 0.059 9.50e-02 1.11e+02 2.69e-02 6.14e-01 pdb=" NE ARGDB 109 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARGDB 109 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARGDB 109 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDB 109 " -0.000 2.00e-02 2.50e+03 ... (remaining 10737 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 11521 2.79 - 3.32: 60913 3.32 - 3.85: 96525 3.85 - 4.37: 104987 4.37 - 4.90: 187453 Nonbonded interactions: 461399 Sorted by model distance: nonbonded pdb=" OG SER D 122 " pdb=" OE2 GLURA 90 " model vdw 2.267 2.440 nonbonded pdb=" OG SER I 122 " pdb=" OE2 GLUGB 90 " model vdw 2.267 2.440 nonbonded pdb=" OE2 GLU H 90 " pdb=" OG SERIA 122 " model vdw 2.267 2.440 nonbonded pdb=" OG SERKA 122 " pdb=" OE2 GLUIB 90 " model vdw 2.267 2.440 nonbonded pdb=" OG SER F 122 " pdb=" OE2 GLU Z 90 " model vdw 2.267 2.440 ... (remaining 461394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.060 Extract box with map and model: 4.440 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 123.790 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.850 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 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 : 0.002 0.024 63000 Z= 0.144 Angle : 0.472 4.531 84540 Z= 0.238 Chirality : 0.042 0.128 10080 Planarity : 0.003 0.027 10740 Dihedral : 15.652 86.717 25680 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.85 (0.10), residues: 7380 helix: 3.18 (0.08), residues: 3540 sheet: 0.27 (0.11), residues: 2160 loop : -1.93 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPJA 52 HIS 0.002 0.001 HISFB 85 PHE 0.003 0.001 PHECB 32 TYR 0.004 0.001 TYRVA 82 ARG 0.007 0.001 ARGQA 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14760 Ramachandran restraints generated. 7380 Oldfield, 0 Emsley, 7380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1504 time to evaluate : 5.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1504 average time/residue: 0.6016 time to fit residues: 1477.0138 Evaluate side-chains 980 residues out of total 7320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.874 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.6106 > 50: distance: 8 - 90: 27.306 distance: 11 - 87: 22.698 distance: 22 - 75: 25.005 distance: 24 - 28: 21.507 distance: 25 - 72: 12.378 distance: 28 - 29: 20.940 distance: 29 - 30: 26.901 distance: 29 - 32: 33.633 distance: 30 - 37: 25.415 distance: 32 - 33: 15.418 distance: 33 - 34: 8.142 distance: 34 - 35: 22.477 distance: 34 - 36: 9.574 distance: 37 - 38: 31.001 distance: 38 - 39: 13.026 distance: 38 - 41: 24.304 distance: 39 - 40: 26.610 distance: 39 - 43: 20.404 distance: 41 - 42: 20.432 distance: 43 - 44: 4.171 distance: 44 - 45: 10.541 distance: 45 - 46: 34.152 distance: 45 - 52: 4.291 distance: 47 - 48: 51.056 distance: 48 - 49: 28.729 distance: 49 - 50: 21.929 distance: 49 - 51: 49.419 distance: 52 - 53: 42.371 distance: 53 - 54: 55.980 distance: 54 - 55: 9.877 distance: 54 - 56: 41.460 distance: 56 - 57: 37.356 distance: 57 - 58: 12.069 distance: 57 - 60: 14.582 distance: 58 - 59: 6.704 distance: 58 - 64: 13.375 distance: 60 - 61: 26.722 distance: 61 - 62: 20.498 distance: 61 - 63: 29.488 distance: 64 - 65: 21.111 distance: 64 - 145: 16.729 distance: 65 - 66: 8.220 distance: 65 - 68: 22.761 distance: 66 - 67: 5.536 distance: 66 - 72: 17.890 distance: 67 - 142: 17.907 distance: 68 - 69: 18.167 distance: 68 - 70: 15.324 distance: 69 - 71: 12.284 distance: 72 - 73: 8.263 distance: 73 - 74: 26.723 distance: 73 - 76: 19.536 distance: 74 - 75: 5.573 distance: 74 - 79: 10.675 distance: 76 - 77: 7.803 distance: 76 - 78: 38.066 distance: 79 - 80: 13.247 distance: 79 - 132: 13.106 distance: 80 - 81: 4.148 distance: 80 - 83: 21.687 distance: 81 - 82: 20.056 distance: 81 - 87: 15.849 distance: 82 - 129: 29.855 distance: 83 - 84: 20.029 distance: 83 - 85: 22.341 distance: 84 - 86: 3.435 distance: 87 - 88: 12.769 distance: 88 - 89: 19.013 distance: 88 - 91: 24.797 distance: 89 - 90: 10.117 distance: 89 - 96: 27.337 distance: 91 - 92: 6.653 distance: 92 - 93: 17.510 distance: 93 - 94: 25.530 distance: 94 - 95: 16.051 distance: 96 - 97: 25.730 distance: 97 - 98: 3.480 distance: 97 - 100: 26.595 distance: 98 - 99: 9.889 distance: 98 - 105: 20.727 distance: 100 - 101: 18.629 distance: 101 - 102: 8.462 distance: 102 - 103: 18.974 distance: 103 - 104: 14.824