Starting phenix.real_space_refine on Thu May 29 20:14:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.map" model { file = "/net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzv_9308/05_2025/6mzv_9308.cif" } resolution = 3.4 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= 0.002 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 126 5.16 5 C 20691 2.51 5 N 5909 2.21 5 O 6107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32833 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "E" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Time building chain proxies: 20.43, per 1000 atoms: 0.62 Number of scatterers: 32833 At special positions: 0 Unit cell: (124.63, 216.3, 192.61, 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 126 16.00 O 6107 8.00 N 5909 7.00 C 20691 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 4.3 seconds 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8074 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 48 sheets defined 44.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 26 Processing helix chain 'A' and resid 47 through 59 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.981A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.851A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'C' and resid 15 through 26 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.953A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 81 through 97 removed outlier: 3.760A pdb=" N VAL D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.830A pdb=" N ARG D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 4.026A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 47 through 59 Processing helix chain 'E' and resid 81 through 96 Processing helix chain 'E' and resid 99 through 103 removed outlier: 3.880A pdb=" N ARG E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 126 removed outlier: 4.055A pdb=" N ILE E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 183 through 199 removed outlier: 3.717A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.851A pdb=" N ARG F 103 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.763A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.812A pdb=" N ALA F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 200 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.807A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 68 removed outlier: 3.707A pdb=" N ALAGA 55 " --> pdb=" O ALAGA 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLUGA 58 " --> pdb=" O LYSGA 54 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALAGA 63 " --> pdb=" O ALAGA 59 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARGGA 66 " --> pdb=" O ARGGA 62 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VALGA 67 " --> pdb=" O ALAGA 63 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 removed outlier: 3.540A pdb=" N ASPGA 84 " --> pdb=" O HISGA 80 " (cutoff:3.500A) Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.535A pdb=" N METGB 16 " --> pdb=" O GLYGB 12 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 3.791A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 removed outlier: 3.591A pdb=" N ASPGB 84 " --> pdb=" O HISGB 80 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALAGB 85 " --> pdb=" O VALGB 81 " (cutoff:3.500A) Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.702A pdb=" N VALGC 24 " --> pdb=" O ALAGC 20 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.782A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALAGC 59 " --> pdb=" O ALAGC 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARGGC 62 " --> pdb=" O GLUGC 58 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 removed outlier: 3.622A pdb=" N ALAGC 86 " --> pdb=" O ASNGC 82 " (cutoff:3.500A) Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.705A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSGD 25 " --> pdb=" O ASPGD 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAGD 27 " --> pdb=" O METGD 23 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 65 removed outlier: 3.565A pdb=" N LYSGD 54 " --> pdb=" O VALGD 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALAGD 55 " --> pdb=" O ALAGD 51 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLUGD 58 " --> pdb=" O LYSGD 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 85 removed outlier: 3.600A pdb=" N ASPGD 84 " --> pdb=" O HISGD 80 " (cutoff:3.500A) Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.739A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYSGE 25 " --> pdb=" O ASPGE 21 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.539A pdb=" N ALAGE 55 " --> pdb=" O ALAGE 51 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALAGE 59 " --> pdb=" O ALAGE 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALAGE 63 " --> pdb=" O ALAGE 59 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.534A pdb=" N METGF 16 " --> pdb=" O GLYGF 12 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VALGF 24 " --> pdb=" O ALAGF 20 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 68 removed outlier: 3.509A pdb=" N LYSGF 54 " --> pdb=" O VALGF 50 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALAGF 55 " --> pdb=" O ALAGF 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALAGF 59 " --> pdb=" O ALAGF 55 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARGGF 66 " --> pdb=" O ARGGF 62 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALGF 67 " --> pdb=" O ALAGF 63 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 removed outlier: 3.511A pdb=" N ALAGF 85 " --> pdb=" O VALGF 81 " (cutoff:3.500A) Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.703A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 3.635A pdb=" N ALAHA 55 " --> pdb=" O ALAHA 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARGHA 62 " --> pdb=" O GLUHA 58 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.792A pdb=" N VALHB 24 " --> pdb=" O ALAHB 20 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 68 removed outlier: 3.598A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALAHB 55 " --> pdb=" O ALAHB 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUHB 58 " --> pdb=" O LYSHB 54 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALAHB 59 " --> pdb=" O ALAHB 55 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARGHB 66 " --> pdb=" O ARGHB 62 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VALHB 67 " --> pdb=" O ALAHB 63 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.610A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSHC 25 " --> pdb=" O ASPHC 21 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALAHC 27 " --> pdb=" O METHC 23 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.508A pdb=" N LYSHC 54 " --> pdb=" O VALHC 50 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THRHC 57 " --> pdb=" O VALHC 53 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALAHC 59 " --> pdb=" O ALAHC 55 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 25 removed outlier: 3.562A pdb=" N METHD 16 " --> pdb=" O GLYHD 12 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 3.747A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALAHD 63 " --> pdb=" O ALAHD 59 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.652A pdb=" N VALHE 24 " --> pdb=" O ALAHE 20 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.838A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALAHE 59 " --> pdb=" O ALAHE 55 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 87 Processing helix chain 'HF' and resid 12 through 26 removed outlier: 3.522A pdb=" N METHF 16 " --> pdb=" O GLYHF 12 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.749A pdb=" N ALAHF 55 " --> pdb=" O ALAHF 51 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALAHF 63 " --> pdb=" O ALAHF 59 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.537A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSIA 25 " --> pdb=" O ASPIA 21 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 68 removed outlier: 3.940A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARGIA 66 " --> pdb=" O ARGIA 62 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VALIA 67 " --> pdb=" O ALAIA 63 " (cutoff:3.500A) Processing helix chain 'IA' and resid 82 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.534A pdb=" N METIB 16 " --> pdb=" O GLYIB 12 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 68 removed outlier: 3.546A pdb=" N LYSIB 54 " --> pdb=" O VALIB 50 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALAIB 59 " --> pdb=" O ALAIB 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARGIB 66 " --> pdb=" O ARGIB 62 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VALIB 67 " --> pdb=" O ALAIB 63 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 removed outlier: 3.529A pdb=" N ASPIB 84 " --> pdb=" O HISIB 80 " (cutoff:3.500A) Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.544A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 68 removed outlier: 3.961A pdb=" N ALAIC 55 " --> pdb=" O ALAIC 51 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLUIC 58 " --> pdb=" O LYSIC 54 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALAIC 59 " --> pdb=" O ALAIC 55 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARGIC 66 " --> pdb=" O ARGIC 62 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VALIC 67 " --> pdb=" O ALAIC 63 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.533A pdb=" N METID 16 " --> pdb=" O GLYID 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VALID 24 " --> pdb=" O ALAID 20 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.626A pdb=" N LYSID 54 " --> pdb=" O VALID 50 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALAID 55 " --> pdb=" O ALAID 51 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLUID 58 " --> pdb=" O LYSID 54 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAID 59 " --> pdb=" O ALAID 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 removed outlier: 3.509A pdb=" N ASPID 84 " --> pdb=" O HISID 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAID 85 " --> pdb=" O VALID 81 " (cutoff:3.500A) Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.652A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.515A pdb=" N THRIE 57 " --> pdb=" O VALIE 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALAIE 63 " --> pdb=" O ALAIE 59 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.839A pdb=" N VALIF 24 " --> pdb=" O ALAIF 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAIF 26 " --> pdb=" O ALAIF 22 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 68 removed outlier: 3.825A pdb=" N ALAIF 55 " --> pdb=" O ALAIF 51 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALAIF 59 " --> pdb=" O ALAIF 55 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARGIF 66 " --> pdb=" O ARGIF 62 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VALIF 67 " --> pdb=" O ALAIF 63 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 removed outlier: 3.566A pdb=" N ASPIF 84 " --> pdb=" O HISIF 80 " (cutoff:3.500A) Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.580A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALAJA 27 " --> pdb=" O METJA 23 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 65 removed outlier: 3.669A pdb=" N ALAJA 55 " --> pdb=" O ALAJA 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THRJA 57 " --> pdb=" O VALJA 53 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGJA 62 " --> pdb=" O GLUJA 58 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.596A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VALJB 24 " --> pdb=" O ALAJB 20 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALAJB 27 " --> pdb=" O METJB 23 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.643A pdb=" N LYSJB 54 " --> pdb=" O VALJB 50 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALAJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALAJB 59 " --> pdb=" O ALAJB 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.585A pdb=" N METJC 16 " --> pdb=" O GLYJC 12 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALAJC 27 " --> pdb=" O METJC 23 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 66 removed outlier: 3.902A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAJC 59 " --> pdb=" O ALAJC 55 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGJC 66 " --> pdb=" O ARGJC 62 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.794A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 3.669A pdb=" N LYSJD 54 " --> pdb=" O VALJD 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 removed outlier: 3.533A pdb=" N ALAJD 86 " --> pdb=" O ASNJD 82 " (cutoff:3.500A) Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.898A pdb=" N VALJE 24 " --> pdb=" O ALAJE 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSJE 25 " --> pdb=" O ASPJE 21 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.507A pdb=" N ALAJE 55 " --> pdb=" O ALAJE 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALAJE 59 " --> pdb=" O ALAJE 55 " (cutoff:3.500A) Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 26 removed outlier: 3.589A pdb=" N METJF 16 " --> pdb=" O GLYJF 12 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.746A pdb=" N ALAJF 55 " --> pdb=" O ALAJF 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALAJF 63 " --> pdb=" O ALAJF 59 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.566A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 68 removed outlier: 3.830A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALAKA 59 " --> pdb=" O ALAKA 55 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALAKA 63 " --> pdb=" O ALAKA 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARGKA 66 " --> pdb=" O ARGKA 62 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VALKA 67 " --> pdb=" O ALAKA 63 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 removed outlier: 3.521A pdb=" N ASPKA 84 " --> pdb=" O HISKA 80 " (cutoff:3.500A) Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.617A pdb=" N METKB 16 " --> pdb=" O GLYKB 12 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.684A pdb=" N LYSKB 54 " --> pdb=" O VALKB 50 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLUKB 58 " --> pdb=" O LYSKB 54 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALAKB 59 " --> pdb=" O ALAKB 55 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.507A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALAKC 27 " --> pdb=" O METKC 23 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 68 removed outlier: 3.951A pdb=" N GLUKC 58 " --> pdb=" O LYSKC 54 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALAKC 59 " --> pdb=" O ALAKC 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARGKC 66 " --> pdb=" O ARGKC 62 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VALKC 67 " --> pdb=" O ALAKC 63 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 removed outlier: 3.631A pdb=" N ALAKC 85 " --> pdb=" O VALKC 81 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALAKC 86 " --> pdb=" O ASNKC 82 " (cutoff:3.500A) Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.590A pdb=" N METKD 16 " --> pdb=" O GLYKD 12 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VALKD 24 " --> pdb=" O ALAKD 20 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSKD 25 " --> pdb=" O ASPKD 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALAKD 27 " --> pdb=" O METKD 23 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.873A pdb=" N ALAKD 55 " --> pdb=" O ALAKD 51 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALAKD 59 " --> pdb=" O ALAKD 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 removed outlier: 3.566A pdb=" N ASPKD 84 " --> pdb=" O HISKD 80 " (cutoff:3.500A) Processing helix chain 'KE' and resid 13 through 26 removed outlier: 4.216A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 3.595A pdb=" N ALAKE 55 " --> pdb=" O ALAKE 51 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALAKE 59 " --> pdb=" O ALAKE 55 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 26 removed outlier: 3.699A pdb=" N VALKF 24 " --> pdb=" O ALAKF 20 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.886A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALAKF 59 " --> pdb=" O ALAKF 55 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 removed outlier: 3.591A pdb=" N ASPKF 84 " --> pdb=" O HISKF 80 " (cutoff:3.500A) Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.661A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 57 removed outlier: 3.587A pdb=" N ALALA 55 " --> pdb=" O ALALA 51 " (cutoff:3.500A) Processing helix chain 'LA' and resid 59 through 65 Processing helix chain 'LA' and resid 80 through 87 removed outlier: 3.522A pdb=" N ASPLA 84 " --> pdb=" O HISLA 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALALA 85 " --> pdb=" O VALLA 81 " (cutoff:3.500A) Processing helix chain 'LB' and resid 12 through 27 removed outlier: 3.600A pdb=" N METLB 16 " --> pdb=" O GLYLB 12 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALLB 24 " --> pdb=" O ALALB 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALALB 27 " --> pdb=" O METLB 23 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.602A pdb=" N ALALB 55 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 removed outlier: 3.566A pdb=" N ALALB 85 " --> pdb=" O VALLB 81 " (cutoff:3.500A) Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.697A pdb=" N VALLC 24 " --> pdb=" O ALALC 20 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALALC 27 " --> pdb=" O METLC 23 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 68 removed outlier: 3.637A pdb=" N LYSLC 54 " --> pdb=" O VALLC 50 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALALC 59 " --> pdb=" O ALALC 55 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGLC 66 " --> pdb=" O ARGLC 62 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VALLC 67 " --> pdb=" O ALALC 63 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.527A pdb=" N METLD 16 " --> pdb=" O GLYLD 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 65 removed outlier: 3.543A pdb=" N LYSLD 54 " --> pdb=" O VALLD 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALALD 63 " --> pdb=" O ALALD 59 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.601A pdb=" N VALLE 24 " --> pdb=" O ALALE 20 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.539A pdb=" N ALALE 55 " --> pdb=" O ALALE 51 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALALE 59 " --> pdb=" O ALALE 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALALE 63 " --> pdb=" O ALALE 59 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.746A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.874A pdb=" N ALALF 55 " --> pdb=" O ALALF 51 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALALF 59 " --> pdb=" O ALALF 55 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 85 removed outlier: 3.590A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 6.754A pdb=" N LEU A 74 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 66 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A 76 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 5.550A pdb=" N VAL A 108 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN A 146 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA A 181 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU A 166 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 removed outlier: 3.558A pdb=" N GLY B 73 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.609A pdb=" N GLU B 144 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N HIS B 111 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 142 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 181 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU B 166 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.007A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS C 78 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 114 removed outlier: 5.837A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR C 179 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 11 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.883A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN D 112 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY D 182 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 181 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 166 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 11 removed outlier: 6.423A pdb=" N LEU E 74 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 66 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU E 76 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 114 removed outlier: 5.947A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN E 112 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN E 168 " --> pdb=" O TYR E 179 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA E 181 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 166 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 11 removed outlier: 6.396A pdb=" N GLU F 41 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR F 8 " --> pdb=" O TRP F 39 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP F 39 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE F 10 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER F 37 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL F 65 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS F 78 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 114 removed outlier: 5.485A pdb=" N VAL F 108 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN F 146 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ARG F 177 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL F 169 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR F 179 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'GA' and resid 31 through 36 removed outlier: 7.404A pdb=" N VALGA 45 " --> pdb=" O ILEGA 32 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYRGA 34 " --> pdb=" O THRGA 43 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THRGA 43 " --> pdb=" O TYRGA 34 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYSGA 36 " --> pdb=" O TYRGA 41 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYRGA 41 " --> pdb=" O LYSGA 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEUGA 5 " --> pdb=" O VALGA 75 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VALGA 75 " --> pdb=" O LEUGA 5 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N METGA 7 " --> pdb=" O VALGA 73 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VALGA 73 " --> pdb=" O METGA 7 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLUGA 9 " --> pdb=" O VALGA 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GB' and resid 31 through 36 removed outlier: 3.867A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GC' and resid 31 through 36 removed outlier: 7.219A pdb=" N VALGC 45 " --> pdb=" O ILEGC 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYRGC 34 " --> pdb=" O THRGC 43 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THRGC 43 " --> pdb=" O TYRGC 34 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LYSGC 36 " --> pdb=" O TYRGC 41 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYRGC 41 " --> pdb=" O LYSGC 36 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEUGC 5 " --> pdb=" O VALGC 75 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VALGC 75 " --> pdb=" O LEUGC 5 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N METGC 7 " --> pdb=" O VALGC 73 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VALGC 73 " --> pdb=" O METGC 7 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLUGC 9 " --> pdb=" O VALGC 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GD' and resid 31 through 36 removed outlier: 4.060A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEUGD 5 " --> pdb=" O VALGD 75 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VALGD 75 " --> pdb=" O LEUGD 5 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N METGD 7 " --> pdb=" O VALGD 73 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VALGD 73 " --> pdb=" O METGD 7 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLUGD 9 " --> pdb=" O VALGD 71 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GE' and resid 31 through 36 removed outlier: 7.362A pdb=" N VALGE 45 " --> pdb=" O ILEGE 32 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYRGE 34 " --> pdb=" O THRGE 43 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THRGE 43 " --> pdb=" O TYRGE 34 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYSGE 36 " --> pdb=" O TYRGE 41 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N TYRGE 41 " --> pdb=" O LYSGE 36 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEUGE 5 " --> pdb=" O VALGE 75 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VALGE 75 " --> pdb=" O LEUGE 5 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N METGE 7 " --> pdb=" O VALGE 73 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VALGE 73 " --> pdb=" O METGE 7 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLUGE 9 " --> pdb=" O VALGE 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GF' and resid 31 through 38 removed outlier: 4.031A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYRGF 41 " --> pdb=" O THRGF 37 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEUGF 5 " --> pdb=" O VALGF 75 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VALGF 75 " --> pdb=" O LEUGF 5 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N METGF 7 " --> pdb=" O VALGF 73 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VALGF 73 " --> pdb=" O METGF 7 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLUGF 9 " --> pdb=" O VALGF 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'HA' and resid 31 through 36 removed outlier: 7.349A pdb=" N VALHA 45 " --> pdb=" O ILEHA 32 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYRHA 34 " --> pdb=" O THRHA 43 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THRHA 43 " --> pdb=" O TYRHA 34 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYSHA 36 " --> pdb=" O TYRHA 41 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYRHA 41 " --> pdb=" O LYSHA 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEUHA 5 " --> pdb=" O VALHA 75 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VALHA 75 " --> pdb=" O LEUHA 5 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N METHA 7 " --> pdb=" O VALHA 73 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VALHA 73 " --> pdb=" O METHA 7 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLUHA 9 " --> pdb=" O VALHA 71 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 31 through 38 removed outlier: 5.775A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYRHB 41 " --> pdb=" O THRHB 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HC' and resid 31 through 36 removed outlier: 5.939A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HD' and resid 31 through 38 removed outlier: 5.778A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALHD 45 " --> pdb=" O GLYHD 33 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYRHD 41 " --> pdb=" O THRHD 37 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HE' and resid 30 through 36 removed outlier: 7.317A pdb=" N VALHE 45 " --> pdb=" O ILEHE 32 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYRHE 34 " --> pdb=" O THRHE 43 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THRHE 43 " --> pdb=" O TYRHE 34 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYSHE 36 " --> pdb=" O TYRHE 41 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYRHE 41 " --> pdb=" O LYSHE 36 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEUHE 5 " --> pdb=" O VALHE 75 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VALHE 75 " --> pdb=" O LEUHE 5 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N METHE 7 " --> pdb=" O VALHE 73 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VALHE 73 " --> pdb=" O METHE 7 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLUHE 9 " --> pdb=" O VALHE 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HF' and resid 31 through 36 removed outlier: 5.981A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEUHF 5 " --> pdb=" O VALHF 75 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VALHF 75 " --> pdb=" O LEUHF 5 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N METHF 7 " --> pdb=" O VALHF 73 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VALHF 73 " --> pdb=" O METHF 7 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUHF 9 " --> pdb=" O VALHF 71 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLUHF 69 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'IA' and resid 31 through 38 removed outlier: 5.824A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYRIA 41 " --> pdb=" O THRIA 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IB' and resid 31 through 38 removed outlier: 5.580A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEUIB 5 " --> pdb=" O VALIB 75 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VALIB 75 " --> pdb=" O LEUIB 5 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N METIB 7 " --> pdb=" O VALIB 73 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VALIB 73 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLUIB 9 " --> pdb=" O VALIB 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IC' and resid 31 through 36 removed outlier: 7.351A pdb=" N VALIC 45 " --> pdb=" O ILEIC 32 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYRIC 34 " --> pdb=" O THRIC 43 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THRIC 43 " --> pdb=" O TYRIC 34 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYSIC 36 " --> pdb=" O TYRIC 41 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYRIC 41 " --> pdb=" O LYSIC 36 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'ID' and resid 31 through 36 removed outlier: 7.332A pdb=" N VALID 45 " --> pdb=" O ILEID 32 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYRID 34 " --> pdb=" O THRID 43 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THRID 43 " --> pdb=" O TYRID 34 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYSID 36 " --> pdb=" O TYRID 41 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYRID 41 " --> pdb=" O LYSID 36 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEUID 5 " --> pdb=" O VALID 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VALID 75 " --> pdb=" O LEUID 5 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N METID 7 " --> pdb=" O VALID 73 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VALID 73 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLUID 9 " --> pdb=" O VALID 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'IE' and resid 31 through 36 removed outlier: 6.060A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALIE 45 " --> pdb=" O GLYIE 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEUIE 5 " --> pdb=" O VALIE 75 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VALIE 75 " --> pdb=" O LEUIE 5 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N METIE 7 " --> pdb=" O VALIE 73 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VALIE 73 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLUIE 9 " --> pdb=" O VALIE 71 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLUIE 69 " --> pdb=" O ARGIE 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IF' and resid 31 through 38 removed outlier: 5.906A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THRIF 37 " --> pdb=" O TYRIF 41 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYRIF 41 " --> pdb=" O THRIF 37 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEUIF 5 " --> pdb=" O VALIF 75 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VALIF 75 " --> pdb=" O LEUIF 5 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N METIF 7 " --> pdb=" O VALIF 73 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VALIF 73 " --> pdb=" O METIF 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLUIF 9 " --> pdb=" O VALIF 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'JA' and resid 31 through 38 removed outlier: 3.959A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYRJA 41 " --> pdb=" O THRJA 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEUJA 5 " --> pdb=" O VALJA 75 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VALJA 75 " --> pdb=" O LEUJA 5 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N METJA 7 " --> pdb=" O VALJA 73 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VALJA 73 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLUJA 9 " --> pdb=" O VALJA 71 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.677A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JC' and resid 31 through 36 removed outlier: 7.239A pdb=" N VALJC 45 " --> pdb=" O ILEJC 32 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYRJC 34 " --> pdb=" O THRJC 43 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THRJC 43 " --> pdb=" O TYRJC 34 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYSJC 36 " --> pdb=" O TYRJC 41 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYRJC 41 " --> pdb=" O LYSJC 36 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JD' and resid 31 through 38 removed outlier: 5.695A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VALJD 45 " --> pdb=" O GLYJD 33 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TYRJD 41 " --> pdb=" O THRJD 37 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEUJD 5 " --> pdb=" O VALJD 75 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VALJD 75 " --> pdb=" O LEUJD 5 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N METJD 7 " --> pdb=" O VALJD 73 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VALJD 73 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLUJD 9 " --> pdb=" O VALJD 71 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.403A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VALJE 45 " --> pdb=" O GLYJE 33 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEUJE 5 " --> pdb=" O VALJE 75 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VALJE 75 " --> pdb=" O LEUJE 5 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N METJE 7 " --> pdb=" O VALJE 73 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VALJE 73 " --> pdb=" O METJE 7 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLUJE 9 " --> pdb=" O VALJE 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JF' and resid 31 through 36 removed outlier: 7.477A pdb=" N VALJF 45 " --> pdb=" O ILEJF 32 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYRJF 34 " --> pdb=" O THRJF 43 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THRJF 43 " --> pdb=" O TYRJF 34 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYSJF 36 " --> pdb=" O TYRJF 41 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYRJF 41 " --> pdb=" O LYSJF 36 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'KA' and resid 31 through 38 removed outlier: 7.311A pdb=" N VALKA 45 " --> pdb=" O ILEKA 32 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYRKA 34 " --> pdb=" O THRKA 43 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THRKA 43 " --> pdb=" O TYRKA 34 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYSKA 36 " --> pdb=" O TYRKA 41 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYRKA 41 " --> pdb=" O LYSKA 36 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KB' and resid 31 through 36 removed outlier: 5.677A pdb=" N LEUKB 31 " --> pdb=" O ARGKB 47 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARGKB 47 " --> pdb=" O LEUKB 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VALKB 45 " --> pdb=" O GLYKB 33 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEUKB 5 " --> pdb=" O VALKB 75 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VALKB 75 " --> pdb=" O LEUKB 5 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N METKB 7 " --> pdb=" O VALKB 73 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VALKB 73 " --> pdb=" O METKB 7 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLUKB 9 " --> pdb=" O VALKB 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KC' and resid 31 through 38 removed outlier: 7.306A pdb=" N VALKC 45 " --> pdb=" O ILEKC 32 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYRKC 34 " --> pdb=" O THRKC 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THRKC 43 " --> pdb=" O TYRKC 34 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYSKC 36 " --> pdb=" O TYRKC 41 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYRKC 41 " --> pdb=" O LYSKC 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KD' and resid 31 through 36 removed outlier: 7.387A pdb=" N VALKD 45 " --> pdb=" O ILEKD 32 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYRKD 34 " --> pdb=" O THRKD 43 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THRKD 43 " --> pdb=" O TYRKD 34 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYSKD 36 " --> pdb=" O TYRKD 41 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TYRKD 41 " --> pdb=" O LYSKD 36 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEUKD 5 " --> pdb=" O VALKD 75 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VALKD 75 " --> pdb=" O LEUKD 5 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N METKD 7 " --> pdb=" O VALKD 73 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VALKD 73 " --> pdb=" O METKD 7 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLUKD 9 " --> pdb=" O VALKD 71 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLUKD 69 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KE' and resid 31 through 36 removed outlier: 6.023A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALKE 45 " --> pdb=" O GLYKE 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEUKE 5 " --> pdb=" O VALKE 75 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VALKE 75 " --> pdb=" O LEUKE 5 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N METKE 7 " --> pdb=" O VALKE 73 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VALKE 73 " --> pdb=" O METKE 7 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLUKE 9 " --> pdb=" O VALKE 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KF' and resid 31 through 38 removed outlier: 5.744A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYRKF 41 " --> pdb=" O THRKF 37 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LA' and resid 31 through 38 removed outlier: 5.815A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALLA 45 " --> pdb=" O GLYLA 33 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEULA 5 " --> pdb=" O VALLA 75 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VALLA 75 " --> pdb=" O LEULA 5 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N METLA 7 " --> pdb=" O VALLA 73 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VALLA 73 " --> pdb=" O METLA 7 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLULA 9 " --> pdb=" O VALLA 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LB' and resid 31 through 36 removed outlier: 5.744A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LC' and resid 31 through 38 removed outlier: 5.611A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYRLC 41 " --> pdb=" O THRLC 37 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LD' and resid 31 through 38 removed outlier: 5.821A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALLD 42 " --> pdb=" O VALLD 10 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LE' and resid 30 through 36 removed outlier: 7.440A pdb=" N VALLE 45 " --> pdb=" O ILELE 32 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYRLE 34 " --> pdb=" O THRLE 43 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THRLE 43 " --> pdb=" O TYRLE 34 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYSLE 36 " --> pdb=" O TYRLE 41 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYRLE 41 " --> pdb=" O LYSLE 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEULE 5 " --> pdb=" O VALLE 75 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VALLE 75 " --> pdb=" O LEULE 5 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N METLE 7 " --> pdb=" O VALLE 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VALLE 73 " --> pdb=" O METLE 7 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLULE 9 " --> pdb=" O VALLE 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LF' and resid 31 through 38 removed outlier: 7.435A pdb=" N VALLF 45 " --> pdb=" O ILELF 32 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYRLF 34 " --> pdb=" O THRLF 43 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THRLF 43 " --> pdb=" O TYRLF 34 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYSLF 36 " --> pdb=" O TYRLF 41 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYRLF 41 " --> pdb=" O LYSLF 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEULF 5 " --> pdb=" O VALLF 75 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VALLF 75 " --> pdb=" O LEULF 5 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N METLF 7 " --> pdb=" O VALLF 73 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VALLF 73 " --> pdb=" O METLF 7 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLULF 9 " --> pdb=" O VALLF 71 " (cutoff:3.500A) 1777 hydrogen bonds defined for protein. 5139 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: 12.23 Time building geometry restraints manager: 8.46 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: 11218 1.34 - 1.45: 3637 1.45 - 1.57: 18170 1.57 - 1.69: 0 1.69 - 1.81: 252 Bond restraints: 33277 Sorted by residual: bond pdb=" C ALAKD 86 " pdb=" N LEUKD 87 " ideal model delta sigma weight residual 1.331 1.275 0.056 2.07e-02 2.33e+03 7.30e+00 bond pdb=" C ALALA 86 " pdb=" N LEULA 87 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.07e-02 2.33e+03 6.08e+00 bond pdb=" C ALAID 86 " pdb=" N LEUID 87 " ideal model delta sigma weight residual 1.331 1.254 0.076 3.12e-02 1.03e+03 5.98e+00 bond pdb=" C ALAIB 86 " pdb=" N LEUIB 87 " ideal model delta sigma weight residual 1.331 1.260 0.071 3.12e-02 1.03e+03 5.18e+00 bond pdb=" CB THR F 20 " pdb=" CG2 THR F 20 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.30e+00 ... (remaining 33272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 43627 1.78 - 3.57: 1452 3.57 - 5.35: 116 5.35 - 7.14: 5 7.14 - 8.92: 3 Bond angle restraints: 45203 Sorted by residual: angle pdb=" C ILE B 114 " pdb=" N ARG B 115 " pdb=" CA ARG B 115 " ideal model delta sigma weight residual 121.31 126.71 -5.40 1.49e+00 4.50e-01 1.31e+01 angle pdb=" N ARG B 115 " pdb=" CA ARG B 115 " pdb=" C ARG B 115 " ideal model delta sigma weight residual 110.35 115.11 -4.76 1.40e+00 5.10e-01 1.16e+01 angle pdb=" C ALA A 71 " pdb=" N TYR A 72 " pdb=" CA TYR A 72 " ideal model delta sigma weight residual 121.76 126.34 -4.58 1.51e+00 4.39e-01 9.21e+00 angle pdb=" CG1 ILE B 114 " pdb=" CB ILE B 114 " pdb=" CG2 ILE B 114 " ideal model delta sigma weight residual 110.70 101.78 8.92 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C ILE F 125 " pdb=" N ASN F 126 " pdb=" CA ASN F 126 " ideal model delta sigma weight residual 122.67 118.33 4.34 1.59e+00 3.96e-01 7.45e+00 ... (remaining 45198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 19418 15.82 - 31.65: 528 31.65 - 47.47: 76 47.47 - 63.29: 10 63.29 - 79.12: 11 Dihedral angle restraints: 20043 sinusoidal: 7380 harmonic: 12663 Sorted by residual: dihedral pdb=" CA ARG A 70 " pdb=" C ARG A 70 " pdb=" N ALA A 71 " pdb=" CA ALA A 71 " ideal model delta harmonic sigma weight residual -180.00 -138.04 -41.96 0 5.00e+00 4.00e-02 7.04e+01 dihedral pdb=" CA ASN E 126 " pdb=" C ASN E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta harmonic sigma weight residual 180.00 147.36 32.64 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ASN F 126 " pdb=" C ASN F 126 " pdb=" N ARG F 127 " pdb=" CA ARG F 127 " ideal model delta harmonic sigma weight residual 180.00 148.10 31.90 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 20040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4138 0.054 - 0.107: 940 0.107 - 0.161: 273 0.161 - 0.215: 60 0.215 - 0.269: 12 Chirality restraints: 5423 Sorted by residual: chirality pdb=" CG LEULF 89 " pdb=" CB LEULF 89 " pdb=" CD1 LEULF 89 " pdb=" CD2 LEULF 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEUHA 89 " pdb=" CB LEUHA 89 " pdb=" CD1 LEUHA 89 " pdb=" CD2 LEUHA 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEUJF 89 " pdb=" CB LEUJF 89 " pdb=" CD1 LEUJF 89 " pdb=" CD2 LEUJF 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 5420 not shown) Planarity restraints: 5939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 62 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO F 63 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO F 63 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 63 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 15 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO C 16 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 16 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 16 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 62 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO D 63 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " 0.031 5.00e-02 4.00e+02 ... (remaining 5936 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10443 2.85 - 3.37: 29052 3.37 - 3.88: 54914 3.88 - 4.39: 61269 4.39 - 4.90: 110060 Nonbonded interactions: 265738 Sorted by model distance: nonbonded pdb=" OG SER C 37 " pdb=" OE2 GLU C 76 " model vdw 2.343 3.040 nonbonded pdb=" ND2 ASN D 126 " pdb=" O ILE D 134 " model vdw 2.360 3.120 nonbonded pdb=" OE1 GLUGB 18 " pdb=" NE2 HISGC 74 " model vdw 2.363 3.120 nonbonded pdb=" OE1 GLUHC 18 " pdb=" NE2 HISHD 74 " model vdw 2.363 3.120 nonbonded pdb=" OE1 GLULC 18 " pdb=" NE2 HISLD 74 " model vdw 2.364 3.120 ... (remaining 265733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 204) selection = (chain 'B' and resid 4 through 204) selection = (chain 'C' and resid 4 through 204) selection = (chain 'D' and resid 4 through 204) selection = (chain 'E' and resid 4 through 204) selection = chain 'F' } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } 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: 8.480 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: 1.380 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 70.610 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.006 0.085 33277 Z= 0.258 Angle : 0.729 8.923 45203 Z= 0.409 Chirality : 0.054 0.269 5423 Planarity : 0.006 0.066 5939 Dihedral : 8.476 79.116 11969 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 0.34 % Allowed : 2.29 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.51 (0.11), residues: 4439 helix: -4.09 (0.07), residues: 1868 sheet: -0.96 (0.16), residues: 1086 loop : -2.66 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 39 HIS 0.011 0.002 HIS F 78 PHE 0.018 0.002 PHE C 29 TYR 0.025 0.003 TYRHE 34 ARG 0.007 0.001 ARG E 70 Details of bonding type rmsd hydrogen bonds : bond 0.29176 ( 1777) hydrogen bonds : angle 8.80537 ( 5139) covalent geometry : bond 0.00645 (33277) covalent geometry : angle 0.72861 (45203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8878 Ramachandran restraints generated. 4439 Oldfield, 0 Emsley, 4439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1264 time to evaluate : 3.512 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: B 76 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 90 SER cc_start: 0.8504 (m) cc_final: 0.7789 (p) REVERT: B 163 ASN cc_start: 0.7507 (t0) cc_final: 0.7299 (t0) REVERT: C 90 SER cc_start: 0.8878 (m) cc_final: 0.8307 (m) REVERT: C 145 THR cc_start: 0.9034 (p) cc_final: 0.8829 (p) REVERT: C 150 TYR cc_start: 0.9194 (m-80) cc_final: 0.8978 (m-80) REVERT: C 177 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8176 (mtt-85) REVERT: C 179 TYR cc_start: 0.8895 (m-10) cc_final: 0.8629 (m-80) REVERT: C 183 SER cc_start: 0.8982 (p) cc_final: 0.8705 (p) REVERT: E 72 TYR cc_start: 0.8380 (m-80) cc_final: 0.8093 (m-80) REVERT: E 90 SER cc_start: 0.8474 (m) cc_final: 0.8128 (m) REVERT: E 139 SER cc_start: 0.9338 (m) cc_final: 0.8913 (p) REVERT: GA 54 LYS cc_start: 0.8238 (tttm) cc_final: 0.7852 (ttpt) REVERT: GC 28 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8528 (mmtm) REVERT: GC 34 TYR cc_start: 0.8963 (p90) cc_final: 0.8719 (p90) REVERT: GC 43 THR cc_start: 0.9358 (m) cc_final: 0.9146 (t) REVERT: GC 65 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7919 (mt-10) REVERT: GD 61 GLN cc_start: 0.8926 (tt0) cc_final: 0.8659 (tt0) REVERT: GF 18 GLU cc_start: 0.8456 (tp30) cc_final: 0.8183 (tp30) REVERT: GF 21 ASP cc_start: 0.8595 (t70) cc_final: 0.8270 (t70) REVERT: HB 3 ASP cc_start: 0.8171 (m-30) cc_final: 0.7958 (m-30) REVERT: HC 28 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8275 (mmtm) REVERT: HC 54 LYS cc_start: 0.8488 (tttm) cc_final: 0.7948 (tttt) REVERT: HC 78 ARG cc_start: 0.8009 (mtp180) cc_final: 0.6664 (mtt90) REVERT: HD 78 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.6906 (mtm-85) REVERT: HF 3 ASP cc_start: 0.8162 (m-30) cc_final: 0.7846 (m-30) REVERT: IB 16 MET cc_start: 0.9080 (tmm) cc_final: 0.8872 (tmm) REVERT: IC 28 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8350 (mptt) REVERT: ID 78 ARG cc_start: 0.8771 (ttt90) cc_final: 0.7611 (ttm170) REVERT: IE 78 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7690 (ptp-170) REVERT: IE 82 ASN cc_start: 0.9129 (t0) cc_final: 0.8800 (t0) REVERT: IF 28 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8326 (ttmt) REVERT: IF 82 ASN cc_start: 0.8886 (t0) cc_final: 0.8603 (t0) REVERT: JA 36 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8134 (mtmm) REVERT: JA 89 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8241 (mt) REVERT: JB 5 LEU cc_start: 0.9114 (tp) cc_final: 0.8909 (tp) REVERT: JC 28 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8134 (mptt) REVERT: JD 61 GLN cc_start: 0.8587 (tt0) cc_final: 0.8379 (tt0) REVERT: JE 16 MET cc_start: 0.8963 (tmm) cc_final: 0.8662 (tmm) REVERT: KA 23 MET cc_start: 0.8689 (mtm) cc_final: 0.8439 (mtp) REVERT: KB 16 MET cc_start: 0.8953 (tmm) cc_final: 0.8596 (tmm) REVERT: KC 23 MET cc_start: 0.8802 (mtm) cc_final: 0.8599 (mtp) REVERT: KC 78 ARG cc_start: 0.7659 (mmm160) cc_final: 0.6642 (ptt180) REVERT: KD 78 ARG cc_start: 0.8616 (ttt90) cc_final: 0.7578 (mtm180) REVERT: KE 16 MET cc_start: 0.8542 (tmm) cc_final: 0.8289 (tmm) REVERT: LA 3 ASP cc_start: 0.8297 (m-30) cc_final: 0.7990 (m-30) REVERT: LA 21 ASP cc_start: 0.9119 (t70) cc_final: 0.8622 (t0) REVERT: LB 21 ASP cc_start: 0.8616 (t70) cc_final: 0.8183 (t0) REVERT: LC 28 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8111 (mptt) REVERT: LC 84 ASP cc_start: 0.8347 (m-30) cc_final: 0.8061 (m-30) REVERT: LD 78 ARG cc_start: 0.7822 (mmm160) cc_final: 0.6981 (mtm-85) REVERT: LE 54 LYS cc_start: 0.9008 (tttm) cc_final: 0.8733 (ttmt) outliers start: 11 outliers final: 0 residues processed: 1269 average time/residue: 0.5738 time to fit residues: 1075.9839 Evaluate side-chains 962 residues out of total 3192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 961 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain JA residue 89 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-dev-5687/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-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1276 > 50: distance: 77 - 85: 29.933 distance: 78 - 107: 23.492 distance: 85 - 86: 9.957 distance: 86 - 87: 14.498 distance: 86 - 89: 27.116 distance: 87 - 88: 26.131 distance: 87 - 92: 31.983 distance: 88 - 115: 29.923 distance: 89 - 90: 17.319 distance: 89 - 91: 45.618 distance: 92 - 93: 16.885 distance: 93 - 94: 46.153 distance: 93 - 96: 21.816 distance: 94 - 95: 16.905 distance: 94 - 100: 4.187 distance: 95 - 120: 58.811 distance: 96 - 97: 36.129 distance: 97 - 98: 11.781 distance: 97 - 99: 24.362 distance: 100 - 101: 3.602 distance: 101 - 102: 27.926 distance: 101 - 104: 32.373 distance: 102 - 103: 22.110 distance: 102 - 107: 32.961 distance: 103 - 125: 63.950 distance: 104 - 105: 23.034 distance: 104 - 106: 41.081 distance: 107 - 108: 13.053 distance: 108 - 109: 11.590 distance: 108 - 111: 16.577 distance: 109 - 110: 15.512 distance: 109 - 115: 12.030 distance: 111 - 112: 7.048 distance: 112 - 113: 43.102 distance: 112 - 114: 6.161 distance: 115 - 116: 23.488 distance: 116 - 117: 32.206 distance: 116 - 119: 9.861 distance: 117 - 118: 41.657 distance: 117 - 120: 29.130 distance: 120 - 121: 45.263 distance: 121 - 122: 36.829 distance: 121 - 124: 45.801 distance: 122 - 125: 39.556 distance: 125 - 126: 16.189 distance: 126 - 127: 19.898 distance: 126 - 129: 41.758 distance: 127 - 128: 3.618 distance: 127 - 133: 50.890 distance: 129 - 130: 28.168 distance: 130 - 131: 24.521 distance: 130 - 132: 34.480 distance: 133 - 134: 37.331 distance: 133 - 139: 25.967 distance: 134 - 135: 19.922 distance: 134 - 137: 37.675 distance: 135 - 136: 27.497 distance: 135 - 140: 19.683 distance: 137 - 138: 40.229 distance: 138 - 139: 11.780 distance: 140 - 141: 16.799 distance: 141 - 142: 4.189 distance: 141 - 144: 29.184 distance: 142 - 143: 27.394 distance: 142 - 148: 30.352 distance: 144 - 145: 30.470 distance: 145 - 146: 4.975 distance: 148 - 149: 42.579 distance: 149 - 150: 46.765 distance: 150 - 151: 36.391 distance: 150 - 152: 34.319