Starting phenix.real_space_refine on Wed Nov 15 22:42:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wc3_8795/11_2023/5wc3_8795.pdb" } resolution = 3.5 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 20130 2.51 5 N 5490 2.21 5 O 6840 1.98 5 H 33390 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 65880 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "B" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "C" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "D" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "E" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "F" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "G" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "H" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "I" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "J" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "K" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "L" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "M" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "N" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "O" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "P" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "Q" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "R" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "S" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "T" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "U" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "V" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "W" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "X" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "Y" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "Z" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "0" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "1" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "2" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Chain: "3" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2196 Classifications: {'peptide': 139} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 132} Time building chain proxies: 20.60, per 1000 atoms: 0.31 Number of scatterers: 65880 At special positions: 0 Unit cell: (230.85, 230.85, 82.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 6840 8.00 N 5490 7.00 C 20130 6.00 H 33390 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.65 Conformation dependent library (CDL) restraints added in 4.8 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7980 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 91 sheets defined 28.8% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 216 No H-bonds generated for 'chain 'D' and resid 214 through 216' Processing helix chain 'E' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP E 95 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 96 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'F' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR F 96 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS F 105 " --> pdb=" O GLU F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR F 202 " --> pdb=" O GLN F 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'G' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR G 202 " --> pdb=" O GLN G 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 216 No H-bonds generated for 'chain 'G' and resid 214 through 216' Processing helix chain 'H' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR H 96 " --> pdb=" O SER H 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN H 103 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR H 202 " --> pdb=" O GLN H 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 203 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL H 210 " --> pdb=" O ALA H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 216 No H-bonds generated for 'chain 'H' and resid 214 through 216' Processing helix chain 'I' and resid 90 through 109 removed outlier: 3.545A pdb=" N ASP I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN I 103 " --> pdb=" O GLU I 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR I 202 " --> pdb=" O GLN I 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 216 No H-bonds generated for 'chain 'I' and resid 214 through 216' Processing helix chain 'J' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 96 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS J 105 " --> pdb=" O GLU J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR J 202 " --> pdb=" O GLN J 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE J 203 " --> pdb=" O ILE J 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG J 209 " --> pdb=" O GLU J 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 216 No H-bonds generated for 'chain 'J' and resid 214 through 216' Processing helix chain 'K' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 103 " --> pdb=" O GLU K 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR K 202 " --> pdb=" O GLN K 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE K 203 " --> pdb=" O ILE K 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL K 210 " --> pdb=" O ALA K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'L' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS L 105 " --> pdb=" O GLU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR L 202 " --> pdb=" O GLN L 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE L 203 " --> pdb=" O ILE L 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 216 No H-bonds generated for 'chain 'L' and resid 214 through 216' Processing helix chain 'M' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP M 95 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR M 96 " --> pdb=" O SER M 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN M 103 " --> pdb=" O GLU M 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 105 " --> pdb=" O GLU M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR M 202 " --> pdb=" O GLN M 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE M 203 " --> pdb=" O ILE M 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG M 209 " --> pdb=" O GLU M 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 216 No H-bonds generated for 'chain 'M' and resid 214 through 216' Processing helix chain 'N' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP N 95 " --> pdb=" O ASP N 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR N 96 " --> pdb=" O SER N 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS N 105 " --> pdb=" O GLU N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR N 202 " --> pdb=" O GLN N 198 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG N 209 " --> pdb=" O GLU N 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 216 No H-bonds generated for 'chain 'N' and resid 214 through 216' Processing helix chain 'O' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP O 95 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR O 96 " --> pdb=" O SER O 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN O 103 " --> pdb=" O GLU O 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS O 105 " --> pdb=" O GLU O 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR O 202 " --> pdb=" O GLN O 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG O 209 " --> pdb=" O GLU O 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL O 210 " --> pdb=" O ALA O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 216 No H-bonds generated for 'chain 'O' and resid 214 through 216' Processing helix chain 'P' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN P 103 " --> pdb=" O GLU P 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS P 105 " --> pdb=" O GLU P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR P 202 " --> pdb=" O GLN P 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE P 203 " --> pdb=" O ILE P 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 216 No H-bonds generated for 'chain 'P' and resid 214 through 216' Processing helix chain 'Q' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR Q 96 " --> pdb=" O SER Q 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Q 103 " --> pdb=" O GLU Q 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR Q 202 " --> pdb=" O GLN Q 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Q 203 " --> pdb=" O ILE Q 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG Q 209 " --> pdb=" O GLU Q 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Q 210 " --> pdb=" O ALA Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 214 through 216 No H-bonds generated for 'chain 'Q' and resid 214 through 216' Processing helix chain 'R' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR R 96 " --> pdb=" O SER R 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN R 103 " --> pdb=" O GLU R 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS R 105 " --> pdb=" O GLU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR R 202 " --> pdb=" O GLN R 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 203 " --> pdb=" O ILE R 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 216 No H-bonds generated for 'chain 'R' and resid 214 through 216' Processing helix chain 'S' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP S 95 " --> pdb=" O ASP S 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR S 96 " --> pdb=" O SER S 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN S 103 " --> pdb=" O GLU S 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 105 " --> pdb=" O GLU S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR S 202 " --> pdb=" O GLN S 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE S 203 " --> pdb=" O ILE S 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG S 209 " --> pdb=" O GLU S 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL S 210 " --> pdb=" O ALA S 206 " (cutoff:3.500A) Processing helix chain 'S' and resid 214 through 216 No H-bonds generated for 'chain 'S' and resid 214 through 216' Processing helix chain 'T' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR T 96 " --> pdb=" O SER T 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN T 103 " --> pdb=" O GLU T 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS T 105 " --> pdb=" O GLU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR T 202 " --> pdb=" O GLN T 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE T 203 " --> pdb=" O ILE T 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG T 209 " --> pdb=" O GLU T 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL T 210 " --> pdb=" O ALA T 206 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 216 No H-bonds generated for 'chain 'T' and resid 214 through 216' Processing helix chain 'U' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR U 96 " --> pdb=" O SER U 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN U 103 " --> pdb=" O GLU U 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 105 " --> pdb=" O GLU U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR U 202 " --> pdb=" O GLN U 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE U 203 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG U 209 " --> pdb=" O GLU U 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 210 " --> pdb=" O ALA U 206 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 216 No H-bonds generated for 'chain 'U' and resid 214 through 216' Processing helix chain 'V' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP V 95 " --> pdb=" O ASP V 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR V 96 " --> pdb=" O SER V 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN V 103 " --> pdb=" O GLU V 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS V 105 " --> pdb=" O GLU V 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE V 203 " --> pdb=" O ILE V 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG V 209 " --> pdb=" O GLU V 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 216 No H-bonds generated for 'chain 'V' and resid 214 through 216' Processing helix chain 'W' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP W 95 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR W 96 " --> pdb=" O SER W 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN W 103 " --> pdb=" O GLU W 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS W 105 " --> pdb=" O GLU W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR W 202 " --> pdb=" O GLN W 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE W 203 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG W 209 " --> pdb=" O GLU W 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL W 210 " --> pdb=" O ALA W 206 " (cutoff:3.500A) Processing helix chain 'W' and resid 214 through 216 No H-bonds generated for 'chain 'W' and resid 214 through 216' Processing helix chain 'X' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP X 95 " --> pdb=" O ASP X 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR X 96 " --> pdb=" O SER X 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN X 103 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR X 202 " --> pdb=" O GLN X 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE X 203 " --> pdb=" O ILE X 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG X 209 " --> pdb=" O GLU X 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL X 210 " --> pdb=" O ALA X 206 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 216 No H-bonds generated for 'chain 'X' and resid 214 through 216' Processing helix chain 'Y' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP Y 95 " --> pdb=" O ASP Y 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR Y 96 " --> pdb=" O SER Y 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Y 103 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Y 105 " --> pdb=" O GLU Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR Y 202 " --> pdb=" O GLN Y 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Y 203 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG Y 209 " --> pdb=" O GLU Y 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 216 No H-bonds generated for 'chain 'Y' and resid 214 through 216' Processing helix chain 'Z' and resid 90 through 109 removed outlier: 3.547A pdb=" N ASP Z 95 " --> pdb=" O ASP Z 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR Z 96 " --> pdb=" O SER Z 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Z 105 " --> pdb=" O GLU Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR Z 202 " --> pdb=" O GLN Z 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE Z 203 " --> pdb=" O ILE Z 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Z 209 " --> pdb=" O GLU Z 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 210 " --> pdb=" O ALA Z 206 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 216 No H-bonds generated for 'chain 'Z' and resid 214 through 216' Processing helix chain '0' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 0 95 " --> pdb=" O ASP 0 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR 0 96 " --> pdb=" O SER 0 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 0 103 " --> pdb=" O GLU 0 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 0 105 " --> pdb=" O GLU 0 101 " (cutoff:3.500A) Processing helix chain '0' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR 0 202 " --> pdb=" O GLN 0 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 0 203 " --> pdb=" O ILE 0 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 0 209 " --> pdb=" O GLU 0 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL 0 210 " --> pdb=" O ALA 0 206 " (cutoff:3.500A) Processing helix chain '0' and resid 214 through 216 No H-bonds generated for 'chain '0' and resid 214 through 216' Processing helix chain '1' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 1 95 " --> pdb=" O ASP 1 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 1 96 " --> pdb=" O SER 1 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN 1 103 " --> pdb=" O GLU 1 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 1 105 " --> pdb=" O GLU 1 101 " (cutoff:3.500A) Processing helix chain '1' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR 1 202 " --> pdb=" O GLN 1 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 1 203 " --> pdb=" O ILE 1 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 1 209 " --> pdb=" O GLU 1 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 1 210 " --> pdb=" O ALA 1 206 " (cutoff:3.500A) Processing helix chain '1' and resid 214 through 216 No H-bonds generated for 'chain '1' and resid 214 through 216' Processing helix chain '2' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 2 95 " --> pdb=" O ASP 2 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 2 96 " --> pdb=" O SER 2 92 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 2 103 " --> pdb=" O GLU 2 99 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 2 105 " --> pdb=" O GLU 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 196 through 212 removed outlier: 3.751A pdb=" N THR 2 202 " --> pdb=" O GLN 2 198 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE 2 203 " --> pdb=" O ILE 2 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG 2 209 " --> pdb=" O GLU 2 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 2 210 " --> pdb=" O ALA 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 216 No H-bonds generated for 'chain '2' and resid 214 through 216' Processing helix chain '3' and resid 90 through 109 removed outlier: 3.546A pdb=" N ASP 3 95 " --> pdb=" O ASP 3 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 3 96 " --> pdb=" O SER 3 92 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN 3 103 " --> pdb=" O GLU 3 99 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 3 105 " --> pdb=" O GLU 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 196 through 212 removed outlier: 3.752A pdb=" N THR 3 202 " --> pdb=" O GLN 3 198 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE 3 203 " --> pdb=" O ILE 3 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG 3 209 " --> pdb=" O GLU 3 205 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL 3 210 " --> pdb=" O ALA 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 216 No H-bonds generated for 'chain '3' and resid 214 through 216' Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA A 219 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY A 186 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN A 178 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 144 removed outlier: 6.320A pdb=" N ILE A 163 " --> pdb=" O LYS 3 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS 3 133 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE 3 163 " --> pdb=" O LYS 2 133 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N LYS 2 133 " --> pdb=" O ILE 3 163 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE 2 163 " --> pdb=" O LYS 1 133 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N LYS 1 133 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE 1 163 " --> pdb=" O LYS 0 133 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LYS 0 133 " --> pdb=" O ILE 1 163 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE 0 163 " --> pdb=" O LYS Z 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS Z 133 " --> pdb=" O ILE 0 163 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE Z 163 " --> pdb=" O LYS Y 133 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N LYS Y 133 " --> pdb=" O ILE Z 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE Y 163 " --> pdb=" O LYS X 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS X 133 " --> pdb=" O ILE Y 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE X 163 " --> pdb=" O LYS W 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS W 133 " --> pdb=" O ILE X 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE W 163 " --> pdb=" O LYS V 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS V 133 " --> pdb=" O ILE W 163 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE V 163 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS U 133 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE U 163 " --> pdb=" O LYS T 133 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N LYS T 133 " --> pdb=" O ILE U 163 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE T 163 " --> pdb=" O LYS S 133 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS S 133 " --> pdb=" O ILE T 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE S 163 " --> pdb=" O LYS R 133 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N LYS R 133 " --> pdb=" O ILE S 163 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE R 163 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LYS Q 133 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE Q 163 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N LYS P 133 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE P 163 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 9.975A pdb=" N LYS O 133 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE O 163 " --> pdb=" O LYS N 133 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS N 133 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE N 163 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LYS M 133 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE M 163 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS L 133 " --> pdb=" O ILE M 163 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE L 163 " --> pdb=" O LYS K 133 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N LYS K 133 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE K 163 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS J 133 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE J 163 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS I 133 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE I 163 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N LYS H 133 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE H 163 " --> pdb=" O LYS G 133 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LYS G 133 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE G 163 " --> pdb=" O LYS F 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS F 133 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE F 163 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N LYS E 133 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE E 163 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS D 133 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE D 163 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N LYS C 133 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 163 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N LYS B 133 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 163 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS A 133 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA B 219 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY B 186 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN B 178 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AA8, first strand: chain 'C' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA C 219 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 186 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN C 178 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 165 through 168 Processing sheet with id=AB2, first strand: chain 'D' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA D 219 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY D 186 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN D 178 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 168 Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA E 219 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY E 186 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN E 178 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 165 through 168 Processing sheet with id=AB8, first strand: chain 'F' and resid 117 through 123 removed outlier: 9.655A pdb=" N ALA F 219 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY F 186 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN F 178 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 165 through 168 Processing sheet with id=AC2, first strand: chain 'G' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA G 219 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY G 186 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN G 178 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA H 219 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY H 186 " --> pdb=" O ALA H 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN H 178 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AC8, first strand: chain 'I' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA I 219 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY I 186 " --> pdb=" O ALA I 219 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 128 through 131 removed outlier: 4.271A pdb=" N GLN I 178 " --> pdb=" O VAL I 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 165 through 168 Processing sheet with id=AD2, first strand: chain 'J' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA J 219 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY J 186 " --> pdb=" O ALA J 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN J 178 " --> pdb=" O VAL J 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 165 through 168 Processing sheet with id=AD5, first strand: chain 'K' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA K 219 " --> pdb=" O ILE K 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 186 " --> pdb=" O ALA K 219 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN K 178 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 165 through 168 Processing sheet with id=AD8, first strand: chain 'L' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA L 219 " --> pdb=" O ILE L 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY L 186 " --> pdb=" O ALA L 219 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN L 178 " --> pdb=" O VAL L 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 165 through 168 Processing sheet with id=AE2, first strand: chain 'M' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA M 219 " --> pdb=" O ILE M 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY M 186 " --> pdb=" O ALA M 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN M 178 " --> pdb=" O VAL M 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 165 through 168 Processing sheet with id=AE5, first strand: chain 'N' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA N 219 " --> pdb=" O ILE N 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY N 186 " --> pdb=" O ALA N 219 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN N 178 " --> pdb=" O VAL N 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 165 through 168 Processing sheet with id=AE8, first strand: chain 'O' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA O 219 " --> pdb=" O ILE O 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY O 186 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN O 178 " --> pdb=" O VAL O 130 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 165 through 168 Processing sheet with id=AF2, first strand: chain 'P' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA P 219 " --> pdb=" O ILE P 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY P 186 " --> pdb=" O ALA P 219 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN P 178 " --> pdb=" O VAL P 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 165 through 168 Processing sheet with id=AF5, first strand: chain 'Q' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA Q 219 " --> pdb=" O ILE Q 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Q 186 " --> pdb=" O ALA Q 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN Q 178 " --> pdb=" O VAL Q 130 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 165 through 168 Processing sheet with id=AF8, first strand: chain 'R' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA R 219 " --> pdb=" O ILE R 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY R 186 " --> pdb=" O ALA R 219 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN R 178 " --> pdb=" O VAL R 130 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 165 through 168 Processing sheet with id=AG2, first strand: chain 'S' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA S 219 " --> pdb=" O ILE S 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY S 186 " --> pdb=" O ALA S 219 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN S 178 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 165 through 168 Processing sheet with id=AG5, first strand: chain 'T' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA T 219 " --> pdb=" O ILE T 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY T 186 " --> pdb=" O ALA T 219 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN T 178 " --> pdb=" O VAL T 130 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 165 through 168 Processing sheet with id=AG8, first strand: chain 'U' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA U 219 " --> pdb=" O ILE U 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY U 186 " --> pdb=" O ALA U 219 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN U 178 " --> pdb=" O VAL U 130 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 165 through 168 Processing sheet with id=AH2, first strand: chain 'V' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA V 219 " --> pdb=" O ILE V 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY V 186 " --> pdb=" O ALA V 219 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN V 178 " --> pdb=" O VAL V 130 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 165 through 168 Processing sheet with id=AH5, first strand: chain 'W' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA W 219 " --> pdb=" O ILE W 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY W 186 " --> pdb=" O ALA W 219 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN W 178 " --> pdb=" O VAL W 130 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 165 through 168 Processing sheet with id=AH8, first strand: chain 'X' and resid 117 through 123 removed outlier: 9.655A pdb=" N ALA X 219 " --> pdb=" O ILE X 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY X 186 " --> pdb=" O ALA X 219 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 128 through 131 removed outlier: 4.271A pdb=" N GLN X 178 " --> pdb=" O VAL X 130 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 165 through 168 Processing sheet with id=AI2, first strand: chain 'Y' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA Y 219 " --> pdb=" O ILE Y 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Y 186 " --> pdb=" O ALA Y 219 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN Y 178 " --> pdb=" O VAL Y 130 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 165 through 168 Processing sheet with id=AI5, first strand: chain 'Z' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA Z 219 " --> pdb=" O ILE Z 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY Z 186 " --> pdb=" O ALA Z 219 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN Z 178 " --> pdb=" O VAL Z 130 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 165 through 168 Processing sheet with id=AI8, first strand: chain '0' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 0 219 " --> pdb=" O ILE 0 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY 0 186 " --> pdb=" O ALA 0 219 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '0' and resid 128 through 131 removed outlier: 4.269A pdb=" N GLN 0 178 " --> pdb=" O VAL 0 130 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '0' and resid 165 through 168 Processing sheet with id=AJ2, first strand: chain '1' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 1 219 " --> pdb=" O ILE 1 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY 1 186 " --> pdb=" O ALA 1 219 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain '1' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 1 178 " --> pdb=" O VAL 1 130 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '1' and resid 165 through 168 Processing sheet with id=AJ5, first strand: chain '2' and resid 117 through 123 removed outlier: 9.657A pdb=" N ALA 2 219 " --> pdb=" O ILE 2 184 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY 2 186 " --> pdb=" O ALA 2 219 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '2' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 2 178 " --> pdb=" O VAL 2 130 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '2' and resid 165 through 168 Processing sheet with id=AJ8, first strand: chain '3' and resid 117 through 123 removed outlier: 9.656A pdb=" N ALA 3 219 " --> pdb=" O ILE 3 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY 3 186 " --> pdb=" O ALA 3 219 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '3' and resid 128 through 131 removed outlier: 4.270A pdb=" N GLN 3 178 " --> pdb=" O VAL 3 130 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain '3' and resid 165 through 168 1680 hydrogen bonds defined for protein. 4770 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: 21.76 Time building geometry restraints manager: 42.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 33390 1.03 - 1.22: 0 1.22 - 1.41: 12076 1.41 - 1.61: 20594 1.61 - 1.80: 60 Bond restraints: 66120 Sorted by residual: bond pdb=" CB VAL U 210 " pdb=" CG2 VAL U 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.35e+00 bond pdb=" CB VAL K 210 " pdb=" CG2 VAL K 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" CB VAL G 210 " pdb=" CG2 VAL G 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.34e+00 bond pdb=" CB VAL S 210 " pdb=" CG2 VAL S 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.33e+00 bond pdb=" CB VAL L 210 " pdb=" CG2 VAL L 210 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.30e+00 ... (remaining 66115 not shown) Histogram of bond angle deviations from ideal: 101.23 - 107.24: 2297 107.24 - 113.25: 84678 113.25 - 119.26: 12115 119.26 - 125.28: 21190 125.28 - 131.29: 650 Bond angle restraints: 120930 Sorted by residual: angle pdb=" C PRO B 222 " pdb=" N LYS B 223 " pdb=" CA LYS B 223 " ideal model delta sigma weight residual 121.54 129.70 -8.16 1.91e+00 2.74e-01 1.83e+01 angle pdb=" C PRO 2 222 " pdb=" N LYS 2 223 " pdb=" CA LYS 2 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO 3 222 " pdb=" N LYS 3 223 " pdb=" CA LYS 3 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO K 222 " pdb=" N LYS K 223 " pdb=" CA LYS K 223 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C PRO U 222 " pdb=" N LYS U 223 " pdb=" CA LYS U 223 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 ... (remaining 120925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 23407 17.94 - 35.87: 1133 35.87 - 53.81: 360 53.81 - 71.75: 600 71.75 - 89.69: 390 Dihedral angle restraints: 25890 sinusoidal: 13230 harmonic: 12660 Sorted by residual: dihedral pdb=" CA ILE Y 111 " pdb=" C ILE Y 111 " pdb=" N ILE Y 112 " pdb=" CA ILE Y 112 " ideal model delta harmonic sigma weight residual 180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE D 111 " pdb=" C ILE D 111 " pdb=" N ILE D 112 " pdb=" CA ILE D 112 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ILE G 111 " pdb=" C ILE G 111 " pdb=" N ILE G 112 " pdb=" CA ILE G 112 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 ... (remaining 25887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3053 0.046 - 0.092: 1648 0.092 - 0.139: 564 0.139 - 0.185: 165 0.185 - 0.231: 30 Chirality restraints: 5460 Sorted by residual: chirality pdb=" CB VAL G 187 " pdb=" CA VAL G 187 " pdb=" CG1 VAL G 187 " pdb=" CG2 VAL G 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL W 187 " pdb=" CA VAL W 187 " pdb=" CG1 VAL W 187 " pdb=" CG2 VAL W 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL 0 187 " pdb=" CA VAL 0 187 " pdb=" CG1 VAL 0 187 " pdb=" CG2 VAL 0 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 5457 not shown) Planarity restraints: 9720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN S 103 " 0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN S 103 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN S 103 " -0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN S 103 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN S 103 " -0.385 2.00e-02 2.50e+03 pdb="HE22 GLN S 103 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN Y 103 " -0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN Y 103 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN Y 103 " 0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN Y 103 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN Y 103 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN Y 103 " -0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 103 " -0.214 2.00e-02 2.50e+03 2.55e-01 9.72e+02 pdb=" CD GLN H 103 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN H 103 " 0.204 2.00e-02 2.50e+03 pdb=" NE2 GLN H 103 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN H 103 " 0.385 2.00e-02 2.50e+03 pdb="HE22 GLN H 103 " -0.391 2.00e-02 2.50e+03 ... (remaining 9717 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3093 2.15 - 2.76: 141585 2.76 - 3.38: 166837 3.38 - 3.99: 218445 3.99 - 4.60: 348110 Nonbonded interactions: 878070 Sorted by model distance: nonbonded pdb=" O LYS 1 90 " pdb=" H ILE 1 93 " model vdw 1.541 1.850 nonbonded pdb=" O LYS Z 90 " pdb=" H ILE Z 93 " model vdw 1.541 1.850 nonbonded pdb=" O LYS Q 90 " pdb=" H ILE Q 93 " model vdw 1.541 1.850 nonbonded pdb=" O LYS N 90 " pdb=" H ILE N 93 " model vdw 1.541 1.850 nonbonded pdb=" O LYS I 90 " pdb=" H ILE I 93 " model vdw 1.541 1.850 ... (remaining 878065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.740 Extract box with map and model: 5.380 Check model and map are aligned: 0.700 Set scattering table: 0.440 Process input model: 153.920 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.430 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.083 32730 Z= 0.980 Angle : 1.179 8.162 44220 Z= 0.686 Chirality : 0.063 0.231 5460 Planarity : 0.006 0.062 5700 Dihedral : 9.370 59.727 12870 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 1.46 % Allowed : 8.03 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.09), residues: 4110 helix: -4.93 (0.06), residues: 960 sheet: -1.37 (0.12), residues: 960 loop : -3.86 (0.09), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.7686 time to fit residues: 516.6668 Evaluate side-chains 133 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 354 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 196 ASN W 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32730 Z= 0.253 Angle : 0.783 5.909 44220 Z= 0.441 Chirality : 0.051 0.163 5460 Planarity : 0.005 0.052 5700 Dihedral : 7.837 35.721 4350 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.92 % Allowed : 7.64 % Favored : 91.44 % Rotamer: Outliers : 0.91 % Allowed : 1.30 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.11), residues: 4110 helix: -2.82 (0.13), residues: 960 sheet: -0.53 (0.14), residues: 960 loop : -3.41 (0.11), residues: 2190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 4.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 31 residues processed: 234 average time/residue: 0.8787 time to fit residues: 325.1432 Evaluate side-chains 161 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.5373 time to fit residues: 36.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 294 optimal weight: 0.4980 chunk 241 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 351 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32730 Z= 0.265 Angle : 0.718 5.944 44220 Z= 0.405 Chirality : 0.049 0.195 5460 Planarity : 0.004 0.041 5700 Dihedral : 6.971 29.902 4350 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.02 % Favored : 88.86 % Rotamer: Outliers : 0.44 % Allowed : 2.94 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.12), residues: 4110 helix: -1.10 (0.17), residues: 1050 sheet: -0.43 (0.15), residues: 780 loop : -3.15 (0.11), residues: 2280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 246 average time/residue: 0.8988 time to fit residues: 359.4526 Evaluate side-chains 148 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 4.043 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5595 time to fit residues: 15.9030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 0.8980 chunk 266 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 356 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32730 Z= 0.232 Angle : 0.683 5.832 44220 Z= 0.383 Chirality : 0.048 0.156 5460 Planarity : 0.004 0.032 5700 Dihedral : 6.475 27.495 4350 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.17 % Favored : 88.71 % Rotamer: Outliers : 0.91 % Allowed : 3.18 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.13), residues: 4110 helix: -0.79 (0.17), residues: 1050 sheet: -1.22 (0.13), residues: 1290 loop : -2.99 (0.13), residues: 1770 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 30 residues processed: 196 average time/residue: 0.7367 time to fit residues: 252.1074 Evaluate side-chains 160 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 4.149 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5847 time to fit residues: 38.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 338 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32730 Z= 0.230 Angle : 0.655 5.638 44220 Z= 0.369 Chirality : 0.048 0.167 5460 Planarity : 0.003 0.030 5700 Dihedral : 6.247 25.086 4350 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.58 % Favored : 88.30 % Rotamer: Outliers : 0.26 % Allowed : 5.34 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 4110 helix: -0.31 (0.19), residues: 960 sheet: -1.19 (0.13), residues: 1290 loop : -2.42 (0.14), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 172 average time/residue: 0.7036 time to fit residues: 214.8857 Evaluate side-chains 134 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 5.343 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6045 time to fit residues: 14.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 313 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 ASN P 102 ASN ** T 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32730 Z= 0.185 Angle : 0.619 5.511 44220 Z= 0.345 Chirality : 0.047 0.160 5460 Planarity : 0.003 0.030 5700 Dihedral : 5.990 25.101 4350 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.85 % Favored : 89.05 % Rotamer: Outliers : 0.76 % Allowed : 6.69 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 4110 helix: -0.18 (0.19), residues: 960 sheet: -1.12 (0.13), residues: 1290 loop : -2.26 (0.14), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 153 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 27 residues processed: 158 average time/residue: 0.6577 time to fit residues: 189.7928 Evaluate side-chains 150 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 4.124 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5517 time to fit residues: 33.4976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 317 optimal weight: 0.2980 chunk 210 optimal weight: 6.9990 chunk 375 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32730 Z= 0.294 Angle : 0.670 5.499 44220 Z= 0.379 Chirality : 0.049 0.205 5460 Planarity : 0.004 0.036 5700 Dihedral : 6.143 23.520 4350 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 1.12 % Allowed : 11.48 % Favored : 87.40 % Rotamer: Outliers : 0.13 % Allowed : 7.63 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 4110 helix: -0.37 (0.18), residues: 960 sheet: -1.22 (0.12), residues: 1500 loop : -2.75 (0.15), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 155 average time/residue: 0.7192 time to fit residues: 194.4832 Evaluate side-chains 136 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 4.102 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5358 time to fit residues: 9.2959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.0470 chunk 150 optimal weight: 0.9990 chunk 224 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN ** N 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32730 Z= 0.152 Angle : 0.591 5.459 44220 Z= 0.328 Chirality : 0.047 0.154 5460 Planarity : 0.003 0.030 5700 Dihedral : 5.837 24.744 4350 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 1.05 % Allowed : 9.83 % Favored : 89.12 % Rotamer: Outliers : 0.52 % Allowed : 7.53 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 4110 helix: -0.09 (0.19), residues: 960 sheet: -1.40 (0.12), residues: 1500 loop : -2.19 (0.15), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 153 average time/residue: 0.7253 time to fit residues: 195.5242 Evaluate side-chains 147 residues out of total 3840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 4.071 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5345 time to fit residues: 23.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6985 > 50: distance: 95 - 420: 8.592 distance: 98 - 417: 9.184 distance: 125 - 389: 17.363 distance: 128 - 386: 14.660 distance: 193 - 300: 33.253 distance: 196 - 297: 11.446 distance: 225 - 269: 16.119 distance: 252 - 266: 8.704 distance: 266 - 267: 5.089 distance: 266 - 275: 13.900 distance: 267 - 268: 11.126 distance: 267 - 270: 20.940 distance: 267 - 276: 13.825 distance: 268 - 269: 11.744 distance: 268 - 283: 6.904 distance: 270 - 271: 12.923 distance: 270 - 277: 20.876 distance: 270 - 278: 12.353 distance: 271 - 272: 8.932 distance: 271 - 279: 9.967 distance: 271 - 280: 12.495 distance: 272 - 273: 14.477 distance: 272 - 274: 17.188 distance: 274 - 281: 16.893 distance: 274 - 282: 5.402 distance: 283 - 284: 9.660 distance: 283 - 290: 16.608 distance: 284 - 285: 17.707 distance: 284 - 287: 5.619 distance: 284 - 291: 6.681 distance: 285 - 286: 19.846 distance: 285 - 297: 20.387 distance: 287 - 288: 10.576 distance: 287 - 289: 7.447 distance: 287 - 292: 10.609 distance: 288 - 293: 6.107 distance: 289 - 294: 7.276 distance: 289 - 295: 16.379 distance: 289 - 296: 11.941 distance: 297 - 298: 18.650 distance: 297 - 306: 9.222 distance: 298 - 299: 30.034 distance: 298 - 301: 26.920 distance: 298 - 307: 19.474 distance: 299 - 300: 24.025 distance: 299 - 319: 28.360 distance: 301 - 302: 13.936 distance: 301 - 308: 23.813 distance: 301 - 309: 6.767 distance: 302 - 303: 11.781 distance: 302 - 310: 16.703 distance: 302 - 311: 15.981 distance: 303 - 304: 9.106 distance: 303 - 312: 23.458 distance: 303 - 313: 18.251 distance: 304 - 305: 15.919 distance: 304 - 314: 15.389 distance: 304 - 315: 20.793 distance: 305 - 316: 5.921 distance: 305 - 317: 9.512 distance: 305 - 318: 10.594 distance: 319 - 320: 31.081 distance: 319 - 328: 44.573 distance: 320 - 321: 29.353 distance: 320 - 323: 31.764 distance: 320 - 329: 18.377 distance: 321 - 322: 24.421 distance: 321 - 341: 14.041 distance: 323 - 324: 8.530 distance: 323 - 330: 21.659 distance: 323 - 331: 25.513 distance: 324 - 325: 6.471 distance: 324 - 332: 9.243 distance: 324 - 333: 10.980 distance: 325 - 326: 17.006 distance: 325 - 334: 9.891 distance: 325 - 335: 12.840 distance: 326 - 327: 5.455 distance: 326 - 336: 14.850 distance: 326 - 337: 10.428 distance: 327 - 338: 4.276 distance: 327 - 339: 6.419 distance: 327 - 340: 5.594 distance: 341 - 342: 9.701 distance: 341 - 347: 11.882 distance: 342 - 343: 18.975 distance: 342 - 345: 15.479 distance: 342 - 348: 23.376 distance: 343 - 344: 15.021 distance: 343 - 355: 28.577 distance: 345 - 346: 10.529 distance: 345 - 349: 4.761 distance: 345 - 350: 9.358 distance: 346 - 347: 11.484 distance: 346 - 351: 5.588 distance: 346 - 352: 10.868 distance: 347 - 353: 14.560 distance: 347 - 354: 15.235 distance: 355 - 356: 18.034 distance: 355 - 363: 18.100 distance: 356 - 357: 20.740 distance: 356 - 359: 24.649 distance: 356 - 364: 10.905 distance: 357 - 358: 13.202 distance: 357 - 367: 18.008 distance: 359 - 360: 29.548 distance: 359 - 365: 10.117 distance: 359 - 366: 6.917 distance: 360 - 361: 19.267 distance: 360 - 362: 21.664 distance: 367 - 368: 8.459 distance: 367 - 375: 14.884 distance: 368 - 369: 23.217 distance: 368 - 371: 27.319 distance: 368 - 376: 25.801 distance: 369 - 370: 18.781 distance: 369 - 386: 13.913 distance: 371 - 372: 29.235 distance: 371 - 373: 14.063 distance: 371 - 377: 12.968 distance: 372 - 374: 7.946 distance: 372 - 378: 27.309 distance: 372 - 379: 30.071 distance: 373 - 380: 19.639 distance: 373 - 381: 11.909 distance: 373 - 382: 6.051 distance: 374 - 383: 12.824 distance: 374 - 384: 16.710 distance: 374 - 385: 14.274 distance: 386 - 387: 14.602 distance: 386 - 397: 35.564 distance: 387 - 388: 11.417 distance: 387 - 390: 9.140 distance: 387 - 398: 17.111 distance: 388 - 389: 16.933 distance: 388 - 410: 12.373 distance: 390 - 391: 22.699 distance: 390 - 399: 24.051 distance: 390 - 400: 30.115 distance: 391 - 392: 17.679 distance: 391 - 401: 33.038 distance: 391 - 402: 14.486 distance: 392 - 393: 5.936 distance: 392 - 403: 4.650 distance: 392 - 404: 18.087 distance: 393 - 394: 14.255 distance: 393 - 405: 16.570 distance: 394 - 395: 13.477 distance: 394 - 396: 11.174 distance: 395 - 406: 6.949 distance: 395 - 407: 8.910 distance: 396 - 408: 7.057 distance: 396 - 409: 8.907 distance: 410 - 411: 8.532 distance: 410 - 414: 21.974 distance: 411 - 412: 14.858 distance: 411 - 415: 9.900 distance: 411 - 416: 8.001 distance: 412 - 413: 16.085 distance: 412 - 417: 16.992 distance: 417 - 418: 10.898 distance: 417 - 424: 7.431 distance: 418 - 419: 7.292 distance: 418 - 421: 7.474 distance: 418 - 425: 11.188 distance: 419 - 420: 11.015 distance: 419 - 433: 3.105 distance: 421 - 422: 4.886 distance: 421 - 423: 10.520 distance: 421 - 426: 10.379 distance: 422 - 427: 6.225 distance: 422 - 428: 8.577 distance: 422 - 429: 6.362 distance: 423 - 430: 4.709 distance: 423 - 431: 11.491 distance: 423 - 432: 10.334