Starting phenix.real_space_refine on Sat Dec 9 04:46:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/12_2023/8oou_17031.pdb" } resolution = 2.9 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= 0.002 sd= 0.058 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 P 140 5.49 5 S 320 5.16 5 C 38620 2.51 5 N 10660 2.21 5 O 12060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ASP 221": "OD1" <-> "OD2" Residue "H GLU 297": "OE1" <-> "OE2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I GLU 130": "OE1" <-> "OE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I ASP 221": "OD1" <-> "OD2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "J ASP 15": "OD1" <-> "OD2" Residue "J PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J ASP 221": "OD1" <-> "OD2" Residue "J GLU 297": "OE1" <-> "OE2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 221": "OD1" <-> "OD2" Residue "K GLU 297": "OE1" <-> "OE2" Residue "L ASP 15": "OD1" <-> "OD2" Residue "L PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L GLU 130": "OE1" <-> "OE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "L GLU 297": "OE1" <-> "OE2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M GLU 130": "OE1" <-> "OE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M ASP 221": "OD1" <-> "OD2" Residue "M GLU 297": "OE1" <-> "OE2" Residue "N ASP 15": "OD1" <-> "OD2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N GLU 130": "OE1" <-> "OE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N ASP 221": "OD1" <-> "OD2" Residue "N GLU 297": "OE1" <-> "OE2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O ASP 221": "OD1" <-> "OD2" Residue "O GLU 297": "OE1" <-> "OE2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 128": "OE1" <-> "OE2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P ASP 155": "OD1" <-> "OD2" Residue "P ASP 221": "OD1" <-> "OD2" Residue "P GLU 297": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "Q ASP 155": "OD1" <-> "OD2" Residue "Q ASP 221": "OD1" <-> "OD2" Residue "Q GLU 297": "OE1" <-> "OE2" Residue "R ASP 15": "OD1" <-> "OD2" Residue "R PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R GLU 130": "OE1" <-> "OE2" Residue "R ASP 155": "OD1" <-> "OD2" Residue "R ASP 221": "OD1" <-> "OD2" Residue "R GLU 297": "OE1" <-> "OE2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 130": "OE1" <-> "OE2" Residue "S ASP 155": "OD1" <-> "OD2" Residue "S ASP 221": "OD1" <-> "OD2" Residue "S GLU 297": "OE1" <-> "OE2" Residue "T ASP 15": "OD1" <-> "OD2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 128": "OE1" <-> "OE2" Residue "T GLU 130": "OE1" <-> "OE2" Residue "T ASP 155": "OD1" <-> "OD2" Residue "T ASP 221": "OD1" <-> "OD2" Residue "T GLU 297": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 61800 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "U" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain: "B" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "C" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "D" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "E" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "F" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "G" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "H" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "I" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "J" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "K" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "e" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain: "L" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "M" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "N" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "O" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "P" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "Q" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "R" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "S" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "T" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Time building chain proxies: 42.43, per 1000 atoms: 0.69 Number of scatterers: 61800 At special positions: 0 Unit cell: (186.635, 186.635, 175.185, 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 320 16.00 P 140 15.00 O 12060 8.00 N 10660 7.00 C 38620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.38 Conformation dependent library (CDL) restraints added in 15.4 seconds 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13920 Finding SS restraints... Secondary structure from input PDB file: 480 helices and 60 sheets defined 71.4% alpha, 5.3% beta 0 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 14.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 53 Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE D 220 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE D 300 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 143 Processing helix chain 'F' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE F 160 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE F 220 " --> pdb=" O HIS F 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU F 282 " --> pdb=" O GLN F 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER F 310 " --> pdb=" O PRO F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 331 Processing helix chain 'F' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 53 Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE G 160 " --> pdb=" O CYS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE G 220 " --> pdb=" O HIS G 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE G 300 " --> pdb=" O GLU G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER G 310 " --> pdb=" O PRO G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 331 Processing helix chain 'G' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU G 359 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 143 Processing helix chain 'H' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE H 160 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 178 through 189 Processing helix chain 'H' and resid 190 through 197 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'H' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP H 221 " --> pdb=" O PRO H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE H 300 " --> pdb=" O GLU H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER H 310 " --> pdb=" O PRO H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 331 Processing helix chain 'H' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 359 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 53 Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 143 Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE I 160 " --> pdb=" O CYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 178 through 189 Processing helix chain 'I' and resid 190 through 197 Processing helix chain 'I' and resid 201 through 216 Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE I 220 " --> pdb=" O HIS I 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 221 " --> pdb=" O PRO I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 248 Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG I 259 " --> pdb=" O GLN I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU I 282 " --> pdb=" O GLN I 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE I 300 " --> pdb=" O GLU I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER I 310 " --> pdb=" O PRO I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 331 Processing helix chain 'I' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU I 359 " --> pdb=" O GLU I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 368 Processing helix chain 'I' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 143 Processing helix chain 'J' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE J 160 " --> pdb=" O CYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 201 through 216 Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE J 220 " --> pdb=" O HIS J 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP J 221 " --> pdb=" O PRO J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 248 Processing helix chain 'J' and resid 249 through 251 No H-bonds generated for 'chain 'J' and resid 249 through 251' Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG J 259 " --> pdb=" O GLN J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU J 282 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE J 300 " --> pdb=" O GLU J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 331 Processing helix chain 'J' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU J 359 " --> pdb=" O GLU J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 368 Processing helix chain 'J' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 9 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 53 Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 143 Processing helix chain 'K' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 190 through 197 Processing helix chain 'K' and resid 201 through 216 Processing helix chain 'K' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE K 220 " --> pdb=" O HIS K 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 248 Processing helix chain 'K' and resid 249 through 251 No H-bonds generated for 'chain 'K' and resid 249 through 251' Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG K 259 " --> pdb=" O GLN K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 331 Processing helix chain 'K' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 359 " --> pdb=" O GLU K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 368 Processing helix chain 'K' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 40 through 53 Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 120 through 143 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE L 160 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 178 through 189 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 201 through 216 Processing helix chain 'L' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE L 220 " --> pdb=" O HIS L 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP L 221 " --> pdb=" O PRO L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 248 Processing helix chain 'L' and resid 249 through 251 No H-bonds generated for 'chain 'L' and resid 249 through 251' Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG L 259 " --> pdb=" O GLN L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU L 282 " --> pdb=" O GLN L 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN L 283 " --> pdb=" O ALA L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE L 300 " --> pdb=" O GLU L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER L 310 " --> pdb=" O PRO L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 331 Processing helix chain 'L' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU L 359 " --> pdb=" O GLU L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 368 Processing helix chain 'L' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE L 378 " --> pdb=" O GLU L 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 53 Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 143 Processing helix chain 'M' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE M 160 " --> pdb=" O CYS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 178 through 189 Processing helix chain 'M' and resid 190 through 197 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE M 220 " --> pdb=" O HIS M 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 248 Processing helix chain 'M' and resid 249 through 251 No H-bonds generated for 'chain 'M' and resid 249 through 251' Processing helix chain 'M' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU M 282 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN M 283 " --> pdb=" O ALA M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE M 300 " --> pdb=" O GLU M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER M 310 " --> pdb=" O PRO M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 331 Processing helix chain 'M' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'M' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 9 through 20 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 40 through 53 Processing helix chain 'N' and resid 61 through 75 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 120 through 143 Processing helix chain 'N' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE N 160 " --> pdb=" O CYS N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 178 through 189 Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 201 through 216 Processing helix chain 'N' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE N 220 " --> pdb=" O HIS N 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP N 221 " --> pdb=" O PRO N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 248 Processing helix chain 'N' and resid 249 through 251 No H-bonds generated for 'chain 'N' and resid 249 through 251' Processing helix chain 'N' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG N 259 " --> pdb=" O GLN N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU N 282 " --> pdb=" O GLN N 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN N 283 " --> pdb=" O ALA N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER N 310 " --> pdb=" O PRO N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 331 Processing helix chain 'N' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU N 359 " --> pdb=" O GLU N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE N 378 " --> pdb=" O GLU N 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'O' and resid 9 through 20 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 53 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 143 Processing helix chain 'O' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE O 160 " --> pdb=" O CYS O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 178 through 189 Processing helix chain 'O' and resid 190 through 197 Processing helix chain 'O' and resid 201 through 216 Processing helix chain 'O' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE O 220 " --> pdb=" O HIS O 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP O 221 " --> pdb=" O PRO O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 248 Processing helix chain 'O' and resid 249 through 251 No H-bonds generated for 'chain 'O' and resid 249 through 251' Processing helix chain 'O' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG O 259 " --> pdb=" O GLN O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU O 282 " --> pdb=" O GLN O 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN O 283 " --> pdb=" O ALA O 279 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE O 300 " --> pdb=" O GLU O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER O 310 " --> pdb=" O PRO O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 331 Processing helix chain 'O' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS O 358 " --> pdb=" O ALA O 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU O 359 " --> pdb=" O GLU O 355 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 368 Processing helix chain 'O' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE O 378 " --> pdb=" O GLU O 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 6 Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 143 Processing helix chain 'P' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE P 160 " --> pdb=" O CYS P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 178 through 189 Processing helix chain 'P' and resid 190 through 197 Processing helix chain 'P' and resid 201 through 216 Processing helix chain 'P' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE P 220 " --> pdb=" O HIS P 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 248 Processing helix chain 'P' and resid 249 through 251 No H-bonds generated for 'chain 'P' and resid 249 through 251' Processing helix chain 'P' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU P 282 " --> pdb=" O GLN P 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN P 283 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE P 300 " --> pdb=" O GLU P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER P 310 " --> pdb=" O PRO P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 331 Processing helix chain 'P' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU P 359 " --> pdb=" O GLU P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 368 Processing helix chain 'P' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE P 378 " --> pdb=" O GLU P 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 53 Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 143 Processing helix chain 'Q' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE Q 160 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 178 through 189 Processing helix chain 'Q' and resid 190 through 197 Processing helix chain 'Q' and resid 201 through 216 Processing helix chain 'Q' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE Q 220 " --> pdb=" O HIS Q 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Q 221 " --> pdb=" O PRO Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 248 Processing helix chain 'Q' and resid 249 through 251 No H-bonds generated for 'chain 'Q' and resid 249 through 251' Processing helix chain 'Q' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG Q 259 " --> pdb=" O GLN Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 273 Processing helix chain 'Q' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU Q 282 " --> pdb=" O GLN Q 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN Q 283 " --> pdb=" O ALA Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER Q 310 " --> pdb=" O PRO Q 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 331 Processing helix chain 'Q' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS Q 358 " --> pdb=" O ALA Q 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU Q 359 " --> pdb=" O GLU Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 368 Processing helix chain 'Q' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 37 through 39 No H-bonds generated for 'chain 'R' and resid 37 through 39' Processing helix chain 'R' and resid 40 through 53 Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 120 through 143 Processing helix chain 'R' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE R 160 " --> pdb=" O CYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 178 through 189 Processing helix chain 'R' and resid 190 through 197 Processing helix chain 'R' and resid 201 through 216 Processing helix chain 'R' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP R 221 " --> pdb=" O PRO R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 248 Processing helix chain 'R' and resid 249 through 251 No H-bonds generated for 'chain 'R' and resid 249 through 251' Processing helix chain 'R' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG R 259 " --> pdb=" O GLN R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 273 Processing helix chain 'R' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU R 282 " --> pdb=" O GLN R 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE R 300 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER R 310 " --> pdb=" O PRO R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 331 Processing helix chain 'R' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS R 358 " --> pdb=" O ALA R 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU R 359 " --> pdb=" O GLU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE R 378 " --> pdb=" O GLU R 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 53 Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 143 Processing helix chain 'S' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE S 160 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 178 through 189 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 201 through 216 Processing helix chain 'S' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE S 220 " --> pdb=" O HIS S 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP S 221 " --> pdb=" O PRO S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 248 Processing helix chain 'S' and resid 249 through 251 No H-bonds generated for 'chain 'S' and resid 249 through 251' Processing helix chain 'S' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG S 259 " --> pdb=" O GLN S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'S' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU S 282 " --> pdb=" O GLN S 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN S 283 " --> pdb=" O ALA S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE S 300 " --> pdb=" O GLU S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER S 310 " --> pdb=" O PRO S 307 " (cutoff:3.500A) Processing helix chain 'S' and resid 317 through 331 Processing helix chain 'S' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS S 358 " --> pdb=" O ALA S 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU S 359 " --> pdb=" O GLU S 355 " (cutoff:3.500A) Processing helix chain 'S' and resid 364 through 368 Processing helix chain 'S' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE S 378 " --> pdb=" O GLU S 374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 9 through 20 Processing helix chain 'T' and resid 37 through 39 No H-bonds generated for 'chain 'T' and resid 37 through 39' Processing helix chain 'T' and resid 40 through 53 Processing helix chain 'T' and resid 61 through 75 Processing helix chain 'T' and resid 75 through 86 Processing helix chain 'T' and resid 120 through 143 Processing helix chain 'T' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE T 160 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 174 No H-bonds generated for 'chain 'T' and resid 172 through 174' Processing helix chain 'T' and resid 178 through 189 Processing helix chain 'T' and resid 190 through 197 Processing helix chain 'T' and resid 201 through 216 Processing helix chain 'T' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP T 221 " --> pdb=" O PRO T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 248 Processing helix chain 'T' and resid 249 through 251 No H-bonds generated for 'chain 'T' and resid 249 through 251' Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG T 259 " --> pdb=" O GLN T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 273 Processing helix chain 'T' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU T 282 " --> pdb=" O GLN T 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN T 283 " --> pdb=" O ALA T 279 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE T 300 " --> pdb=" O GLU T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER T 310 " --> pdb=" O PRO T 307 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 331 Processing helix chain 'T' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS T 358 " --> pdb=" O ALA T 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU T 359 " --> pdb=" O GLU T 355 " (cutoff:3.500A) Processing helix chain 'T' and resid 364 through 368 Processing helix chain 'T' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE T 378 " --> pdb=" O GLU T 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE C 33 " --> pdb=" O ASN C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG D 27 " --> pdb=" O HIS D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 97 through 104 Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG E 27 " --> pdb=" O HIS E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 97 through 104 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG F 27 " --> pdb=" O HIS F 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE F 33 " --> pdb=" O ASN F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 104 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG G 27 " --> pdb=" O HIS G 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE G 33 " --> pdb=" O ASN G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 97 through 104 Processing sheet with id=AC4, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG H 27 " --> pdb=" O HIS H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE H 33 " --> pdb=" O ASN H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 97 through 104 Processing sheet with id=AC7, first strand: chain 'I' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG I 27 " --> pdb=" O HIS I 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE I 33 " --> pdb=" O ASN I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 97 through 104 Processing sheet with id=AD1, first strand: chain 'J' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG J 27 " --> pdb=" O HIS J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE J 33 " --> pdb=" O ASN J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 97 through 104 Processing sheet with id=AD4, first strand: chain 'K' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG K 27 " --> pdb=" O HIS K 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE K 33 " --> pdb=" O ASN K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 97 through 104 Processing sheet with id=AD7, first strand: chain 'L' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG L 27 " --> pdb=" O HIS L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'L' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE L 33 " --> pdb=" O ASN L 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'L' and resid 97 through 104 Processing sheet with id=AE1, first strand: chain 'M' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG M 27 " --> pdb=" O HIS M 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE M 33 " --> pdb=" O ASN M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 97 through 104 Processing sheet with id=AE4, first strand: chain 'N' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG N 27 " --> pdb=" O HIS N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE N 33 " --> pdb=" O ASN N 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'N' and resid 97 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG O 27 " --> pdb=" O HIS O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'O' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE O 33 " --> pdb=" O ASN O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 97 through 104 Processing sheet with id=AF1, first strand: chain 'P' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG P 27 " --> pdb=" O HIS P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE P 33 " --> pdb=" O ASN P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'P' and resid 97 through 104 Processing sheet with id=AF4, first strand: chain 'Q' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG Q 27 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'Q' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE Q 33 " --> pdb=" O ASN Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Q' and resid 97 through 104 Processing sheet with id=AF7, first strand: chain 'R' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG R 27 " --> pdb=" O HIS R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE R 33 " --> pdb=" O ASN R 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'R' and resid 97 through 104 Processing sheet with id=AG1, first strand: chain 'S' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG S 27 " --> pdb=" O HIS S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'S' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE S 33 " --> pdb=" O ASN S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'S' and resid 97 through 104 Processing sheet with id=AG4, first strand: chain 'T' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG T 27 " --> pdb=" O HIS T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'T' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE T 33 " --> pdb=" O ASN T 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'T' and resid 97 through 104 3580 hydrogen bonds defined for protein. 9940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 20.71 Time building geometry restraints manager: 19.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 62048 1.54 - 1.86: 1012 1.86 - 2.18: 0 2.18 - 2.50: 0 2.50 - 2.82: 18 Bond restraints: 63078 Sorted by residual: bond pdb=" O3' C U1014 " pdb=" P C U1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1014 " pdb=" P C e1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C U1049 " pdb=" P C U1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1049 " pdb=" P C e1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1007 " pdb=" P C e1008 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.51e+03 ... (remaining 63073 not shown) Histogram of bond angle deviations from ideal: 75.63 - 90.70: 36 90.70 - 105.77: 1320 105.77 - 120.84: 66566 120.84 - 135.92: 17672 135.92 - 150.99: 18 Bond angle restraints: 85612 Sorted by residual: angle pdb=" O3' C e1014 " pdb=" P C e1015 " pdb=" O5' C e1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1014 " pdb=" P C U1015 " pdb=" O5' C U1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1049 " pdb=" P C U1050 " pdb=" O5' C U1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1049 " pdb=" P C e1050 " pdb=" O5' C e1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1028 " pdb=" P C e1029 " pdb=" O5' C e1029 " ideal model delta sigma weight residual 104.00 75.64 28.36 1.50e+00 4.44e-01 3.57e+02 ... (remaining 85607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 35058 17.76 - 35.53: 2776 35.53 - 53.29: 400 53.29 - 71.05: 160 71.05 - 88.81: 180 Dihedral angle restraints: 38574 sinusoidal: 16754 harmonic: 21820 Sorted by residual: dihedral pdb=" CA ARG O 338 " pdb=" C ARG O 338 " pdb=" N GLY O 339 " pdb=" CA GLY O 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG T 338 " pdb=" C ARG T 338 " pdb=" N GLY T 339 " pdb=" CA GLY T 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG E 338 " pdb=" C ARG E 338 " pdb=" N GLY E 339 " pdb=" CA GLY E 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 38571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 5780 0.034 - 0.069: 2960 0.069 - 0.103: 740 0.103 - 0.137: 320 0.137 - 0.172: 20 Chirality restraints: 9820 Sorted by residual: chirality pdb=" CB VAL S 284 " pdb=" CA VAL S 284 " pdb=" CG1 VAL S 284 " pdb=" CG2 VAL S 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL N 284 " pdb=" CA VAL N 284 " pdb=" CG1 VAL N 284 " pdb=" CG2 VAL N 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL D 284 " pdb=" CA VAL D 284 " pdb=" CG1 VAL D 284 " pdb=" CG2 VAL D 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 9817 not shown) Planarity restraints: 10520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR L 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR L 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR L 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR L 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR L 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 149 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 149 " -0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR G 149 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 149 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 149 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 149 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 149 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 149 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 149 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR B 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 149 " 0.002 2.00e-02 2.50e+03 ... (remaining 10517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7168 2.74 - 3.28: 60942 3.28 - 3.82: 104240 3.82 - 4.36: 134256 4.36 - 4.90: 217416 Nonbonded interactions: 524022 Sorted by model distance: nonbonded pdb=" OE1 GLU G 297 " pdb=" OH TYR G 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU L 297 " pdb=" OH TYR L 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR B 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU Q 297 " pdb=" OH TYR Q 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU J 297 " pdb=" OH TYR J 301 " model vdw 2.204 2.440 ... (remaining 524017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'B' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'C' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'D' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'E' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'F' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'G' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'H' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'I' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'J' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'K' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'L' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'M' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'N' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'O' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'P' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'Q' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'R' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'S' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'T' and (resid 2 through 99 or resid 101 through 379)) } ncs_group { reference = chain 'U' selection = chain 'e' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.040 Extract box with map and model: 16.460 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 157.340 Find NCS groups from input model: 3.490 Set up NCS constraints: 0.270 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 194.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.021 1.211 63078 Z= 1.282 Angle : 1.033 42.987 85612 Z= 0.504 Chirality : 0.044 0.172 9820 Planarity : 0.003 0.034 10520 Dihedral : 14.494 88.812 24654 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 7540 helix: 0.86 (0.07), residues: 4720 sheet: 0.74 (0.22), residues: 440 loop : -0.15 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 260 HIS 0.006 0.001 HIS E 225 PHE 0.019 0.002 PHE S 219 TYR 0.022 0.002 TYR G 149 ARG 0.004 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.529 Fit side-chains outliers start: 0 outliers final: 4 residues processed: 980 average time/residue: 1.8622 time to fit residues: 2232.1140 Evaluate side-chains 784 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 780 time to evaluate : 5.108 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 6.8859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 636 optimal weight: 0.9980 chunk 571 optimal weight: 0.0050 chunk 317 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 305 optimal weight: 0.6980 chunk 590 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 359 optimal weight: 0.5980 chunk 439 optimal weight: 0.9980 chunk 684 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 HIS ** A 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 89 HIS ** B 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN D 26 GLN D 89 HIS ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN E 26 GLN E 89 HIS E 319 HIS E 343 ASN F 26 GLN F 89 HIS ** F 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 89 HIS ** G 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN I 26 GLN I 89 HIS I 151 HIS I 356 GLN J 26 GLN J 89 HIS J 319 HIS J 343 ASN K 26 GLN K 89 HIS ** K 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 GLN L 89 HIS ** L 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 HIS M 356 GLN N 26 GLN N 89 HIS ** N 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN O 26 GLN O 89 HIS O 319 HIS O 343 ASN P 26 GLN P 89 HIS ** P 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN Q 89 HIS ** Q 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS R 356 GLN S 26 GLN S 89 HIS ** S 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN T 26 GLN T 89 HIS T 319 HIS T 343 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.179 Angle : 0.507 5.441 85612 Z= 0.276 Chirality : 0.040 0.152 9820 Planarity : 0.004 0.035 10520 Dihedral : 11.270 73.818 10454 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.85 % Allowed : 8.54 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.10), residues: 7540 helix: 1.38 (0.07), residues: 4720 sheet: 0.73 (0.25), residues: 300 loop : 0.19 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 260 HIS 0.004 0.001 HIS G 225 PHE 0.010 0.002 PHE G 219 TYR 0.009 0.001 TYR P 337 ARG 0.009 0.001 ARG S 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 812 time to evaluate : 5.106 Fit side-chains outliers start: 180 outliers final: 80 residues processed: 916 average time/residue: 1.8819 time to fit residues: 2128.2804 Evaluate side-chains 812 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 732 time to evaluate : 5.121 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 48 residues processed: 32 average time/residue: 1.0405 time to fit residues: 54.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 380 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 569 optimal weight: 4.9990 chunk 466 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 685 optimal weight: 1.9990 chunk 741 optimal weight: 1.9990 chunk 610 optimal weight: 0.5980 chunk 680 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 550 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 216 HIS ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN F 89 HIS F 216 HIS ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN K 89 HIS K 216 HIS ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN P 89 HIS P 216 HIS ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63078 Z= 0.204 Angle : 0.504 6.827 85612 Z= 0.268 Chirality : 0.040 0.147 9820 Planarity : 0.004 0.038 10520 Dihedral : 11.145 73.822 10454 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.04 % Allowed : 11.01 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.10), residues: 7540 helix: 1.46 (0.07), residues: 4720 sheet: 0.73 (0.26), residues: 300 loop : 0.29 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 260 HIS 0.006 0.001 HIS L 225 PHE 0.009 0.002 PHE H 226 TYR 0.012 0.001 TYR T 337 ARG 0.008 0.001 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 764 time to evaluate : 5.233 Fit side-chains outliers start: 192 outliers final: 96 residues processed: 868 average time/residue: 1.8197 time to fit residues: 1946.7803 Evaluate side-chains 808 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 712 time to evaluate : 5.055 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 64 residues processed: 32 average time/residue: 1.1290 time to fit residues: 56.1597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 677 optimal weight: 0.6980 chunk 515 optimal weight: 3.9990 chunk 355 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 327 optimal weight: 2.9990 chunk 460 optimal weight: 0.6980 chunk 688 optimal weight: 3.9990 chunk 728 optimal weight: 0.6980 chunk 359 optimal weight: 0.8980 chunk 652 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS B 26 GLN B 89 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN F 89 HIS G 26 GLN G 89 HIS ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN K 89 HIS L 26 GLN L 89 HIS ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN P 89 HIS Q 26 GLN Q 89 HIS ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.196 Angle : 0.503 7.383 85612 Z= 0.267 Chirality : 0.040 0.145 9820 Planarity : 0.004 0.044 10520 Dihedral : 11.079 73.871 10454 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.39 % Allowed : 12.99 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 7540 helix: 1.50 (0.07), residues: 4720 sheet: 0.52 (0.26), residues: 260 loop : 0.23 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 260 HIS 0.005 0.001 HIS G 225 PHE 0.009 0.002 PHE H 226 TYR 0.012 0.001 TYR P 337 ARG 0.011 0.001 ARG E 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 748 time to evaluate : 5.250 Fit side-chains outliers start: 151 outliers final: 100 residues processed: 820 average time/residue: 1.8341 time to fit residues: 1857.2138 Evaluate side-chains 796 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 696 time to evaluate : 5.278 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 72 residues processed: 28 average time/residue: 0.7712 time to fit residues: 40.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 606 optimal weight: 4.9990 chunk 413 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 542 optimal weight: 3.9990 chunk 300 optimal weight: 0.4980 chunk 621 optimal weight: 0.9980 chunk 503 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 372 optimal weight: 0.6980 chunk 654 optimal weight: 0.1980 chunk 183 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN D 356 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 356 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN N 356 GLN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 GLN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 GLN S 356 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 63078 Z= 0.157 Angle : 0.475 8.611 85612 Z= 0.250 Chirality : 0.038 0.152 9820 Planarity : 0.003 0.045 10520 Dihedral : 11.028 73.819 10454 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.17 % Allowed : 14.67 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.10), residues: 7540 helix: 1.68 (0.07), residues: 4700 sheet: 1.20 (0.26), residues: 220 loop : 0.22 (0.13), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 260 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE H 226 TYR 0.009 0.001 TYR T 337 ARG 0.010 0.001 ARG O 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 736 time to evaluate : 5.154 Fit side-chains outliers start: 137 outliers final: 96 residues processed: 812 average time/residue: 1.8296 time to fit residues: 1838.9761 Evaluate side-chains 806 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 710 time to evaluate : 5.148 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 72 residues processed: 24 average time/residue: 0.9999 time to fit residues: 41.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 245 optimal weight: 0.7980 chunk 656 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 427 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 729 optimal weight: 0.5980 chunk 605 optimal weight: 3.9990 chunk 337 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 241 optimal weight: 0.8980 chunk 382 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN D 364 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 GLN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 292 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN I 364 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 GLN ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN N 364 ASN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 356 GLN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN S 364 ASN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 356 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.201 Angle : 0.508 8.804 85612 Z= 0.267 Chirality : 0.040 0.144 9820 Planarity : 0.004 0.054 10520 Dihedral : 11.029 73.970 10454 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.91 % Allowed : 16.11 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 7540 helix: 1.58 (0.07), residues: 4700 sheet: 1.37 (0.27), residues: 220 loop : 0.16 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 260 HIS 0.005 0.001 HIS S 225 PHE 0.010 0.002 PHE R 226 TYR 0.010 0.001 TYR T 288 ARG 0.014 0.001 ARG I 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 711 time to evaluate : 5.094 Fit side-chains outliers start: 121 outliers final: 89 residues processed: 791 average time/residue: 1.8382 time to fit residues: 1795.5886 Evaluate side-chains 786 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 697 time to evaluate : 5.130 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 71 residues processed: 18 average time/residue: 0.4854 time to fit residues: 23.2021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 703 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 415 optimal weight: 4.9990 chunk 532 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 614 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 726 optimal weight: 2.9990 chunk 454 optimal weight: 0.0170 chunk 443 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 ASN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** S 192 ASN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 63078 Z= 0.408 Angle : 0.623 9.291 85612 Z= 0.326 Chirality : 0.047 0.244 9820 Planarity : 0.005 0.058 10520 Dihedral : 11.199 74.340 10454 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.56 % Allowed : 15.98 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7540 helix: 1.02 (0.07), residues: 4720 sheet: 0.35 (0.21), residues: 460 loop : 0.13 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 260 HIS 0.010 0.002 HIS B 225 PHE 0.015 0.003 PHE P 243 TYR 0.015 0.002 TYR A 337 ARG 0.015 0.001 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 711 time to evaluate : 5.180 Fit side-chains outliers start: 162 outliers final: 99 residues processed: 814 average time/residue: 1.8390 time to fit residues: 1845.8094 Evaluate side-chains 798 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 699 time to evaluate : 5.168 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 64 residues processed: 35 average time/residue: 1.0284 time to fit residues: 57.6266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 449 optimal weight: 0.9980 chunk 290 optimal weight: 0.5980 chunk 434 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 462 optimal weight: 0.6980 chunk 495 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 571 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.194 Angle : 0.520 9.877 85612 Z= 0.274 Chirality : 0.040 0.150 9820 Planarity : 0.004 0.075 10520 Dihedral : 11.078 73.857 10454 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.47 % Allowed : 17.15 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.09), residues: 7540 helix: 1.39 (0.07), residues: 4700 sheet: 1.37 (0.28), residues: 220 loop : 0.01 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 260 HIS 0.004 0.001 HIS G 225 PHE 0.009 0.002 PHE H 226 TYR 0.010 0.001 TYR O 353 ARG 0.016 0.001 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 738 time to evaluate : 5.199 Fit side-chains outliers start: 93 outliers final: 76 residues processed: 814 average time/residue: 1.8672 time to fit residues: 1872.7354 Evaluate side-chains 792 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 716 time to evaluate : 5.157 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 5 average time/residue: 1.1420 time to fit residues: 14.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 661 optimal weight: 0.6980 chunk 696 optimal weight: 0.5980 chunk 635 optimal weight: 1.9990 chunk 677 optimal weight: 0.9980 chunk 407 optimal weight: 0.1980 chunk 295 optimal weight: 0.6980 chunk 531 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 611 optimal weight: 0.1980 chunk 640 optimal weight: 0.7980 chunk 674 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 ASN M 151 HIS ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN R 151 HIS ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 63078 Z= 0.155 Angle : 0.497 11.046 85612 Z= 0.260 Chirality : 0.038 0.151 9820 Planarity : 0.003 0.078 10520 Dihedral : 11.022 73.776 10454 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 17.33 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.09), residues: 7540 helix: 1.66 (0.07), residues: 4700 sheet: 1.32 (0.28), residues: 220 loop : 0.06 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 260 HIS 0.004 0.001 HIS T 89 PHE 0.009 0.001 PHE L 223 TYR 0.011 0.001 TYR H 88 ARG 0.016 0.001 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 743 time to evaluate : 5.074 Fit side-chains outliers start: 91 outliers final: 80 residues processed: 814 average time/residue: 1.8163 time to fit residues: 1824.2343 Evaluate side-chains 798 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 718 time to evaluate : 5.068 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 68 residues processed: 12 average time/residue: 1.4517 time to fit residues: 29.3299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 444 optimal weight: 2.9990 chunk 716 optimal weight: 0.6980 chunk 437 optimal weight: 0.8980 chunk 339 optimal weight: 0.7980 chunk 497 optimal weight: 0.4980 chunk 751 optimal weight: 5.9990 chunk 691 optimal weight: 2.9990 chunk 598 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 462 optimal weight: 0.4980 chunk 366 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN B 89 HIS ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 HIS I 364 ASN ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 GLN L 89 HIS ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 HIS ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.187 Angle : 0.524 11.181 85612 Z= 0.273 Chirality : 0.039 0.144 9820 Planarity : 0.004 0.055 10520 Dihedral : 11.018 73.873 10454 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.11 % Allowed : 17.91 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 7540 helix: 1.61 (0.07), residues: 4720 sheet: 1.44 (0.28), residues: 220 loop : 0.06 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP M 260 HIS 0.007 0.001 HIS M 89 PHE 0.009 0.002 PHE L 223 TYR 0.010 0.001 TYR J 353 ARG 0.016 0.001 ARG J 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 715 time to evaluate : 5.164 Fit side-chains outliers start: 70 outliers final: 68 residues processed: 783 average time/residue: 1.8590 time to fit residues: 1793.2154 Evaluate side-chains 766 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 698 time to evaluate : 5.170 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 68 residues processed: 0 time to fit residues: 7.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 475 optimal weight: 6.9990 chunk 637 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 551 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 599 optimal weight: 0.6980 chunk 250 optimal weight: 0.8980 chunk 615 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112319 restraints weight = 129987.399| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.66 r_work: 0.2880 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 63078 Z= 0.201 Angle : 0.526 11.186 85612 Z= 0.275 Chirality : 0.040 0.145 9820 Planarity : 0.004 0.069 10520 Dihedral : 11.004 73.904 10454 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.31 % Allowed : 17.72 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 7540 helix: 1.56 (0.07), residues: 4720 sheet: 1.51 (0.28), residues: 220 loop : 0.05 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 260 HIS 0.006 0.001 HIS H 89 PHE 0.010 0.002 PHE Q 223 TYR 0.010 0.001 TYR O 353 ARG 0.015 0.001 ARG E 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25044.37 seconds wall clock time: 434 minutes 56.26 seconds (26096.26 seconds total)