Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 20 01:25:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/08_2023/7qg0_13951.pdb" } resolution = 4.02 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 384 5.16 5 C 49856 2.51 5 N 14160 2.21 5 O 14480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 445": "NH1" <-> "NH2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ARG 463": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C ARG 463": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C GLU 525": "OE1" <-> "OE2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 664": "OE1" <-> "OE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 450": "OE1" <-> "OE2" Residue "D ARG 463": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D GLU 525": "OE1" <-> "OE2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D GLU 661": "OE1" <-> "OE2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E GLU 450": "OE1" <-> "OE2" Residue "E ARG 463": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E ARG 537": "NH1" <-> "NH2" Residue "E GLU 661": "OE1" <-> "OE2" Residue "E GLU 664": "OE1" <-> "OE2" Residue "E GLU 670": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 217": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F ARG 445": "NH1" <-> "NH2" Residue "F GLU 450": "OE1" <-> "OE2" Residue "F ARG 463": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ARG 537": "NH1" <-> "NH2" Residue "F GLU 661": "OE1" <-> "OE2" Residue "F GLU 664": "OE1" <-> "OE2" Residue "F GLU 670": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 217": "NH1" <-> "NH2" Residue "G ARG 395": "NH1" <-> "NH2" Residue "G ARG 445": "NH1" <-> "NH2" Residue "G GLU 450": "OE1" <-> "OE2" Residue "G ARG 463": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "G GLU 525": "OE1" <-> "OE2" Residue "G ARG 537": "NH1" <-> "NH2" Residue "G GLU 661": "OE1" <-> "OE2" Residue "G GLU 664": "OE1" <-> "OE2" Residue "G GLU 670": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H ARG 445": "NH1" <-> "NH2" Residue "H GLU 450": "OE1" <-> "OE2" Residue "H ARG 463": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Residue "H GLU 525": "OE1" <-> "OE2" Residue "H ARG 537": "NH1" <-> "NH2" Residue "H GLU 661": "OE1" <-> "OE2" Residue "H GLU 664": "OE1" <-> "OE2" Residue "H GLU 670": "OE1" <-> "OE2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "I GLU 149": "OE1" <-> "OE2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 217": "NH1" <-> "NH2" Residue "I ARG 395": "NH1" <-> "NH2" Residue "I ARG 445": "NH1" <-> "NH2" Residue "I GLU 450": "OE1" <-> "OE2" Residue "I ARG 463": "NH1" <-> "NH2" Residue "I ARG 512": "NH1" <-> "NH2" Residue "I GLU 525": "OE1" <-> "OE2" Residue "I ARG 537": "NH1" <-> "NH2" Residue "I GLU 661": "OE1" <-> "OE2" Residue "I GLU 664": "OE1" <-> "OE2" Residue "I GLU 670": "OE1" <-> "OE2" Residue "J GLU 137": "OE1" <-> "OE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J ARG 217": "NH1" <-> "NH2" Residue "J ARG 395": "NH1" <-> "NH2" Residue "J ARG 445": "NH1" <-> "NH2" Residue "J GLU 450": "OE1" <-> "OE2" Residue "J ARG 463": "NH1" <-> "NH2" Residue "J ARG 512": "NH1" <-> "NH2" Residue "J GLU 525": "OE1" <-> "OE2" Residue "J ARG 537": "NH1" <-> "NH2" Residue "J GLU 661": "OE1" <-> "OE2" Residue "J GLU 664": "OE1" <-> "OE2" Residue "J GLU 670": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K GLU 149": "OE1" <-> "OE2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K ARG 217": "NH1" <-> "NH2" Residue "K ARG 395": "NH1" <-> "NH2" Residue "K ARG 445": "NH1" <-> "NH2" Residue "K GLU 450": "OE1" <-> "OE2" Residue "K ARG 463": "NH1" <-> "NH2" Residue "K ARG 512": "NH1" <-> "NH2" Residue "K GLU 525": "OE1" <-> "OE2" Residue "K ARG 537": "NH1" <-> "NH2" Residue "K GLU 661": "OE1" <-> "OE2" Residue "K GLU 664": "OE1" <-> "OE2" Residue "K GLU 670": "OE1" <-> "OE2" Residue "L GLU 137": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 395": "NH1" <-> "NH2" Residue "L ARG 445": "NH1" <-> "NH2" Residue "L GLU 450": "OE1" <-> "OE2" Residue "L ARG 463": "NH1" <-> "NH2" Residue "L ARG 512": "NH1" <-> "NH2" Residue "L GLU 525": "OE1" <-> "OE2" Residue "L ARG 537": "NH1" <-> "NH2" Residue "L GLU 661": "OE1" <-> "OE2" Residue "L GLU 664": "OE1" <-> "OE2" Residue "L GLU 670": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M GLU 149": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ARG 217": "NH1" <-> "NH2" Residue "M ARG 395": "NH1" <-> "NH2" Residue "M ARG 445": "NH1" <-> "NH2" Residue "M GLU 450": "OE1" <-> "OE2" Residue "M ARG 463": "NH1" <-> "NH2" Residue "M ARG 512": "NH1" <-> "NH2" Residue "M GLU 525": "OE1" <-> "OE2" Residue "M ARG 537": "NH1" <-> "NH2" Residue "M GLU 661": "OE1" <-> "OE2" Residue "M GLU 664": "OE1" <-> "OE2" Residue "M GLU 670": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "N GLU 149": "OE1" <-> "OE2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N ARG 217": "NH1" <-> "NH2" Residue "N ARG 395": "NH1" <-> "NH2" Residue "N ARG 445": "NH1" <-> "NH2" Residue "N GLU 450": "OE1" <-> "OE2" Residue "N ARG 463": "NH1" <-> "NH2" Residue "N ARG 512": "NH1" <-> "NH2" Residue "N GLU 525": "OE1" <-> "OE2" Residue "N ARG 537": "NH1" <-> "NH2" Residue "N GLU 661": "OE1" <-> "OE2" Residue "N GLU 664": "OE1" <-> "OE2" Residue "N GLU 670": "OE1" <-> "OE2" Residue "O GLU 137": "OE1" <-> "OE2" Residue "O GLU 149": "OE1" <-> "OE2" Residue "O ARG 182": "NH1" <-> "NH2" Residue "O ARG 217": "NH1" <-> "NH2" Residue "O ARG 395": "NH1" <-> "NH2" Residue "O ARG 445": "NH1" <-> "NH2" Residue "O GLU 450": "OE1" <-> "OE2" Residue "O ARG 463": "NH1" <-> "NH2" Residue "O ARG 512": "NH1" <-> "NH2" Residue "O GLU 525": "OE1" <-> "OE2" Residue "O ARG 537": "NH1" <-> "NH2" Residue "O GLU 661": "OE1" <-> "OE2" Residue "O GLU 664": "OE1" <-> "OE2" Residue "O GLU 670": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 149": "OE1" <-> "OE2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 217": "NH1" <-> "NH2" Residue "P ARG 395": "NH1" <-> "NH2" Residue "P ARG 445": "NH1" <-> "NH2" Residue "P GLU 450": "OE1" <-> "OE2" Residue "P ARG 463": "NH1" <-> "NH2" Residue "P ARG 512": "NH1" <-> "NH2" Residue "P GLU 525": "OE1" <-> "OE2" Residue "P ARG 537": "NH1" <-> "NH2" Residue "P GLU 661": "OE1" <-> "OE2" Residue "P GLU 664": "OE1" <-> "OE2" Residue "P GLU 670": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 78880 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "C" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "D" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "E" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "F" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "G" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "H" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "I" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "J" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "K" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "L" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "M" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "N" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "O" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Chain: "P" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4930 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 2 Time building chain proxies: 27.73, per 1000 atoms: 0.35 Number of scatterers: 78880 At special positions: 0 Unit cell: (208.911, 208.911, 138.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 384 16.00 O 14480 8.00 N 14160 7.00 C 49856 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: 28.10 Conformation dependent library (CDL) restraints added in 8.8 seconds 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18784 Finding SS restraints... Secondary structure from input PDB file: 656 helices and 16 sheets defined 73.2% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.04 Creating SS restraints... Processing helix chain 'A' and resid 56 through 81 removed outlier: 4.265A pdb=" N GLU A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.889A pdb=" N GLN A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 250 through 259 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA A 294 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS A 428 " --> pdb=" O GLY A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 605 through 614 removed outlier: 3.906A pdb=" N GLN A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA A 674 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 675 " --> pdb=" O MET A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 81 Proline residue: B 70 - end of helix removed outlier: 3.889A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 250 through 259 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA B 294 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 425 through 428 removed outlier: 4.903A pdb=" N LYS B 428 " --> pdb=" O GLY B 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 428' Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 459 through 477 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 Processing helix chain 'B' and resid 573 through 587 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA B 674 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 675 " --> pdb=" O MET B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 81 Proline residue: C 70 - end of helix removed outlier: 3.890A pdb=" N GLN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 137 through 152 Processing helix chain 'C' and resid 153 through 173 removed outlier: 3.655A pdb=" N LEU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 167 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 248 Processing helix chain 'C' and resid 250 through 259 Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA C 294 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 360 removed outlier: 3.565A pdb=" N GLN C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.565A pdb=" N ASP C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 375 removed outlier: 4.031A pdb=" N SER C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.636A pdb=" N SER C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 397 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS C 428 " --> pdb=" O GLY C 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 428' Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 447 through 455 Processing helix chain 'C' and resid 459 through 477 Processing helix chain 'C' and resid 486 through 495 Processing helix chain 'C' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.611A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU C 523 " --> pdb=" O SER C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 Processing helix chain 'C' and resid 573 through 587 Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA C 674 " --> pdb=" O ASP C 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 675 " --> pdb=" O MET C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 Proline residue: D 70 - end of helix removed outlier: 3.890A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 104 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 137 through 152 Processing helix chain 'D' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 219 through 238 removed outlier: 4.520A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 250 through 259 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA D 294 " --> pdb=" O GLY D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 291 through 294' Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP D 367 " --> pdb=" O LYS D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 424 Processing helix chain 'D' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS D 428 " --> pdb=" O GLY D 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 428' Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'D' and resid 459 through 477 Processing helix chain 'D' and resid 486 through 495 Processing helix chain 'D' and resid 497 through 500 removed outlier: 3.931A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 497 through 500' Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU D 523 " --> pdb=" O SER D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 546 Processing helix chain 'D' and resid 573 through 587 Processing helix chain 'D' and resid 605 through 614 removed outlier: 3.906A pdb=" N GLN D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 649 Processing helix chain 'D' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA D 674 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL D 675 " --> pdb=" O MET D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 81 Proline residue: E 70 - end of helix removed outlier: 3.889A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 Processing helix chain 'E' and resid 109 through 123 Processing helix chain 'E' and resid 126 through 135 Processing helix chain 'E' and resid 137 through 152 Processing helix chain 'E' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 208 through 214 Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 Processing helix chain 'E' and resid 250 through 259 Proline residue: E 256 - end of helix Processing helix chain 'E' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU E 286 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA E 294 " --> pdb=" O GLY E 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.636A pdb=" N LEU E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN E 342 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 removed outlier: 3.565A pdb=" N ASP E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER E 379 " --> pdb=" O LYS E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS E 428 " --> pdb=" O GLY E 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 428' Processing helix chain 'E' and resid 429 through 437 Processing helix chain 'E' and resid 447 through 455 Processing helix chain 'E' and resid 459 through 477 Processing helix chain 'E' and resid 486 through 495 Processing helix chain 'E' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 497 through 500' Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU E 523 " --> pdb=" O SER E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 546 Processing helix chain 'E' and resid 573 through 587 Processing helix chain 'E' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN E 609 " --> pdb=" O ASP E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 649 Processing helix chain 'E' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA E 674 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 675 " --> pdb=" O MET E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE E 698 " --> pdb=" O LYS E 694 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 81 Proline residue: F 70 - end of helix removed outlier: 3.889A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 126 through 135 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 153 through 173 removed outlier: 3.655A pdb=" N LEU F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY F 166 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 219 through 238 removed outlier: 4.522A pdb=" N GLY F 238 " --> pdb=" O ALA F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 250 through 259 Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU F 286 " --> pdb=" O GLU F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA F 294 " --> pdb=" O GLY F 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP F 367 " --> pdb=" O LYS F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 375 removed outlier: 4.031A pdb=" N SER F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER F 379 " --> pdb=" O LYS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 424 Processing helix chain 'F' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS F 428 " --> pdb=" O GLY F 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 428' Processing helix chain 'F' and resid 429 through 437 Processing helix chain 'F' and resid 447 through 455 Processing helix chain 'F' and resid 459 through 477 Processing helix chain 'F' and resid 486 through 495 Processing helix chain 'F' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 497 through 500' Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU F 523 " --> pdb=" O SER F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 546 Processing helix chain 'F' and resid 573 through 587 Processing helix chain 'F' and resid 605 through 614 removed outlier: 3.905A pdb=" N GLN F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 649 Processing helix chain 'F' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA F 674 " --> pdb=" O ASP F 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 675 " --> pdb=" O MET F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE F 698 " --> pdb=" O LYS F 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 81 Proline residue: G 70 - end of helix removed outlier: 3.888A pdb=" N GLN G 81 " --> pdb=" O SER G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 104 Processing helix chain 'G' and resid 109 through 123 Processing helix chain 'G' and resid 126 through 135 Processing helix chain 'G' and resid 137 through 152 Processing helix chain 'G' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 192 Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 208 through 214 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY G 238 " --> pdb=" O ALA G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 250 through 259 Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 263 through 278 removed outlier: 3.881A pdb=" N ARG G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU G 286 " --> pdb=" O GLU G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA G 294 " --> pdb=" O GLY G 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 291 through 294' Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN G 342 " --> pdb=" O ARG G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP G 367 " --> pdb=" O LYS G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER G 373 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER G 379 " --> pdb=" O LYS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 397 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 425 through 428 removed outlier: 4.903A pdb=" N LYS G 428 " --> pdb=" O GLY G 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 428' Processing helix chain 'G' and resid 429 through 437 Processing helix chain 'G' and resid 447 through 455 Processing helix chain 'G' and resid 459 through 477 Processing helix chain 'G' and resid 486 through 495 Processing helix chain 'G' and resid 497 through 500 removed outlier: 3.931A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 497 through 500' Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU G 523 " --> pdb=" O SER G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 546 Processing helix chain 'G' and resid 573 through 587 Processing helix chain 'G' and resid 605 through 614 removed outlier: 3.906A pdb=" N GLN G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 649 Processing helix chain 'G' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA G 674 " --> pdb=" O ASP G 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL G 675 " --> pdb=" O MET G 672 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE G 698 " --> pdb=" O LYS G 694 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 81 Proline residue: H 70 - end of helix removed outlier: 3.889A pdb=" N GLN H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 104 Processing helix chain 'H' and resid 109 through 123 Processing helix chain 'H' and resid 126 through 135 Processing helix chain 'H' and resid 137 through 152 Processing helix chain 'H' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 168 " --> pdb=" O GLY H 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 192 Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 208 through 214 Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 250 through 259 Proline residue: H 256 - end of helix Processing helix chain 'H' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU H 286 " --> pdb=" O GLU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA H 294 " --> pdb=" O GLY H 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 291 through 294' Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU H 334 " --> pdb=" O LEU H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 360 removed outlier: 3.567A pdb=" N GLN H 342 " --> pdb=" O ARG H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP H 367 " --> pdb=" O LYS H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER H 373 " --> pdb=" O GLY H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER H 379 " --> pdb=" O LYS H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 424 Processing helix chain 'H' and resid 425 through 428 removed outlier: 4.901A pdb=" N LYS H 428 " --> pdb=" O GLY H 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 425 through 428' Processing helix chain 'H' and resid 429 through 437 Processing helix chain 'H' and resid 447 through 455 Processing helix chain 'H' and resid 459 through 477 Processing helix chain 'H' and resid 486 through 495 Processing helix chain 'H' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 497 through 500' Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.611A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU H 523 " --> pdb=" O SER H 519 " (cutoff:3.500A) Processing helix chain 'H' and resid 531 through 546 Processing helix chain 'H' and resid 573 through 587 Processing helix chain 'H' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN H 609 " --> pdb=" O ASP H 605 " (cutoff:3.500A) Processing helix chain 'H' and resid 637 through 649 Processing helix chain 'H' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL H 675 " --> pdb=" O MET H 672 " (cutoff:3.500A) Processing helix chain 'H' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE H 698 " --> pdb=" O LYS H 694 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 81 Proline residue: I 70 - end of helix removed outlier: 3.890A pdb=" N GLN I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 104 Processing helix chain 'I' and resid 109 through 123 Processing helix chain 'I' and resid 126 through 135 Processing helix chain 'I' and resid 137 through 152 Processing helix chain 'I' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY I 166 " --> pdb=" O ARG I 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 167 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE I 168 " --> pdb=" O GLY I 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 192 Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 208 through 214 Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 248 Processing helix chain 'I' and resid 250 through 259 Proline residue: I 256 - end of helix Processing helix chain 'I' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG I 267 " --> pdb=" O ASP I 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL I 274 " --> pdb=" O ALA I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU I 286 " --> pdb=" O GLU I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA I 294 " --> pdb=" O GLY I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 291 through 294' Processing helix chain 'I' and resid 295 through 303 Processing helix chain 'I' and resid 305 through 310 Processing helix chain 'I' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN I 342 " --> pdb=" O ARG I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 369 removed outlier: 3.565A pdb=" N ASP I 367 " --> pdb=" O LYS I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER I 373 " --> pdb=" O GLY I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER I 379 " --> pdb=" O LYS I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 397 Processing helix chain 'I' and resid 408 through 412 Processing helix chain 'I' and resid 413 through 424 Processing helix chain 'I' and resid 425 through 428 removed outlier: 4.901A pdb=" N LYS I 428 " --> pdb=" O GLY I 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 428' Processing helix chain 'I' and resid 429 through 437 Processing helix chain 'I' and resid 447 through 455 Processing helix chain 'I' and resid 459 through 477 Processing helix chain 'I' and resid 486 through 495 Processing helix chain 'I' and resid 497 through 500 removed outlier: 3.931A pdb=" N GLN I 500 " --> pdb=" O ARG I 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 497 through 500' Processing helix chain 'I' and resid 501 through 507 Processing helix chain 'I' and resid 514 through 518 removed outlier: 3.611A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU I 523 " --> pdb=" O SER I 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 546 Processing helix chain 'I' and resid 573 through 587 Processing helix chain 'I' and resid 605 through 614 removed outlier: 3.905A pdb=" N GLN I 609 " --> pdb=" O ASP I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 637 through 649 Processing helix chain 'I' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA I 674 " --> pdb=" O ASP I 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL I 675 " --> pdb=" O MET I 672 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE I 698 " --> pdb=" O LYS I 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 81 Proline residue: J 70 - end of helix removed outlier: 3.889A pdb=" N GLN J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 104 Processing helix chain 'J' and resid 109 through 123 Processing helix chain 'J' and resid 126 through 135 Processing helix chain 'J' and resid 137 through 152 Processing helix chain 'J' and resid 153 through 173 removed outlier: 3.655A pdb=" N LEU J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY J 166 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL J 167 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 192 Processing helix chain 'J' and resid 195 through 205 Processing helix chain 'J' and resid 208 through 214 Processing helix chain 'J' and resid 215 through 217 No H-bonds generated for 'chain 'J' and resid 215 through 217' Processing helix chain 'J' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY J 238 " --> pdb=" O ALA J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 248 Processing helix chain 'J' and resid 250 through 259 Proline residue: J 256 - end of helix Processing helix chain 'J' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG J 267 " --> pdb=" O ASP J 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL J 274 " --> pdb=" O ALA J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA J 294 " --> pdb=" O GLY J 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 291 through 294' Processing helix chain 'J' and resid 295 through 303 Processing helix chain 'J' and resid 305 through 310 Processing helix chain 'J' and resid 330 through 335 removed outlier: 3.638A pdb=" N LEU J 334 " --> pdb=" O LEU J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN J 342 " --> pdb=" O ARG J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 363 through 369 removed outlier: 3.565A pdb=" N ASP J 367 " --> pdb=" O LYS J 363 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 375 removed outlier: 4.031A pdb=" N SER J 373 " --> pdb=" O GLY J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 375 through 380 removed outlier: 3.636A pdb=" N SER J 379 " --> pdb=" O LYS J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 408 through 412 Processing helix chain 'J' and resid 413 through 424 Processing helix chain 'J' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS J 428 " --> pdb=" O GLY J 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 425 through 428' Processing helix chain 'J' and resid 429 through 437 Processing helix chain 'J' and resid 447 through 455 Processing helix chain 'J' and resid 459 through 477 Processing helix chain 'J' and resid 486 through 495 Processing helix chain 'J' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN J 500 " --> pdb=" O ARG J 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 497 through 500' Processing helix chain 'J' and resid 501 through 507 Processing helix chain 'J' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG J 517 " --> pdb=" O LEU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU J 523 " --> pdb=" O SER J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 546 Processing helix chain 'J' and resid 573 through 587 Processing helix chain 'J' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN J 609 " --> pdb=" O ASP J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 637 through 649 Processing helix chain 'J' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA J 674 " --> pdb=" O ASP J 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 675 " --> pdb=" O MET J 672 " (cutoff:3.500A) Processing helix chain 'J' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE J 698 " --> pdb=" O LYS J 694 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 81 Proline residue: K 70 - end of helix removed outlier: 3.888A pdb=" N GLN K 81 " --> pdb=" O SER K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 104 Processing helix chain 'K' and resid 109 through 123 Processing helix chain 'K' and resid 126 through 135 Processing helix chain 'K' and resid 137 through 152 Processing helix chain 'K' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY K 166 " --> pdb=" O ARG K 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL K 167 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE K 168 " --> pdb=" O GLY K 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 192 Processing helix chain 'K' and resid 195 through 205 Processing helix chain 'K' and resid 208 through 214 Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 219 through 238 removed outlier: 4.522A pdb=" N GLY K 238 " --> pdb=" O ALA K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 248 Processing helix chain 'K' and resid 250 through 259 Proline residue: K 256 - end of helix Processing helix chain 'K' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG K 267 " --> pdb=" O ASP K 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL K 274 " --> pdb=" O ALA K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA K 294 " --> pdb=" O GLY K 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 291 through 294' Processing helix chain 'K' and resid 295 through 303 Processing helix chain 'K' and resid 305 through 310 Processing helix chain 'K' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU K 334 " --> pdb=" O LEU K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN K 342 " --> pdb=" O ARG K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP K 367 " --> pdb=" O LYS K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 375 removed outlier: 4.033A pdb=" N SER K 373 " --> pdb=" O GLY K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER K 379 " --> pdb=" O LYS K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 397 Processing helix chain 'K' and resid 408 through 412 Processing helix chain 'K' and resid 413 through 424 Processing helix chain 'K' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS K 428 " --> pdb=" O GLY K 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 425 through 428' Processing helix chain 'K' and resid 429 through 437 Processing helix chain 'K' and resid 447 through 455 Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 486 through 495 Processing helix chain 'K' and resid 497 through 500 removed outlier: 3.933A pdb=" N GLN K 500 " --> pdb=" O ARG K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 497 through 500' Processing helix chain 'K' and resid 501 through 507 Processing helix chain 'K' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG K 517 " --> pdb=" O LEU K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU K 523 " --> pdb=" O SER K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 546 Processing helix chain 'K' and resid 573 through 587 Processing helix chain 'K' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN K 609 " --> pdb=" O ASP K 605 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 649 Processing helix chain 'K' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA K 674 " --> pdb=" O ASP K 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL K 675 " --> pdb=" O MET K 672 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE K 698 " --> pdb=" O LYS K 694 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 81 Proline residue: L 70 - end of helix removed outlier: 3.889A pdb=" N GLN L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 104 Processing helix chain 'L' and resid 109 through 123 Processing helix chain 'L' and resid 126 through 135 Processing helix chain 'L' and resid 137 through 152 Processing helix chain 'L' and resid 153 through 173 removed outlier: 3.655A pdb=" N LEU L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY L 166 " --> pdb=" O ARG L 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 195 through 205 Processing helix chain 'L' and resid 208 through 214 Processing helix chain 'L' and resid 215 through 217 No H-bonds generated for 'chain 'L' and resid 215 through 217' Processing helix chain 'L' and resid 219 through 238 removed outlier: 4.522A pdb=" N GLY L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 248 Processing helix chain 'L' and resid 250 through 259 Proline residue: L 256 - end of helix Processing helix chain 'L' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL L 274 " --> pdb=" O ALA L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU L 286 " --> pdb=" O GLU L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 294 removed outlier: 5.247A pdb=" N ALA L 294 " --> pdb=" O GLY L 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 291 through 294' Processing helix chain 'L' and resid 295 through 303 Processing helix chain 'L' and resid 305 through 310 Processing helix chain 'L' and resid 330 through 335 removed outlier: 3.636A pdb=" N LEU L 334 " --> pdb=" O LEU L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN L 342 " --> pdb=" O ARG L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP L 367 " --> pdb=" O LYS L 363 " (cutoff:3.500A) Processing helix chain 'L' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER L 373 " --> pdb=" O GLY L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER L 379 " --> pdb=" O LYS L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 397 Processing helix chain 'L' and resid 408 through 412 Processing helix chain 'L' and resid 413 through 424 Processing helix chain 'L' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS L 428 " --> pdb=" O GLY L 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 425 through 428' Processing helix chain 'L' and resid 429 through 437 Processing helix chain 'L' and resid 447 through 455 Processing helix chain 'L' and resid 459 through 477 Processing helix chain 'L' and resid 486 through 495 Processing helix chain 'L' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN L 500 " --> pdb=" O ARG L 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 497 through 500' Processing helix chain 'L' and resid 501 through 507 Processing helix chain 'L' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG L 517 " --> pdb=" O LEU L 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 526 removed outlier: 3.528A pdb=" N LEU L 523 " --> pdb=" O SER L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 546 Processing helix chain 'L' and resid 573 through 587 Processing helix chain 'L' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN L 609 " --> pdb=" O ASP L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 637 through 649 Processing helix chain 'L' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA L 674 " --> pdb=" O ASP L 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 675 " --> pdb=" O MET L 672 " (cutoff:3.500A) Processing helix chain 'L' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE L 698 " --> pdb=" O LYS L 694 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 81 Proline residue: M 70 - end of helix removed outlier: 3.889A pdb=" N GLN M 81 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 104 Processing helix chain 'M' and resid 109 through 123 Processing helix chain 'M' and resid 126 through 135 Processing helix chain 'M' and resid 137 through 152 Processing helix chain 'M' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY M 166 " --> pdb=" O ARG M 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL M 167 " --> pdb=" O ILE M 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE M 168 " --> pdb=" O GLY M 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 192 Processing helix chain 'M' and resid 195 through 205 Processing helix chain 'M' and resid 208 through 214 Processing helix chain 'M' and resid 215 through 217 No H-bonds generated for 'chain 'M' and resid 215 through 217' Processing helix chain 'M' and resid 219 through 238 removed outlier: 4.520A pdb=" N GLY M 238 " --> pdb=" O ALA M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 248 Processing helix chain 'M' and resid 250 through 259 Proline residue: M 256 - end of helix Processing helix chain 'M' and resid 263 through 278 removed outlier: 3.881A pdb=" N ARG M 267 " --> pdb=" O ASP M 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL M 274 " --> pdb=" O ALA M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 290 removed outlier: 4.034A pdb=" N ARG M 285 " --> pdb=" O LYS M 281 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU M 286 " --> pdb=" O GLU M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA M 294 " --> pdb=" O GLY M 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 291 through 294' Processing helix chain 'M' and resid 295 through 303 Processing helix chain 'M' and resid 305 through 310 Processing helix chain 'M' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU M 334 " --> pdb=" O LEU M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN M 342 " --> pdb=" O ARG M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP M 367 " --> pdb=" O LYS M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER M 373 " --> pdb=" O GLY M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER M 379 " --> pdb=" O LYS M 375 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 397 Processing helix chain 'M' and resid 408 through 412 Processing helix chain 'M' and resid 413 through 424 Processing helix chain 'M' and resid 425 through 428 removed outlier: 4.903A pdb=" N LYS M 428 " --> pdb=" O GLY M 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 425 through 428' Processing helix chain 'M' and resid 429 through 437 Processing helix chain 'M' and resid 447 through 455 Processing helix chain 'M' and resid 459 through 477 Processing helix chain 'M' and resid 486 through 495 Processing helix chain 'M' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN M 500 " --> pdb=" O ARG M 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 497 through 500' Processing helix chain 'M' and resid 501 through 507 Processing helix chain 'M' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG M 517 " --> pdb=" O LEU M 514 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU M 523 " --> pdb=" O SER M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 531 through 546 Processing helix chain 'M' and resid 573 through 587 Processing helix chain 'M' and resid 605 through 614 removed outlier: 3.906A pdb=" N GLN M 609 " --> pdb=" O ASP M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 637 through 649 Processing helix chain 'M' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA M 674 " --> pdb=" O ASP M 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL M 675 " --> pdb=" O MET M 672 " (cutoff:3.500A) Processing helix chain 'M' and resid 687 through 698 removed outlier: 3.645A pdb=" N PHE M 698 " --> pdb=" O LYS M 694 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 81 Proline residue: N 70 - end of helix removed outlier: 3.889A pdb=" N GLN N 81 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 123 Processing helix chain 'N' and resid 126 through 135 Processing helix chain 'N' and resid 137 through 152 Processing helix chain 'N' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU N 165 " --> pdb=" O ALA N 161 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY N 166 " --> pdb=" O ARG N 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE N 168 " --> pdb=" O GLY N 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 192 Processing helix chain 'N' and resid 195 through 205 Processing helix chain 'N' and resid 208 through 214 Processing helix chain 'N' and resid 215 through 217 No H-bonds generated for 'chain 'N' and resid 215 through 217' Processing helix chain 'N' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY N 238 " --> pdb=" O ALA N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 248 Processing helix chain 'N' and resid 250 through 259 Proline residue: N 256 - end of helix Processing helix chain 'N' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG N 267 " --> pdb=" O ASP N 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL N 274 " --> pdb=" O ALA N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG N 285 " --> pdb=" O LYS N 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU N 286 " --> pdb=" O GLU N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA N 294 " --> pdb=" O GLY N 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 291 through 294' Processing helix chain 'N' and resid 295 through 303 Processing helix chain 'N' and resid 305 through 310 Processing helix chain 'N' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU N 334 " --> pdb=" O LEU N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN N 342 " --> pdb=" O ARG N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP N 367 " --> pdb=" O LYS N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER N 373 " --> pdb=" O GLY N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER N 379 " --> pdb=" O LYS N 375 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 397 Processing helix chain 'N' and resid 408 through 412 Processing helix chain 'N' and resid 413 through 424 Processing helix chain 'N' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS N 428 " --> pdb=" O GLY N 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 425 through 428' Processing helix chain 'N' and resid 429 through 437 Processing helix chain 'N' and resid 447 through 455 Processing helix chain 'N' and resid 459 through 477 Processing helix chain 'N' and resid 486 through 495 Processing helix chain 'N' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN N 500 " --> pdb=" O ARG N 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 497 through 500' Processing helix chain 'N' and resid 501 through 507 Processing helix chain 'N' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG N 517 " --> pdb=" O LEU N 514 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU N 523 " --> pdb=" O SER N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 531 through 546 Processing helix chain 'N' and resid 573 through 587 Processing helix chain 'N' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN N 609 " --> pdb=" O ASP N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 637 through 649 Processing helix chain 'N' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA N 674 " --> pdb=" O ASP N 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL N 675 " --> pdb=" O MET N 672 " (cutoff:3.500A) Processing helix chain 'N' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE N 698 " --> pdb=" O LYS N 694 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 81 Proline residue: O 70 - end of helix removed outlier: 3.889A pdb=" N GLN O 81 " --> pdb=" O SER O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 104 Processing helix chain 'O' and resid 109 through 123 Processing helix chain 'O' and resid 126 through 135 Processing helix chain 'O' and resid 137 through 152 Processing helix chain 'O' and resid 153 through 173 removed outlier: 3.654A pdb=" N LEU O 165 " --> pdb=" O ALA O 161 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL O 167 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE O 168 " --> pdb=" O GLY O 164 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS O 173 " --> pdb=" O LEU O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 192 Processing helix chain 'O' and resid 195 through 205 Processing helix chain 'O' and resid 208 through 214 Processing helix chain 'O' and resid 215 through 217 No H-bonds generated for 'chain 'O' and resid 215 through 217' Processing helix chain 'O' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY O 238 " --> pdb=" O ALA O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 248 Processing helix chain 'O' and resid 250 through 259 Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 263 through 278 removed outlier: 3.880A pdb=" N ARG O 267 " --> pdb=" O ASP O 263 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL O 274 " --> pdb=" O ALA O 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG O 285 " --> pdb=" O LYS O 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU O 286 " --> pdb=" O GLU O 282 " (cutoff:3.500A) Processing helix chain 'O' and resid 291 through 294 removed outlier: 5.249A pdb=" N ALA O 294 " --> pdb=" O GLY O 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 291 through 294' Processing helix chain 'O' and resid 295 through 303 Processing helix chain 'O' and resid 305 through 310 Processing helix chain 'O' and resid 330 through 335 removed outlier: 3.638A pdb=" N LEU O 334 " --> pdb=" O LEU O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 360 removed outlier: 3.566A pdb=" N GLN O 342 " --> pdb=" O ARG O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 369 removed outlier: 3.564A pdb=" N ASP O 367 " --> pdb=" O LYS O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER O 373 " --> pdb=" O GLY O 369 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 380 removed outlier: 3.636A pdb=" N SER O 379 " --> pdb=" O LYS O 375 " (cutoff:3.500A) Processing helix chain 'O' and resid 383 through 397 Processing helix chain 'O' and resid 408 through 412 Processing helix chain 'O' and resid 413 through 424 Processing helix chain 'O' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS O 428 " --> pdb=" O GLY O 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 425 through 428' Processing helix chain 'O' and resid 429 through 437 Processing helix chain 'O' and resid 447 through 455 Processing helix chain 'O' and resid 459 through 477 Processing helix chain 'O' and resid 486 through 495 Processing helix chain 'O' and resid 497 through 500 removed outlier: 3.931A pdb=" N GLN O 500 " --> pdb=" O ARG O 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 497 through 500' Processing helix chain 'O' and resid 501 through 507 Processing helix chain 'O' and resid 514 through 518 removed outlier: 3.613A pdb=" N ARG O 517 " --> pdb=" O LEU O 514 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU O 523 " --> pdb=" O SER O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 531 through 546 Processing helix chain 'O' and resid 573 through 587 Processing helix chain 'O' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN O 609 " --> pdb=" O ASP O 605 " (cutoff:3.500A) Processing helix chain 'O' and resid 637 through 649 Processing helix chain 'O' and resid 669 through 678 removed outlier: 5.156A pdb=" N ALA O 674 " --> pdb=" O ASP O 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL O 675 " --> pdb=" O MET O 672 " (cutoff:3.500A) Processing helix chain 'O' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE O 698 " --> pdb=" O LYS O 694 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 81 Proline residue: P 70 - end of helix removed outlier: 3.889A pdb=" N GLN P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 104 Processing helix chain 'P' and resid 109 through 123 Processing helix chain 'P' and resid 126 through 135 Processing helix chain 'P' and resid 137 through 152 Processing helix chain 'P' and resid 153 through 173 removed outlier: 3.655A pdb=" N LEU P 165 " --> pdb=" O ALA P 161 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLY P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL P 167 " --> pdb=" O ILE P 163 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE P 168 " --> pdb=" O GLY P 164 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS P 173 " --> pdb=" O LEU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 192 Processing helix chain 'P' and resid 195 through 205 Processing helix chain 'P' and resid 208 through 214 Processing helix chain 'P' and resid 215 through 217 No H-bonds generated for 'chain 'P' and resid 215 through 217' Processing helix chain 'P' and resid 219 through 238 removed outlier: 4.521A pdb=" N GLY P 238 " --> pdb=" O ALA P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 250 through 259 Proline residue: P 256 - end of helix Processing helix chain 'P' and resid 263 through 278 removed outlier: 3.879A pdb=" N ARG P 267 " --> pdb=" O ASP P 263 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL P 274 " --> pdb=" O ALA P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 290 removed outlier: 4.033A pdb=" N ARG P 285 " --> pdb=" O LYS P 281 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU P 286 " --> pdb=" O GLU P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 291 through 294 removed outlier: 5.248A pdb=" N ALA P 294 " --> pdb=" O GLY P 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 291 through 294' Processing helix chain 'P' and resid 295 through 303 Processing helix chain 'P' and resid 305 through 310 Processing helix chain 'P' and resid 330 through 335 removed outlier: 3.637A pdb=" N LEU P 334 " --> pdb=" O LEU P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 360 removed outlier: 3.567A pdb=" N GLN P 342 " --> pdb=" O ARG P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 369 removed outlier: 3.565A pdb=" N ASP P 367 " --> pdb=" O LYS P 363 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 375 removed outlier: 4.032A pdb=" N SER P 373 " --> pdb=" O GLY P 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 380 removed outlier: 3.637A pdb=" N SER P 379 " --> pdb=" O LYS P 375 " (cutoff:3.500A) Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 408 through 412 Processing helix chain 'P' and resid 413 through 424 Processing helix chain 'P' and resid 425 through 428 removed outlier: 4.902A pdb=" N LYS P 428 " --> pdb=" O GLY P 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 425 through 428' Processing helix chain 'P' and resid 429 through 437 Processing helix chain 'P' and resid 447 through 455 Processing helix chain 'P' and resid 459 through 477 Processing helix chain 'P' and resid 486 through 495 Processing helix chain 'P' and resid 497 through 500 removed outlier: 3.932A pdb=" N GLN P 500 " --> pdb=" O ARG P 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 497 through 500' Processing helix chain 'P' and resid 501 through 507 Processing helix chain 'P' and resid 514 through 518 removed outlier: 3.612A pdb=" N ARG P 517 " --> pdb=" O LEU P 514 " (cutoff:3.500A) Processing helix chain 'P' and resid 519 through 526 removed outlier: 3.529A pdb=" N LEU P 523 " --> pdb=" O SER P 519 " (cutoff:3.500A) Processing helix chain 'P' and resid 531 through 546 Processing helix chain 'P' and resid 573 through 587 Processing helix chain 'P' and resid 605 through 614 removed outlier: 3.907A pdb=" N GLN P 609 " --> pdb=" O ASP P 605 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 649 Processing helix chain 'P' and resid 669 through 678 removed outlier: 5.155A pdb=" N ALA P 674 " --> pdb=" O ASP P 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL P 675 " --> pdb=" O MET P 672 " (cutoff:3.500A) Processing helix chain 'P' and resid 687 through 698 removed outlier: 3.644A pdb=" N PHE P 698 " --> pdb=" O LYS P 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 591 through 592 removed outlier: 6.699A pdb=" N VAL A 564 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE A 565 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 620 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER A 567 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL C 564 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE C 565 " --> pdb=" O VAL C 618 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL C 620 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER C 567 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL D 564 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE D 565 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL D 620 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER D 567 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 591 through 592 removed outlier: 6.699A pdb=" N VAL E 564 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE E 565 " --> pdb=" O VAL E 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL E 620 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER E 567 " --> pdb=" O VAL E 620 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL F 564 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE F 565 " --> pdb=" O VAL F 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL F 620 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER F 567 " --> pdb=" O VAL F 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 591 through 592 removed outlier: 6.697A pdb=" N VAL G 564 " --> pdb=" O PHE G 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE G 565 " --> pdb=" O VAL G 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL G 620 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER G 567 " --> pdb=" O VAL G 620 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 591 through 592 removed outlier: 6.699A pdb=" N VAL H 564 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE H 565 " --> pdb=" O VAL H 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL H 620 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER H 567 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL I 564 " --> pdb=" O PHE I 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE I 565 " --> pdb=" O VAL I 618 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL I 620 " --> pdb=" O PHE I 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER I 567 " --> pdb=" O VAL I 620 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 591 through 592 removed outlier: 6.697A pdb=" N VAL J 564 " --> pdb=" O PHE J 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE J 565 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL J 620 " --> pdb=" O PHE J 565 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER J 567 " --> pdb=" O VAL J 620 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL K 564 " --> pdb=" O PHE K 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE K 565 " --> pdb=" O VAL K 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL K 620 " --> pdb=" O PHE K 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER K 567 " --> pdb=" O VAL K 620 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL L 564 " --> pdb=" O PHE L 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE L 565 " --> pdb=" O VAL L 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL L 620 " --> pdb=" O PHE L 565 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER L 567 " --> pdb=" O VAL L 620 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL M 564 " --> pdb=" O PHE M 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE M 565 " --> pdb=" O VAL M 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL M 620 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER M 567 " --> pdb=" O VAL M 620 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 591 through 592 removed outlier: 6.699A pdb=" N VAL N 564 " --> pdb=" O PHE N 592 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE N 565 " --> pdb=" O VAL N 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL N 620 " --> pdb=" O PHE N 565 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER N 567 " --> pdb=" O VAL N 620 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 591 through 592 removed outlier: 6.699A pdb=" N VAL O 564 " --> pdb=" O PHE O 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE O 565 " --> pdb=" O VAL O 618 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL O 620 " --> pdb=" O PHE O 565 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER O 567 " --> pdb=" O VAL O 620 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 591 through 592 removed outlier: 6.698A pdb=" N VAL P 564 " --> pdb=" O PHE P 592 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE P 565 " --> pdb=" O VAL P 618 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL P 620 " --> pdb=" O PHE P 565 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER P 567 " --> pdb=" O VAL P 620 " (cutoff:3.500A) 4496 hydrogen bonds defined for protein. 13056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.64 Time building geometry restraints manager: 30.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 26892 1.34 - 1.46: 12172 1.46 - 1.57: 40632 1.57 - 1.69: 0 1.69 - 1.81: 496 Bond restraints: 80192 Sorted by residual: bond pdb=" C ARG C 517 " pdb=" N VAL C 518 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.79e+00 bond pdb=" C ARG M 517 " pdb=" N VAL M 518 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.78e+00 bond pdb=" C ARG P 517 " pdb=" N VAL P 518 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.75e+00 bond pdb=" C ARG N 517 " pdb=" N VAL N 518 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.69e+00 bond pdb=" C ARG H 517 " pdb=" N VAL H 518 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.60e+00 ... (remaining 80187 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.99: 1958 106.99 - 113.77: 47010 113.77 - 120.55: 32360 120.55 - 127.33: 26283 127.33 - 134.11: 805 Bond angle restraints: 108416 Sorted by residual: angle pdb=" N GLY C 207 " pdb=" CA GLY C 207 " pdb=" C GLY C 207 " ideal model delta sigma weight residual 115.32 109.40 5.92 1.31e+00 5.83e-01 2.04e+01 angle pdb=" N GLY L 207 " pdb=" CA GLY L 207 " pdb=" C GLY L 207 " ideal model delta sigma weight residual 115.32 109.41 5.91 1.31e+00 5.83e-01 2.04e+01 angle pdb=" N GLY B 207 " pdb=" CA GLY B 207 " pdb=" C GLY B 207 " ideal model delta sigma weight residual 115.32 109.41 5.91 1.31e+00 5.83e-01 2.04e+01 angle pdb=" N GLY E 207 " pdb=" CA GLY E 207 " pdb=" C GLY E 207 " ideal model delta sigma weight residual 115.32 109.41 5.91 1.31e+00 5.83e-01 2.03e+01 angle pdb=" N GLY J 207 " pdb=" CA GLY J 207 " pdb=" C GLY J 207 " ideal model delta sigma weight residual 115.32 109.42 5.90 1.31e+00 5.83e-01 2.03e+01 ... (remaining 108411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 43577 17.78 - 35.56: 4287 35.56 - 53.34: 776 53.34 - 71.12: 176 71.12 - 88.90: 64 Dihedral angle restraints: 48880 sinusoidal: 19904 harmonic: 28976 Sorted by residual: dihedral pdb=" CA TRP E 253 " pdb=" C TRP E 253 " pdb=" N LEU E 254 " pdb=" CA LEU E 254 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP H 253 " pdb=" C TRP H 253 " pdb=" N LEU H 254 " pdb=" CA LEU H 254 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TRP G 253 " pdb=" C TRP G 253 " pdb=" N LEU G 254 " pdb=" CA LEU G 254 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 48877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 6696 0.030 - 0.059: 3677 0.059 - 0.089: 1581 0.089 - 0.118: 382 0.118 - 0.148: 80 Chirality restraints: 12416 Sorted by residual: chirality pdb=" CA GLU E 94 " pdb=" N GLU E 94 " pdb=" C GLU E 94 " pdb=" CB GLU E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA GLU O 94 " pdb=" N GLU O 94 " pdb=" C GLU O 94 " pdb=" CB GLU O 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA GLU A 94 " pdb=" N GLU A 94 " pdb=" C GLU A 94 " pdb=" CB GLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 12413 not shown) Planarity restraints: 14064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR O 561 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO O 562 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO O 562 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO O 562 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 561 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 562 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 562 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 562 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 561 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO J 562 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 562 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 562 " -0.023 5.00e-02 4.00e+02 ... (remaining 14061 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1817 2.63 - 3.20: 84997 3.20 - 3.76: 131405 3.76 - 4.33: 186336 4.33 - 4.90: 274331 Nonbonded interactions: 678886 Sorted by model distance: nonbonded pdb=" NH2 ARG C 465 " pdb=" OE1 GLN D 437 " model vdw 2.062 2.520 nonbonded pdb=" OE1 GLN I 437 " pdb=" NH2 ARG P 465 " model vdw 2.073 2.520 nonbonded pdb=" NH2 ARG N 465 " pdb=" OE1 GLN O 437 " model vdw 2.111 2.520 nonbonded pdb=" O ARG M 468 " pdb=" OG1 THR M 471 " model vdw 2.139 2.440 nonbonded pdb=" O ARG O 468 " pdb=" OG1 THR O 471 " model vdw 2.139 2.440 ... (remaining 678881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 18.170 Check model and map are aligned: 0.850 Set scattering table: 0.500 Process input model: 166.290 Find NCS groups from input model: 4.230 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 80192 Z= 0.380 Angle : 0.835 7.119 108416 Z= 0.494 Chirality : 0.042 0.148 12416 Planarity : 0.004 0.041 14064 Dihedral : 14.917 88.904 30096 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer Outliers : 1.71 % 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: -4.81 (0.06), residues: 10000 helix: -3.09 (0.04), residues: 6896 sheet: -3.12 (0.22), residues: 304 loop : -2.77 (0.10), residues: 2800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1606 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1462 time to evaluate : 6.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 41 residues processed: 1573 average time/residue: 0.7913 time to fit residues: 2058.4572 Evaluate side-chains 911 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 870 time to evaluate : 6.735 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5570 time to fit residues: 53.4457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 851 optimal weight: 6.9990 chunk 764 optimal weight: 7.9990 chunk 423 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 515 optimal weight: 4.9990 chunk 408 optimal weight: 6.9990 chunk 790 optimal weight: 8.9990 chunk 305 optimal weight: 0.0370 chunk 480 optimal weight: 5.9990 chunk 588 optimal weight: 6.9990 chunk 915 optimal weight: 6.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 422 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 ASN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 HIS ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN D 328 GLN D 422 GLN ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 679 ASN E 150 GLN ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 547 HIS E 679 ASN ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 547 HIS ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN G 150 GLN G 337 ASN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 HIS G 679 ASN H 232 ASN H 422 GLN ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 547 HIS ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 679 ASN I 337 ASN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 547 HIS ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 679 ASN ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 547 HIS ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 679 ASN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 HIS ** K 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 679 ASN L 328 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 547 HIS ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 679 ASN ** M 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 547 HIS ** M 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 679 ASN N 150 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 547 HIS N 679 ASN ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 547 HIS ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 ASN P 337 ASN ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 547 HIS ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 679 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 80192 Z= 0.283 Angle : 0.668 8.650 108416 Z= 0.341 Chirality : 0.042 0.181 12416 Planarity : 0.005 0.145 14064 Dihedral : 5.107 18.430 10960 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.08), residues: 10000 helix: -1.32 (0.06), residues: 7040 sheet: -2.39 (0.22), residues: 304 loop : -1.87 (0.11), residues: 2656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1309 time to evaluate : 6.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 6 residues processed: 1327 average time/residue: 0.7406 time to fit residues: 1668.2238 Evaluate side-chains 878 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 872 time to evaluate : 6.719 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6408 time to fit residues: 16.2035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 508 optimal weight: 5.9990 chunk 284 optimal weight: 6.9990 chunk 761 optimal weight: 20.0000 chunk 623 optimal weight: 8.9990 chunk 252 optimal weight: 40.0000 chunk 917 optimal weight: 0.9990 chunk 990 optimal weight: 3.9990 chunk 816 optimal weight: 0.9980 chunk 909 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 735 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN B 328 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN D 328 GLN ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 679 ASN F 328 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN G 150 GLN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 679 ASN H 97 GLN H 328 GLN ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 328 GLN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 679 ASN J 97 GLN J 328 GLN ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 GLN L 328 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 ASN ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 ASN ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 ASN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 80192 Z= 0.216 Angle : 0.590 8.646 108416 Z= 0.303 Chirality : 0.040 0.206 12416 Planarity : 0.005 0.078 14064 Dihedral : 4.704 22.378 10960 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.07 % 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: -1.05 (0.08), residues: 10000 helix: -0.26 (0.06), residues: 6960 sheet: -1.69 (0.23), residues: 304 loop : -1.38 (0.12), residues: 2736 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1359 time to evaluate : 6.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 1365 average time/residue: 0.7450 time to fit residues: 1727.9367 Evaluate side-chains 941 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 941 time to evaluate : 6.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.2954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 906 optimal weight: 5.9990 chunk 689 optimal weight: 6.9990 chunk 475 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 615 optimal weight: 10.0000 chunk 920 optimal weight: 2.9990 chunk 974 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 872 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN G 150 GLN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 587 HIS ** H 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN ** I 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 GLN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 679 ASN ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 GLN ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN ** K 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 GLN K 328 GLN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 232 ASN ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 ASN O 232 ASN O 328 GLN ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 ASN P 328 GLN P 337 ASN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 80192 Z= 0.298 Angle : 0.639 9.222 108416 Z= 0.329 Chirality : 0.042 0.220 12416 Planarity : 0.005 0.062 14064 Dihedral : 4.790 19.819 10960 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer Outliers : 0.05 % 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: -0.81 (0.08), residues: 10000 helix: -0.08 (0.06), residues: 6944 sheet: -1.78 (0.23), residues: 304 loop : -1.25 (0.12), residues: 2752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1216 time to evaluate : 6.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 1220 average time/residue: 0.7712 time to fit residues: 1605.4952 Evaluate side-chains 876 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 876 time to evaluate : 6.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.1311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 811 optimal weight: 8.9990 chunk 553 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 725 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 831 optimal weight: 8.9990 chunk 673 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 497 optimal weight: 20.0000 chunk 874 optimal weight: 0.9990 chunk 245 optimal weight: 30.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 328 GLN ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 GLN G 150 GLN G 328 GLN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 522 GLN ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 328 GLN N 150 GLN N 170 ASN N 328 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 80192 Z= 0.290 Angle : 0.639 7.729 108416 Z= 0.328 Chirality : 0.042 0.230 12416 Planarity : 0.005 0.060 14064 Dihedral : 4.772 22.775 10960 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer Outliers : 0.01 % 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: -0.61 (0.08), residues: 10000 helix: 0.03 (0.06), residues: 6944 sheet: -1.71 (0.24), residues: 304 loop : -1.07 (0.12), residues: 2752 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1232 time to evaluate : 6.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1233 average time/residue: 0.7768 time to fit residues: 1638.6842 Evaluate side-chains 873 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 873 time to evaluate : 7.574 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.3268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 327 optimal weight: 10.0000 chunk 877 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 572 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 975 optimal weight: 8.9990 chunk 809 optimal weight: 10.0000 chunk 451 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 512 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 80192 Z= 0.237 Angle : 0.595 7.976 108416 Z= 0.304 Chirality : 0.040 0.208 12416 Planarity : 0.004 0.053 14064 Dihedral : 4.630 20.654 10960 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.01 % 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: -0.26 (0.09), residues: 10000 helix: 0.28 (0.06), residues: 6960 sheet: -1.67 (0.24), residues: 304 loop : -0.90 (0.13), residues: 2736 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1238 time to evaluate : 6.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 1239 average time/residue: 0.7500 time to fit residues: 1584.0827 Evaluate side-chains 881 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 881 time to evaluate : 6.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 940 optimal weight: 40.0000 chunk 109 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 712 optimal weight: 6.9990 chunk 551 optimal weight: 0.8980 chunk 820 optimal weight: 5.9990 chunk 544 optimal weight: 1.9990 chunk 971 optimal weight: 0.2980 chunk 608 optimal weight: 2.9990 chunk 592 optimal weight: 6.9990 chunk 448 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 383 ASN ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 534 HIS ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 437 GLN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 437 GLN ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 80192 Z= 0.197 Angle : 0.577 9.492 108416 Z= 0.293 Chirality : 0.039 0.236 12416 Planarity : 0.005 0.177 14064 Dihedral : 4.442 21.617 10960 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 10000 helix: 0.52 (0.06), residues: 6848 sheet: -1.62 (0.24), residues: 304 loop : -0.59 (0.13), residues: 2848 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1271 time to evaluate : 6.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1273 average time/residue: 0.7589 time to fit residues: 1639.7969 Evaluate side-chains 895 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 895 time to evaluate : 6.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.4747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 601 optimal weight: 0.0970 chunk 387 optimal weight: 9.9990 chunk 580 optimal weight: 0.9980 chunk 292 optimal weight: 4.9990 chunk 190 optimal weight: 0.4980 chunk 188 optimal weight: 9.9990 chunk 617 optimal weight: 4.9990 chunk 661 optimal weight: 3.9990 chunk 480 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 763 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN E 383 ASN F 437 GLN ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 170 ASN J 239 GLN ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 583 HIS ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 80192 Z= 0.180 Angle : 0.575 10.819 108416 Z= 0.291 Chirality : 0.039 0.254 12416 Planarity : 0.004 0.068 14064 Dihedral : 4.296 18.407 10960 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 10000 helix: 0.66 (0.07), residues: 6752 sheet: -1.48 (0.25), residues: 304 loop : -0.41 (0.13), residues: 2944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1309 time to evaluate : 6.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1311 average time/residue: 0.7678 time to fit residues: 1706.7491 Evaluate side-chains 900 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 900 time to evaluate : 6.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.4824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 883 optimal weight: 7.9990 chunk 930 optimal weight: 3.9990 chunk 849 optimal weight: 5.9990 chunk 905 optimal weight: 0.9990 chunk 544 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 710 optimal weight: 6.9990 chunk 277 optimal weight: 0.0270 chunk 818 optimal weight: 10.0000 chunk 856 optimal weight: 3.9990 chunk 902 optimal weight: 7.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN E 150 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 80192 Z= 0.225 Angle : 0.610 11.261 108416 Z= 0.308 Chirality : 0.040 0.216 12416 Planarity : 0.005 0.162 14064 Dihedral : 4.351 20.512 10960 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 10000 helix: 0.50 (0.06), residues: 6848 sheet: -1.41 (0.26), residues: 304 loop : -0.41 (0.13), residues: 2848 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1227 time to evaluate : 6.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1227 average time/residue: 0.7797 time to fit residues: 1613.0456 Evaluate side-chains 886 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 886 time to evaluate : 6.847 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.2621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 594 optimal weight: 5.9990 chunk 957 optimal weight: 9.9990 chunk 584 optimal weight: 5.9990 chunk 454 optimal weight: 7.9990 chunk 665 optimal weight: 2.9990 chunk 1004 optimal weight: 20.0000 chunk 924 optimal weight: 0.3980 chunk 799 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 617 optimal weight: 8.9990 chunk 490 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN B 150 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS G 150 GLN ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 GLN ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 80192 Z= 0.234 Angle : 0.618 9.431 108416 Z= 0.314 Chirality : 0.041 0.205 12416 Planarity : 0.005 0.112 14064 Dihedral : 4.399 21.378 10960 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.09), residues: 10000 helix: 0.43 (0.06), residues: 6880 sheet: -1.48 (0.26), residues: 304 loop : -0.42 (0.13), residues: 2816 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20000 Ramachandran restraints generated. 10000 Oldfield, 0 Emsley, 10000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1185 time to evaluate : 7.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1185 average time/residue: 0.7947 time to fit residues: 1585.5795 Evaluate side-chains 855 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 6.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 9.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 635 optimal weight: 9.9990 chunk 851 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 737 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 800 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 822 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 685 HIS ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 609 GLN ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 685 HIS ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 452 GLN ** L 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.122930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091666 restraints weight = 263941.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094310 restraints weight = 154945.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095995 restraints weight = 108607.853| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 80192 Z= 0.263 Angle : 0.647 10.495 108416 Z= 0.329 Chirality : 0.042 0.209 12416 Planarity : 0.005 0.121 14064 Dihedral : 4.503 21.751 10960 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.01 % 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: -0.09 (0.09), residues: 10000 helix: 0.35 (0.06), residues: 6848 sheet: -1.58 (0.26), residues: 304 loop : -0.59 (0.12), residues: 2848 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22492.35 seconds wall clock time: 394 minutes 6.28 seconds (23646.28 seconds total)