Starting phenix.real_space_refine on Sun Mar 17 12:36:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/03_2024/7qg0_13951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/03_2024/7qg0_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_13951/03_2024/7qg0_13951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/03_2024/7qg0_13951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/03_2024/7qg0_13951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg0_13951/03_2024/7qg0_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: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 29.86, per 1000 atoms: 0.38 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: 24.85 Conformation dependent library (CDL) restraints added in 10.1 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: 6.87 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: 38.43 Time building geometry restraints manager: 27.16 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: 3.830 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: 0.100 Extract box with map and model: 16.510 Check model and map are aligned: 0.840 Set scattering table: 0.600 Process input model: 168.850 Find NCS groups from input model: 4.300 Set up NCS constraints: 0.580 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: 0.030 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.110 ------------------------------------------------------------------------------- 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 % Allowed : 6.86 % Favored : 91.43 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 638 HIS 0.006 0.002 HIS B 516 PHE 0.014 0.002 PHE L 308 TYR 0.007 0.002 TYR K 479 ARG 0.004 0.001 ARG I 463 *********************** 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 : 6.802 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: A 94 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8952 (pp20) REVERT: A 98 LEU cc_start: 0.9122 (mt) cc_final: 0.8908 (mt) REVERT: A 193 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8997 (mtmm) REVERT: A 325 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8149 (p0) REVERT: A 420 TRP cc_start: 0.8672 (t60) cc_final: 0.8252 (t60) REVERT: A 442 LEU cc_start: 0.9440 (mt) cc_final: 0.9123 (tp) REVERT: A 511 ASP cc_start: 0.8770 (p0) cc_final: 0.8483 (p0) REVERT: B 94 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8914 (pp20) REVERT: B 159 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7792 (mmm160) REVERT: B 325 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8135 (p0) REVERT: B 442 LEU cc_start: 0.9440 (mt) cc_final: 0.9196 (tp) REVERT: B 511 ASP cc_start: 0.8690 (p0) cc_final: 0.8345 (p0) REVERT: B 693 GLU cc_start: 0.9462 (pt0) cc_final: 0.9191 (tp30) REVERT: C 94 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9039 (pp20) REVERT: C 325 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8159 (p0) REVERT: C 511 ASP cc_start: 0.8784 (p0) cc_final: 0.8477 (p0) REVERT: C 667 VAL cc_start: 0.6626 (OUTLIER) cc_final: 0.6419 (p) REVERT: D 94 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8937 (pp20) REVERT: D 159 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.7821 (mmm160) REVERT: D 162 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8596 (mtm180) REVERT: D 325 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8093 (p0) REVERT: D 442 LEU cc_start: 0.9415 (mt) cc_final: 0.9139 (tp) REVERT: D 511 ASP cc_start: 0.8717 (p0) cc_final: 0.8347 (p0) REVERT: E 62 GLN cc_start: 0.8210 (mt0) cc_final: 0.7855 (tp40) REVERT: E 66 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8383 (mt-10) REVERT: E 325 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8233 (p0) REVERT: E 511 ASP cc_start: 0.8781 (p0) cc_final: 0.8332 (p0) REVERT: E 667 VAL cc_start: 0.6735 (OUTLIER) cc_final: 0.6453 (p) REVERT: E 683 TRP cc_start: 0.8451 (t-100) cc_final: 0.8137 (t-100) REVERT: F 159 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.7847 (mmm160) REVERT: F 325 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8097 (p0) REVERT: F 437 GLN cc_start: 0.9000 (mp10) cc_final: 0.8737 (mp10) REVERT: F 511 ASP cc_start: 0.8691 (p0) cc_final: 0.8314 (p0) REVERT: G 325 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8171 (p0) REVERT: G 511 ASP cc_start: 0.8855 (p0) cc_final: 0.8364 (p0) REVERT: G 565 PHE cc_start: 0.8361 (t80) cc_final: 0.7763 (t80) REVERT: H 159 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8109 (mmm160) REVERT: H 325 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8220 (p0) REVERT: H 511 ASP cc_start: 0.8723 (p0) cc_final: 0.8384 (p0) REVERT: H 693 GLU cc_start: 0.9467 (pt0) cc_final: 0.9146 (tp30) REVERT: I 94 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8890 (pp20) REVERT: I 159 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7863 (mmm160) REVERT: I 325 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8087 (p0) REVERT: I 511 ASP cc_start: 0.8760 (p0) cc_final: 0.8426 (p0) REVERT: J 94 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8953 (pp20) REVERT: J 98 LEU cc_start: 0.9146 (mt) cc_final: 0.8944 (mt) REVERT: J 193 LYS cc_start: 0.9236 (ttmt) cc_final: 0.9012 (mtmm) REVERT: J 325 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8190 (p0) REVERT: J 381 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8576 (p) REVERT: J 420 TRP cc_start: 0.8690 (t60) cc_final: 0.8226 (t60) REVERT: J 442 LEU cc_start: 0.9449 (mt) cc_final: 0.9160 (tp) REVERT: J 511 ASP cc_start: 0.8761 (p0) cc_final: 0.8472 (p0) REVERT: J 667 VAL cc_start: 0.6397 (OUTLIER) cc_final: 0.6171 (p) REVERT: K 94 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9031 (pp20) REVERT: K 159 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8066 (mmm160) REVERT: K 162 ARG cc_start: 0.8863 (mtm180) cc_final: 0.8622 (mtm180) REVERT: K 257 LEU cc_start: 0.9249 (mm) cc_final: 0.8882 (mm) REVERT: K 325 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8011 (p0) REVERT: K 381 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (t) REVERT: K 511 ASP cc_start: 0.8830 (p0) cc_final: 0.8502 (p0) REVERT: K 693 GLU cc_start: 0.9394 (pt0) cc_final: 0.9097 (tp30) REVERT: L 94 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9042 (pp20) REVERT: L 325 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8130 (p0) REVERT: L 381 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8597 (p) REVERT: L 420 TRP cc_start: 0.8697 (t60) cc_final: 0.8220 (t60) REVERT: L 511 ASP cc_start: 0.8825 (p0) cc_final: 0.8526 (p0) REVERT: L 667 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.6457 (p) REVERT: M 62 GLN cc_start: 0.8257 (mt0) cc_final: 0.7956 (tt0) REVERT: M 66 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8514 (mt-10) REVERT: M 110 ARG cc_start: 0.5589 (ttt90) cc_final: 0.5301 (ttm-80) REVERT: M 157 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.7134 (mtt180) REVERT: M 420 TRP cc_start: 0.8452 (t60) cc_final: 0.8231 (t60) REVERT: M 511 ASP cc_start: 0.8763 (p0) cc_final: 0.8379 (p0) REVERT: M 693 GLU cc_start: 0.9392 (pt0) cc_final: 0.9103 (tp30) REVERT: N 62 GLN cc_start: 0.8230 (mt0) cc_final: 0.7730 (tp40) REVERT: N 193 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8944 (mtmm) REVERT: N 325 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8271 (p0) REVERT: N 511 ASP cc_start: 0.8853 (p0) cc_final: 0.8445 (p0) REVERT: N 693 GLU cc_start: 0.9347 (pt0) cc_final: 0.9114 (tp30) REVERT: O 159 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: O 325 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8128 (p0) REVERT: O 511 ASP cc_start: 0.8804 (p0) cc_final: 0.8432 (p0) REVERT: P 66 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8293 (mt-10) REVERT: P 94 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9023 (pp20) REVERT: P 98 LEU cc_start: 0.9063 (mt) cc_final: 0.8840 (mt) REVERT: P 159 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8225 (tpt170) REVERT: P 325 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8123 (p0) REVERT: P 381 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8627 (p) REVERT: P 420 TRP cc_start: 0.8641 (t60) cc_final: 0.8309 (t60) REVERT: P 511 ASP cc_start: 0.8789 (p0) cc_final: 0.8479 (p0) outliers start: 144 outliers final: 41 residues processed: 1573 average time/residue: 0.7892 time to fit residues: 2059.9892 Evaluate side-chains 965 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 901 time to evaluate : 6.865 ------------------------------------------------------------------------------- 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: 1.9990 chunk 260 optimal weight: 7.9990 chunk 515 optimal weight: 4.9990 chunk 408 optimal weight: 6.9990 chunk 790 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 480 optimal weight: 5.9990 chunk 588 optimal weight: 6.9990 chunk 915 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** 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 337 ASN ** 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 337 ASN ** 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 337 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 337 ASN ** 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 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: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 80192 Z= 0.318 Angle : 0.697 8.804 108416 Z= 0.357 Chirality : 0.043 0.178 12416 Planarity : 0.005 0.130 14064 Dihedral : 5.202 18.686 10960 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.27 % Allowed : 5.65 % Favored : 94.07 % 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: -2.61 (0.07), residues: 10000 helix: -1.44 (0.06), residues: 7024 sheet: -2.44 (0.22), residues: 304 loop : -1.92 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 638 HIS 0.004 0.001 HIS B 516 PHE 0.017 0.002 PHE D 426 TYR 0.016 0.002 TYR D 429 ARG 0.010 0.001 ARG D 465 *********************** 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 1291 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1268 time to evaluate : 6.718 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: A 94 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8853 (pp20) REVERT: A 193 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8987 (mtmm) REVERT: A 420 TRP cc_start: 0.8703 (t60) cc_final: 0.8401 (t60) REVERT: A 511 ASP cc_start: 0.8749 (p0) cc_final: 0.8518 (p0) REVERT: B 94 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8819 (pp20) REVERT: B 127 ASP cc_start: 0.8162 (p0) cc_final: 0.7933 (m-30) REVERT: B 150 GLN cc_start: 0.7892 (mm110) cc_final: 0.7565 (tp-100) REVERT: B 473 LEU cc_start: 0.9011 (tp) cc_final: 0.8700 (tp) REVERT: B 511 ASP cc_start: 0.8695 (p0) cc_final: 0.8451 (p0) REVERT: B 545 MET cc_start: 0.8702 (tpp) cc_final: 0.8456 (tpp) REVERT: C 66 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 159 ARG cc_start: 0.8712 (mmm160) cc_final: 0.8351 (mmm160) REVERT: C 193 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8978 (mtmm) REVERT: C 420 TRP cc_start: 0.8710 (t60) cc_final: 0.8322 (t60) REVERT: C 511 ASP cc_start: 0.8760 (p0) cc_final: 0.8488 (p0) REVERT: C 683 TRP cc_start: 0.8036 (t-100) cc_final: 0.7814 (t-100) REVERT: D 66 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8181 (mt-10) REVERT: D 94 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8924 (pp20) REVERT: D 150 GLN cc_start: 0.7961 (mm110) cc_final: 0.7573 (tp-100) REVERT: D 159 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7764 (mmm160) REVERT: D 162 ARG cc_start: 0.8815 (mtm180) cc_final: 0.8614 (mtm180) REVERT: D 420 TRP cc_start: 0.8771 (t60) cc_final: 0.8411 (t60) REVERT: D 511 ASP cc_start: 0.8695 (p0) cc_final: 0.8444 (p0) REVERT: D 545 MET cc_start: 0.8600 (tpp) cc_final: 0.8335 (tpp) REVERT: E 62 GLN cc_start: 0.8178 (mt0) cc_final: 0.7773 (tp40) REVERT: E 66 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 159 ARG cc_start: 0.8962 (tpt170) cc_final: 0.8482 (mmm160) REVERT: E 162 ARG cc_start: 0.8812 (mtm180) cc_final: 0.8594 (mtm180) REVERT: E 214 TRP cc_start: 0.8555 (m-10) cc_final: 0.8345 (m-10) REVERT: E 395 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7995 (ptt90) REVERT: E 511 ASP cc_start: 0.8759 (p0) cc_final: 0.8452 (p0) REVERT: E 565 PHE cc_start: 0.8370 (t80) cc_final: 0.7561 (t80) REVERT: E 682 LYS cc_start: 0.9271 (mttt) cc_final: 0.8920 (tptt) REVERT: E 683 TRP cc_start: 0.8529 (t-100) cc_final: 0.7846 (t-100) REVERT: F 127 ASP cc_start: 0.8213 (p0) cc_final: 0.7975 (m-30) REVERT: F 150 GLN cc_start: 0.7883 (mm110) cc_final: 0.7503 (tp-100) REVERT: F 193 LYS cc_start: 0.9167 (ttmt) cc_final: 0.8919 (mtmm) REVERT: F 257 LEU cc_start: 0.8915 (mm) cc_final: 0.8589 (mm) REVERT: F 511 ASP cc_start: 0.8702 (p0) cc_final: 0.8473 (p0) REVERT: F 545 MET cc_start: 0.8643 (tpp) cc_final: 0.8378 (tpp) REVERT: G 62 GLN cc_start: 0.8188 (mt0) cc_final: 0.7617 (tp40) REVERT: G 66 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8386 (mt-10) REVERT: G 97 GLN cc_start: 0.9378 (pt0) cc_final: 0.9128 (pp30) REVERT: G 98 LEU cc_start: 0.8961 (mt) cc_final: 0.8474 (mt) REVERT: G 268 LEU cc_start: 0.9149 (tp) cc_final: 0.8945 (tp) REVERT: G 395 ARG cc_start: 0.8344 (ptt90) cc_final: 0.8073 (ptt90) REVERT: G 565 PHE cc_start: 0.8451 (t80) cc_final: 0.7856 (t80) REVERT: G 683 TRP cc_start: 0.8370 (t-100) cc_final: 0.8005 (t-100) REVERT: H 150 GLN cc_start: 0.7799 (mm110) cc_final: 0.7408 (tp-100) REVERT: H 159 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7705 (mmm160) REVERT: H 420 TRP cc_start: 0.8742 (t60) cc_final: 0.8526 (t60) REVERT: H 473 LEU cc_start: 0.8995 (tp) cc_final: 0.8732 (tp) REVERT: H 511 ASP cc_start: 0.8737 (p0) cc_final: 0.8500 (p0) REVERT: H 545 MET cc_start: 0.8661 (tpp) cc_final: 0.8429 (tpp) REVERT: I 150 GLN cc_start: 0.7872 (mm110) cc_final: 0.7493 (tp-100) REVERT: I 437 GLN cc_start: 0.8971 (mp10) cc_final: 0.8576 (mp10) REVERT: I 511 ASP cc_start: 0.8686 (p0) cc_final: 0.8465 (p0) REVERT: I 545 MET cc_start: 0.8580 (tpp) cc_final: 0.8366 (tpp) REVERT: J 94 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8853 (pp20) REVERT: J 193 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8977 (mtmm) REVERT: J 420 TRP cc_start: 0.8688 (t60) cc_final: 0.8357 (t60) REVERT: J 511 ASP cc_start: 0.8768 (p0) cc_final: 0.8502 (p0) REVERT: K 66 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8378 (mt-10) REVERT: K 94 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8966 (pp20) REVERT: K 159 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7886 (mmm160) REVERT: K 162 ARG cc_start: 0.8822 (mtm180) cc_final: 0.8613 (mtm180) REVERT: K 293 LEU cc_start: 0.8691 (mt) cc_final: 0.8489 (mt) REVERT: K 420 TRP cc_start: 0.8632 (t60) cc_final: 0.8232 (t60) REVERT: K 545 MET cc_start: 0.8566 (tpp) cc_final: 0.8353 (tpp) REVERT: L 66 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8206 (mt-10) REVERT: L 94 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8927 (pp20) REVERT: L 193 LYS cc_start: 0.9217 (ttmt) cc_final: 0.9012 (mtmm) REVERT: L 420 TRP cc_start: 0.8709 (t60) cc_final: 0.8382 (t60) REVERT: L 511 ASP cc_start: 0.8759 (p0) cc_final: 0.8525 (p0) REVERT: L 538 ILE cc_start: 0.9339 (mt) cc_final: 0.9106 (tp) REVERT: L 683 TRP cc_start: 0.8070 (t-100) cc_final: 0.7839 (t-100) REVERT: M 62 GLN cc_start: 0.8237 (mt0) cc_final: 0.7873 (tt0) REVERT: M 66 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8389 (mt-10) REVERT: M 98 LEU cc_start: 0.8819 (mt) cc_final: 0.8418 (mt) REVERT: M 110 ARG cc_start: 0.5513 (ttt90) cc_final: 0.5235 (ttm-80) REVERT: M 127 ASP cc_start: 0.8416 (p0) cc_final: 0.8123 (p0) REVERT: M 159 ARG cc_start: 0.8982 (tpt170) cc_final: 0.8268 (mmm160) REVERT: M 214 TRP cc_start: 0.8323 (m-10) cc_final: 0.8075 (m-10) REVERT: M 233 CYS cc_start: 0.8437 (t) cc_final: 0.8072 (t) REVERT: M 245 MET cc_start: 0.8800 (mtm) cc_final: 0.8554 (mtp) REVERT: M 293 LEU cc_start: 0.8631 (mt) cc_final: 0.8427 (mt) REVERT: M 420 TRP cc_start: 0.8578 (t60) cc_final: 0.8148 (t60) REVERT: M 545 MET cc_start: 0.8640 (tpp) cc_final: 0.8439 (tpp) REVERT: N 62 GLN cc_start: 0.8202 (mt0) cc_final: 0.7809 (tp40) REVERT: N 66 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8230 (mt-10) REVERT: N 511 ASP cc_start: 0.8792 (p0) cc_final: 0.8570 (p0) REVERT: N 565 PHE cc_start: 0.8398 (t80) cc_final: 0.7601 (t80) REVERT: O 159 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7828 (mmm160) REVERT: O 162 ARG cc_start: 0.8635 (mtm180) cc_final: 0.8424 (mtm180) REVERT: O 511 ASP cc_start: 0.8709 (p0) cc_final: 0.8458 (p0) REVERT: O 545 MET cc_start: 0.8637 (tpp) cc_final: 0.8420 (tpp) REVERT: O 565 PHE cc_start: 0.8380 (t80) cc_final: 0.7643 (t80) REVERT: P 66 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8264 (mt-10) REVERT: P 94 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8947 (pp20) REVERT: P 257 LEU cc_start: 0.9008 (mm) cc_final: 0.8694 (mm) REVERT: P 420 TRP cc_start: 0.8672 (t60) cc_final: 0.8405 (t60) REVERT: P 511 ASP cc_start: 0.8749 (p0) cc_final: 0.8501 (p0) REVERT: P 683 TRP cc_start: 0.7960 (t-100) cc_final: 0.7731 (t-100) outliers start: 23 outliers final: 4 residues processed: 1287 average time/residue: 0.7337 time to fit residues: 1604.5622 Evaluate side-chains 899 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 895 time to evaluate : 6.705 ------------------------------------------------------------------------------- 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: 6.9990 chunk 284 optimal weight: 5.9990 chunk 761 optimal weight: 10.0000 chunk 623 optimal weight: 30.0000 chunk 252 optimal weight: 40.0000 chunk 917 optimal weight: 3.9990 chunk 990 optimal weight: 0.8980 chunk 816 optimal weight: 20.0000 chunk 909 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 735 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN 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 328 GLN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 679 ASN F 328 GLN ** F 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 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 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** ** L 688 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 328 GLN ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 ASN P 337 ASN ** 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 80192 Z= 0.229 Angle : 0.599 8.756 108416 Z= 0.308 Chirality : 0.040 0.146 12416 Planarity : 0.005 0.081 14064 Dihedral : 4.777 17.606 10960 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % 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: -1.14 (0.08), residues: 10000 helix: -0.33 (0.06), residues: 6960 sheet: -1.53 (0.25), residues: 304 loop : -1.43 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 638 HIS 0.004 0.001 HIS J 640 PHE 0.017 0.002 PHE P 678 TYR 0.014 0.001 TYR E 429 ARG 0.007 0.000 ARG L 465 *********************** 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 1385 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1376 time to evaluate : 6.891 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: A 94 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8883 (pt0) REVERT: A 420 TRP cc_start: 0.8639 (t60) cc_final: 0.8376 (t60) REVERT: A 594 ASP cc_start: 0.8163 (t0) cc_final: 0.7955 (t70) REVERT: B 94 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8816 (pt0) REVERT: B 150 GLN cc_start: 0.7744 (mm110) cc_final: 0.7448 (tp-100) REVERT: B 159 ARG cc_start: 0.8596 (mmm160) cc_final: 0.7683 (mmm160) REVERT: B 162 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8366 (mtm180) REVERT: B 245 MET cc_start: 0.8941 (mtm) cc_final: 0.8685 (mtm) REVERT: B 395 ARG cc_start: 0.8071 (ptt90) cc_final: 0.7793 (ptt90) REVERT: B 594 ASP cc_start: 0.8324 (t0) cc_final: 0.8082 (t70) REVERT: B 682 LYS cc_start: 0.9162 (mttt) cc_final: 0.8844 (tptt) REVERT: B 683 TRP cc_start: 0.8023 (t-100) cc_final: 0.7670 (t-100) REVERT: C 66 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8190 (mt-10) REVERT: C 94 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8923 (pt0) REVERT: C 127 ASP cc_start: 0.8788 (m-30) cc_final: 0.8232 (m-30) REVERT: C 420 TRP cc_start: 0.8591 (t60) cc_final: 0.8257 (t60) REVERT: D 66 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8175 (mt-10) REVERT: D 94 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9028 (pt0) REVERT: D 127 ASP cc_start: 0.8678 (m-30) cc_final: 0.8106 (m-30) REVERT: D 159 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.7576 (mmm160) REVERT: D 245 MET cc_start: 0.8937 (mtm) cc_final: 0.8702 (mtm) REVERT: D 395 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7792 (ptt90) REVERT: D 522 GLN cc_start: 0.8605 (mt0) cc_final: 0.8319 (mm-40) REVERT: D 545 MET cc_start: 0.8679 (tpp) cc_final: 0.8462 (tpp) REVERT: E 62 GLN cc_start: 0.8170 (mt0) cc_final: 0.7761 (tp40) REVERT: E 66 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8169 (mt-10) REVERT: E 159 ARG cc_start: 0.8983 (tpt170) cc_final: 0.8163 (mmm160) REVERT: E 214 TRP cc_start: 0.8522 (m-10) cc_final: 0.8219 (m-10) REVERT: E 395 ARG cc_start: 0.8267 (ptt90) cc_final: 0.7951 (ptt90) REVERT: E 511 ASP cc_start: 0.8798 (p0) cc_final: 0.8501 (p0) REVERT: E 522 GLN cc_start: 0.8486 (mt0) cc_final: 0.8239 (mm-40) REVERT: E 565 PHE cc_start: 0.8443 (t80) cc_final: 0.7605 (t80) REVERT: E 683 TRP cc_start: 0.8468 (t-100) cc_final: 0.8193 (t-100) REVERT: F 94 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8807 (pt0) REVERT: F 159 ARG cc_start: 0.8580 (mmm160) cc_final: 0.7851 (mmm160) REVERT: F 162 ARG cc_start: 0.8657 (mtm180) cc_final: 0.8318 (mtm180) REVERT: F 245 MET cc_start: 0.8919 (mtm) cc_final: 0.8675 (mtm) REVERT: F 395 ARG cc_start: 0.8027 (ptt90) cc_final: 0.7754 (ptt90) REVERT: F 511 ASP cc_start: 0.8739 (p0) cc_final: 0.8524 (p0) REVERT: F 545 MET cc_start: 0.8715 (tpp) cc_final: 0.8496 (tpp) REVERT: F 609 GLN cc_start: 0.9089 (mt0) cc_final: 0.8772 (mt0) REVERT: G 62 GLN cc_start: 0.8169 (mt0) cc_final: 0.7578 (tp40) REVERT: G 66 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8285 (mt-10) REVERT: G 159 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8384 (mmm160) REVERT: G 395 ARG cc_start: 0.8307 (ptt90) cc_final: 0.7995 (ptt90) REVERT: G 565 PHE cc_start: 0.8288 (t80) cc_final: 0.7406 (t80) REVERT: G 682 LYS cc_start: 0.9235 (mttt) cc_final: 0.8872 (tptt) REVERT: G 683 TRP cc_start: 0.8310 (t-100) cc_final: 0.7458 (t-100) REVERT: H 66 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8238 (mt-10) REVERT: H 94 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8779 (pt0) REVERT: H 150 GLN cc_start: 0.7746 (mm110) cc_final: 0.7399 (tp-100) REVERT: H 159 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7994 (mmt180) REVERT: H 545 MET cc_start: 0.8713 (tpp) cc_final: 0.8507 (tpp) REVERT: H 594 ASP cc_start: 0.8418 (t0) cc_final: 0.8215 (t70) REVERT: I 66 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8183 (mt-10) REVERT: I 94 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8801 (pt0) REVERT: I 127 ASP cc_start: 0.8651 (m-30) cc_final: 0.8127 (m-30) REVERT: I 159 ARG cc_start: 0.8636 (mmm160) cc_final: 0.7836 (mmm160) REVERT: I 162 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8259 (mtm180) REVERT: I 245 MET cc_start: 0.8743 (mtt) cc_final: 0.8464 (mtp) REVERT: I 395 ARG cc_start: 0.8060 (ptt90) cc_final: 0.7805 (ptt90) REVERT: I 437 GLN cc_start: 0.9002 (mp10) cc_final: 0.8744 (mp10) REVERT: I 511 ASP cc_start: 0.8730 (p0) cc_final: 0.8508 (p0) REVERT: I 545 MET cc_start: 0.8634 (tpp) cc_final: 0.8399 (tpp) REVERT: J 94 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8887 (pt0) REVERT: J 127 ASP cc_start: 0.8843 (m-30) cc_final: 0.8202 (m-30) REVERT: J 420 TRP cc_start: 0.8590 (t60) cc_final: 0.8246 (t60) REVERT: K 94 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8934 (pt0) REVERT: K 127 ASP cc_start: 0.8617 (m-30) cc_final: 0.7993 (m-30) REVERT: K 159 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7887 (mmm160) REVERT: K 233 CYS cc_start: 0.8517 (t) cc_final: 0.8193 (t) REVERT: K 245 MET cc_start: 0.8684 (mtm) cc_final: 0.8309 (mtp) REVERT: K 293 LEU cc_start: 0.8638 (mt) cc_final: 0.8400 (mt) REVERT: K 420 TRP cc_start: 0.8552 (t60) cc_final: 0.8157 (t60) REVERT: K 545 MET cc_start: 0.8591 (tpp) cc_final: 0.8358 (tpp) REVERT: L 66 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8188 (mt-10) REVERT: L 94 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8909 (pt0) REVERT: L 127 ASP cc_start: 0.8768 (m-30) cc_final: 0.8185 (m-30) REVERT: L 420 TRP cc_start: 0.8631 (t60) cc_final: 0.8360 (t60) REVERT: L 457 MET cc_start: 0.6104 (ttp) cc_final: 0.5896 (ptm) REVERT: L 683 TRP cc_start: 0.7977 (t-100) cc_final: 0.7754 (t-100) REVERT: M 62 GLN cc_start: 0.8261 (mt0) cc_final: 0.7891 (tt0) REVERT: M 66 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8321 (mt-10) REVERT: M 110 ARG cc_start: 0.5574 (ttt90) cc_final: 0.5246 (ttm-80) REVERT: M 150 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7334 (tp-100) REVERT: M 157 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7234 (mtt180) REVERT: M 163 ILE cc_start: 0.8709 (pt) cc_final: 0.8378 (pt) REVERT: M 233 CYS cc_start: 0.8323 (t) cc_final: 0.7945 (t) REVERT: M 245 MET cc_start: 0.8704 (mtm) cc_final: 0.8476 (mtp) REVERT: M 386 LYS cc_start: 0.8622 (ptmm) cc_final: 0.8396 (pttt) REVERT: M 420 TRP cc_start: 0.8444 (t60) cc_final: 0.8014 (t60) REVERT: M 545 MET cc_start: 0.8685 (tpp) cc_final: 0.8475 (tpp) REVERT: N 66 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8340 (mt-10) REVERT: N 94 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8854 (pt0) REVERT: N 511 ASP cc_start: 0.8798 (p0) cc_final: 0.8503 (p0) REVERT: N 522 GLN cc_start: 0.8550 (mt0) cc_final: 0.8270 (mm-40) REVERT: O 66 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8233 (mt-10) REVERT: O 94 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8797 (pt0) REVERT: O 245 MET cc_start: 0.8764 (mtt) cc_final: 0.8473 (mtp) REVERT: O 395 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7805 (ptt90) REVERT: O 511 ASP cc_start: 0.8736 (p0) cc_final: 0.8501 (p0) REVERT: O 545 MET cc_start: 0.8656 (tpp) cc_final: 0.8419 (tpp) REVERT: P 94 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8879 (pt0) REVERT: P 420 TRP cc_start: 0.8592 (t60) cc_final: 0.8295 (t60) REVERT: P 594 ASP cc_start: 0.8071 (t0) cc_final: 0.7727 (t70) REVERT: P 683 TRP cc_start: 0.7944 (t-100) cc_final: 0.7738 (t-100) outliers start: 9 outliers final: 2 residues processed: 1385 average time/residue: 0.7327 time to fit residues: 1726.9470 Evaluate side-chains 965 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 963 time to evaluate : 6.670 ------------------------------------------------------------------------------- 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: 6.9990 chunk 689 optimal weight: 1.9990 chunk 475 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 437 optimal weight: 20.0000 chunk 615 optimal weight: 6.9990 chunk 920 optimal weight: 4.9990 chunk 974 optimal weight: 9.9990 chunk 480 optimal weight: 2.9990 chunk 872 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 640 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 328 GLN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN E 337 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** 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** ** 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 328 GLN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 679 ASN ** 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 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 328 GLN M 337 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** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 679 ASN P 328 GLN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 80192 Z= 0.245 Angle : 0.598 9.455 108416 Z= 0.306 Chirality : 0.040 0.229 12416 Planarity : 0.005 0.145 14064 Dihedral : 4.681 21.147 10960 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % 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: -0.59 (0.08), residues: 10000 helix: 0.07 (0.06), residues: 6928 sheet: -1.33 (0.26), residues: 304 loop : -1.17 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 420 HIS 0.003 0.001 HIS H 640 PHE 0.013 0.002 PHE D 617 TYR 0.013 0.001 TYR H 429 ARG 0.010 0.000 ARG C 465 *********************** 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 1303 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1300 time to evaluate : 6.896 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: A 94 GLU cc_start: 0.9314 (mt-10) cc_final: 0.8953 (pt0) REVERT: A 127 ASP cc_start: 0.8428 (m-30) cc_final: 0.7457 (m-30) REVERT: A 150 GLN cc_start: 0.7886 (mm110) cc_final: 0.7591 (tp-100) REVERT: A 159 ARG cc_start: 0.8656 (mmm160) cc_final: 0.8424 (mmm160) REVERT: A 245 MET cc_start: 0.9057 (mtp) cc_final: 0.8676 (mtp) REVERT: A 594 ASP cc_start: 0.8172 (t0) cc_final: 0.7956 (t70) REVERT: B 66 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8355 (mt-10) REVERT: B 94 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8893 (pt0) REVERT: B 150 GLN cc_start: 0.7838 (mm110) cc_final: 0.7480 (tp-100) REVERT: B 159 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8364 (mmm160) REVERT: B 163 ILE cc_start: 0.8628 (pt) cc_final: 0.8426 (pt) REVERT: B 420 TRP cc_start: 0.8665 (t60) cc_final: 0.8201 (t60) REVERT: B 522 GLN cc_start: 0.8621 (mt0) cc_final: 0.8311 (mm-40) REVERT: C 66 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8185 (mt-10) REVERT: C 94 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8975 (pt0) REVERT: C 245 MET cc_start: 0.8770 (mtt) cc_final: 0.8448 (mtp) REVERT: C 457 MET cc_start: 0.6023 (tmm) cc_final: 0.5116 (ppp) REVERT: D 66 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 94 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8917 (pt0) REVERT: D 395 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7800 (ptt90) REVERT: D 522 GLN cc_start: 0.8595 (mt0) cc_final: 0.8356 (mm-40) REVERT: D 538 ILE cc_start: 0.9262 (mt) cc_final: 0.9034 (tp) REVERT: D 545 MET cc_start: 0.8708 (tpp) cc_final: 0.8483 (tpp) REVERT: D 594 ASP cc_start: 0.8068 (t0) cc_final: 0.7864 (t70) REVERT: E 159 ARG cc_start: 0.8778 (tpt170) cc_final: 0.7865 (tpp-160) REVERT: E 163 ILE cc_start: 0.8146 (pt) cc_final: 0.7673 (pt) REVERT: E 522 GLN cc_start: 0.8549 (mt0) cc_final: 0.8280 (mm-40) REVERT: E 683 TRP cc_start: 0.8475 (t-100) cc_final: 0.8201 (t-100) REVERT: F 94 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8779 (pt0) REVERT: F 150 GLN cc_start: 0.7867 (mm110) cc_final: 0.7493 (tp-100) REVERT: F 159 ARG cc_start: 0.8584 (mmm160) cc_final: 0.8330 (mmm160) REVERT: F 245 MET cc_start: 0.8797 (mtm) cc_final: 0.8527 (mtp) REVERT: F 538 ILE cc_start: 0.9245 (mt) cc_final: 0.9021 (tp) REVERT: F 545 MET cc_start: 0.8721 (tpp) cc_final: 0.8505 (tpp) REVERT: G 66 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8270 (mt-10) REVERT: G 395 ARG cc_start: 0.8315 (ptt90) cc_final: 0.7989 (ptt90) REVERT: G 565 PHE cc_start: 0.8222 (t80) cc_final: 0.7281 (t80) REVERT: G 683 TRP cc_start: 0.8323 (t-100) cc_final: 0.7991 (t-100) REVERT: H 66 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8203 (mt-10) REVERT: H 94 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8859 (pt0) REVERT: H 150 GLN cc_start: 0.7817 (mm110) cc_final: 0.7415 (tp-100) REVERT: H 159 ARG cc_start: 0.8282 (mmm-85) cc_final: 0.8034 (mmt180) REVERT: H 162 ARG cc_start: 0.8472 (mtm180) cc_final: 0.8027 (mtm180) REVERT: H 395 ARG cc_start: 0.8020 (ptt90) cc_final: 0.7812 (ptt90) REVERT: H 420 TRP cc_start: 0.8661 (t60) cc_final: 0.8223 (t60) REVERT: H 511 ASP cc_start: 0.8632 (p0) cc_final: 0.8413 (p0) REVERT: I 66 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8154 (mt-10) REVERT: I 94 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8787 (pt0) REVERT: I 150 GLN cc_start: 0.7853 (mm110) cc_final: 0.7523 (tp-100) REVERT: I 159 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8420 (mmm160) REVERT: I 245 MET cc_start: 0.8790 (mtt) cc_final: 0.8371 (mtm) REVERT: I 437 GLN cc_start: 0.8995 (mp10) cc_final: 0.8754 (mp10) REVERT: I 511 ASP cc_start: 0.8728 (p0) cc_final: 0.8490 (p0) REVERT: I 538 ILE cc_start: 0.9254 (mt) cc_final: 0.9018 (tp) REVERT: I 545 MET cc_start: 0.8669 (tpp) cc_final: 0.8430 (tpp) REVERT: J 94 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8919 (pt0) REVERT: J 159 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8397 (mmm160) REVERT: K 94 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8963 (pt0) REVERT: K 150 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7380 (tp-100) REVERT: K 245 MET cc_start: 0.8658 (mtm) cc_final: 0.8312 (mtp) REVERT: K 293 LEU cc_start: 0.8625 (mt) cc_final: 0.8351 (mt) REVERT: K 420 TRP cc_start: 0.8495 (t60) cc_final: 0.8091 (t60) REVERT: K 522 GLN cc_start: 0.8592 (mt0) cc_final: 0.8282 (mm-40) REVERT: K 538 ILE cc_start: 0.9278 (mt) cc_final: 0.9045 (tp) REVERT: K 545 MET cc_start: 0.8674 (tpp) cc_final: 0.8458 (tpp) REVERT: L 66 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8169 (mt-10) REVERT: L 94 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8926 (pt0) REVERT: L 159 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8480 (mmm160) REVERT: L 457 MET cc_start: 0.6110 (ttp) cc_final: 0.5852 (ptm) REVERT: L 683 TRP cc_start: 0.8027 (t-100) cc_final: 0.7791 (t-100) REVERT: M 62 GLN cc_start: 0.8211 (mt0) cc_final: 0.7923 (tt0) REVERT: M 66 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8198 (mt-10) REVERT: M 110 ARG cc_start: 0.5637 (ttt90) cc_final: 0.5302 (ttm-80) REVERT: M 150 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7365 (tp-100) REVERT: M 159 ARG cc_start: 0.9044 (tpt170) cc_final: 0.8033 (mmp80) REVERT: M 233 CYS cc_start: 0.8302 (t) cc_final: 0.7947 (t) REVERT: M 245 MET cc_start: 0.8634 (mtm) cc_final: 0.8419 (mtp) REVERT: M 293 LEU cc_start: 0.8640 (mt) cc_final: 0.8410 (mt) REVERT: M 420 TRP cc_start: 0.8457 (t60) cc_final: 0.8016 (t60) REVERT: M 511 ASP cc_start: 0.8770 (p0) cc_final: 0.8421 (p0) REVERT: M 522 GLN cc_start: 0.8575 (mt0) cc_final: 0.8276 (mm-40) REVERT: M 545 MET cc_start: 0.8769 (tpp) cc_final: 0.8553 (tpp) REVERT: M 683 TRP cc_start: 0.8326 (t-100) cc_final: 0.8113 (t-100) REVERT: N 66 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8340 (mp0) REVERT: N 127 ASP cc_start: 0.8512 (m-30) cc_final: 0.7692 (m-30) REVERT: N 245 MET cc_start: 0.8984 (mtp) cc_final: 0.8603 (mtp) REVERT: N 511 ASP cc_start: 0.8722 (p0) cc_final: 0.8447 (p0) REVERT: O 66 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8204 (mt-10) REVERT: O 94 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8794 (pt0) REVERT: O 245 MET cc_start: 0.8777 (mtt) cc_final: 0.8352 (mtm) REVERT: O 395 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7776 (ptt90) REVERT: O 522 GLN cc_start: 0.8599 (mt0) cc_final: 0.8319 (mm-40) REVERT: O 545 MET cc_start: 0.8745 (tpp) cc_final: 0.8522 (tpp) REVERT: P 94 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8911 (pt0) REVERT: P 245 MET cc_start: 0.8704 (mtt) cc_final: 0.8322 (mtm) REVERT: P 420 TRP cc_start: 0.8595 (t60) cc_final: 0.8355 (t60) REVERT: P 594 ASP cc_start: 0.8066 (t0) cc_final: 0.7737 (t70) REVERT: P 683 TRP cc_start: 0.7959 (t-100) cc_final: 0.7729 (t-100) outliers start: 3 outliers final: 0 residues processed: 1303 average time/residue: 0.7454 time to fit residues: 1669.0031 Evaluate side-chains 920 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 920 time to evaluate : 6.754 ------------------------------------------------------------------------------- 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: 20.0000 chunk 553 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 725 optimal weight: 5.9990 chunk 402 optimal weight: 1.9990 chunk 831 optimal weight: 5.9990 chunk 673 optimal weight: 0.0870 chunk 1 optimal weight: 6.9990 chunk 497 optimal weight: 9.9990 chunk 874 optimal weight: 20.0000 chunk 245 optimal weight: 30.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 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** ** C 642 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 328 GLN ** E 534 HIS ** 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 328 GLN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 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 640 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 170 ASN N 328 GLN N 437 GLN ** N 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 150 GLN ** P 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7998 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 80192 Z= 0.236 Angle : 0.587 7.154 108416 Z= 0.301 Chirality : 0.040 0.215 12416 Planarity : 0.004 0.077 14064 Dihedral : 4.570 20.045 10960 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.93 % 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: -0.32 (0.09), residues: 10000 helix: 0.23 (0.06), residues: 6960 sheet: -1.25 (0.26), residues: 304 loop : -0.95 (0.13), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 420 HIS 0.007 0.001 HIS P 190 PHE 0.013 0.001 PHE O 565 TYR 0.018 0.001 TYR A 429 ARG 0.013 0.000 ARG G 465 *********************** 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 1311 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1308 time to evaluate : 8.432 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: A 94 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8974 (pt0) REVERT: A 159 ARG cc_start: 0.8688 (mmm160) cc_final: 0.8390 (mmm160) REVERT: A 245 MET cc_start: 0.8990 (mtp) cc_final: 0.8563 (mtp) REVERT: A 594 ASP cc_start: 0.8175 (t0) cc_final: 0.7963 (t70) REVERT: B 94 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8891 (pt0) REVERT: B 150 GLN cc_start: 0.7907 (mm110) cc_final: 0.7534 (tp-100) REVERT: B 159 ARG cc_start: 0.8580 (mmm160) cc_final: 0.8342 (mmm160) REVERT: B 163 ILE cc_start: 0.8636 (pt) cc_final: 0.8432 (pt) REVERT: B 245 MET cc_start: 0.8920 (mtp) cc_final: 0.8432 (mtp) REVERT: B 395 ARG cc_start: 0.8030 (ptt90) cc_final: 0.7732 (ptt90) REVERT: B 420 TRP cc_start: 0.8567 (t60) cc_final: 0.8131 (t60) REVERT: B 522 GLN cc_start: 0.8583 (mt0) cc_final: 0.8293 (mm-40) REVERT: C 66 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8199 (mt-10) REVERT: C 94 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8944 (pt0) REVERT: C 245 MET cc_start: 0.8828 (mtt) cc_final: 0.8586 (mtp) REVERT: D 66 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8174 (mt-10) REVERT: D 94 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8914 (pt0) REVERT: D 245 MET cc_start: 0.8926 (mtp) cc_final: 0.8364 (mtp) REVERT: D 522 GLN cc_start: 0.8567 (mt0) cc_final: 0.8321 (mm-40) REVERT: D 545 MET cc_start: 0.8712 (tpp) cc_final: 0.8502 (tpp) REVERT: E 150 GLN cc_start: 0.7766 (tp40) cc_final: 0.7446 (tp-100) REVERT: E 159 ARG cc_start: 0.8822 (tpt170) cc_final: 0.7986 (tpp-160) REVERT: E 163 ILE cc_start: 0.8206 (pt) cc_final: 0.7626 (pt) REVERT: E 214 TRP cc_start: 0.8421 (m-10) cc_final: 0.8166 (m-10) REVERT: E 386 LYS cc_start: 0.8447 (ptmm) cc_final: 0.8174 (pttt) REVERT: E 522 GLN cc_start: 0.8505 (mt0) cc_final: 0.8271 (mm-40) REVERT: E 565 PHE cc_start: 0.8371 (t80) cc_final: 0.7488 (t80) REVERT: E 683 TRP cc_start: 0.8473 (t-100) cc_final: 0.8210 (t-100) REVERT: F 66 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8267 (mt-10) REVERT: F 94 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8809 (pt0) REVERT: F 150 GLN cc_start: 0.7808 (mm110) cc_final: 0.7503 (tp-100) REVERT: F 245 MET cc_start: 0.8735 (mtm) cc_final: 0.8519 (mtm) REVERT: F 545 MET cc_start: 0.8736 (tpp) cc_final: 0.8523 (tpp) REVERT: G 66 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8232 (mt-10) REVERT: G 214 TRP cc_start: 0.8373 (m-10) cc_final: 0.8138 (m-10) REVERT: G 395 ARG cc_start: 0.8340 (ptt90) cc_final: 0.7998 (ptt90) REVERT: G 522 GLN cc_start: 0.8552 (mt0) cc_final: 0.8273 (mm-40) REVERT: G 565 PHE cc_start: 0.8224 (t80) cc_final: 0.7204 (t80) REVERT: G 683 TRP cc_start: 0.8341 (t-100) cc_final: 0.8015 (t-100) REVERT: H 66 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8212 (mt-10) REVERT: H 94 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8860 (pt0) REVERT: H 150 GLN cc_start: 0.7824 (mm110) cc_final: 0.7444 (tp-100) REVERT: H 189 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8199 (pt0) REVERT: I 66 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8288 (mt-10) REVERT: I 94 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8807 (pt0) REVERT: I 150 GLN cc_start: 0.7901 (mm110) cc_final: 0.7533 (tp-100) REVERT: I 167 VAL cc_start: 0.9119 (t) cc_final: 0.8754 (p) REVERT: I 233 CYS cc_start: 0.8364 (t) cc_final: 0.8116 (t) REVERT: I 245 MET cc_start: 0.8769 (mtt) cc_final: 0.8303 (mtp) REVERT: I 437 GLN cc_start: 0.8971 (mp10) cc_final: 0.8717 (mp10) REVERT: I 522 GLN cc_start: 0.8621 (mt0) cc_final: 0.8339 (mm-40) REVERT: I 538 ILE cc_start: 0.9316 (mt) cc_final: 0.9112 (tp) REVERT: I 545 MET cc_start: 0.8692 (tpp) cc_final: 0.8462 (tpp) REVERT: J 94 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8968 (pt0) REVERT: J 245 MET cc_start: 0.8833 (mtt) cc_final: 0.8494 (mtp) REVERT: K 94 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8981 (pt0) REVERT: K 150 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7390 (tp-100) REVERT: K 159 ARG cc_start: 0.8609 (mmm160) cc_final: 0.7740 (mmm160) REVERT: K 162 ARG cc_start: 0.8654 (mtm180) cc_final: 0.8180 (mtm180) REVERT: K 420 TRP cc_start: 0.8513 (t60) cc_final: 0.8112 (t60) REVERT: K 538 ILE cc_start: 0.9312 (mt) cc_final: 0.9101 (tp) REVERT: K 545 MET cc_start: 0.8667 (tpp) cc_final: 0.8429 (tpp) REVERT: L 66 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8127 (mt-10) REVERT: L 94 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8922 (pt0) REVERT: L 159 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8407 (mmm160) REVERT: L 245 MET cc_start: 0.8857 (mtt) cc_final: 0.8633 (mtm) REVERT: L 683 TRP cc_start: 0.8045 (t-100) cc_final: 0.7790 (t-100) REVERT: M 62 GLN cc_start: 0.8207 (mt0) cc_final: 0.7909 (tt0) REVERT: M 66 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8167 (mt-10) REVERT: M 110 ARG cc_start: 0.5732 (ttt90) cc_final: 0.5397 (ttm-80) REVERT: M 150 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7483 (tp-100) REVERT: M 159 ARG cc_start: 0.9068 (tpt170) cc_final: 0.8171 (tpp-160) REVERT: M 163 ILE cc_start: 0.8358 (pt) cc_final: 0.7715 (pt) REVERT: M 233 CYS cc_start: 0.8245 (t) cc_final: 0.7922 (t) REVERT: M 245 MET cc_start: 0.8637 (mtm) cc_final: 0.8391 (mtp) REVERT: M 293 LEU cc_start: 0.8627 (mt) cc_final: 0.8413 (mt) REVERT: M 420 TRP cc_start: 0.8451 (t60) cc_final: 0.8050 (t60) REVERT: M 511 ASP cc_start: 0.8659 (p0) cc_final: 0.8363 (p0) REVERT: M 522 GLN cc_start: 0.8568 (mt0) cc_final: 0.8283 (mm-40) REVERT: M 609 GLN cc_start: 0.9034 (mt0) cc_final: 0.8776 (mt0) REVERT: N 66 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8342 (mp0) REVERT: N 94 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8838 (pt0) REVERT: N 150 GLN cc_start: 0.7805 (tp40) cc_final: 0.7397 (tp-100) REVERT: N 245 MET cc_start: 0.8910 (mtp) cc_final: 0.8475 (mtp) REVERT: N 683 TRP cc_start: 0.8548 (t-100) cc_final: 0.8224 (t-100) REVERT: O 86 ARG cc_start: 0.9050 (mpp-170) cc_final: 0.8800 (mpp-170) REVERT: O 94 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8817 (pt0) REVERT: O 245 MET cc_start: 0.8734 (mtt) cc_final: 0.8377 (mtm) REVERT: O 420 TRP cc_start: 0.8633 (t60) cc_final: 0.7844 (t60) REVERT: O 522 GLN cc_start: 0.8553 (mt0) cc_final: 0.8226 (mm-40) REVERT: O 545 MET cc_start: 0.8811 (tpp) cc_final: 0.8604 (tpp) REVERT: P 94 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8827 (pt0) REVERT: P 98 LEU cc_start: 0.9101 (mt) cc_final: 0.8797 (mt) REVERT: P 245 MET cc_start: 0.8775 (mtm) cc_final: 0.8575 (mtp) REVERT: P 420 TRP cc_start: 0.8503 (t60) cc_final: 0.8293 (t60) outliers start: 3 outliers final: 0 residues processed: 1311 average time/residue: 0.7346 time to fit residues: 1637.4930 Evaluate side-chains 933 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 933 time to evaluate : 6.682 ------------------------------------------------------------------------------- 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: 20.0000 chunk 877 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 572 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 975 optimal weight: 1.9990 chunk 809 optimal weight: 0.9980 chunk 451 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 chunk 512 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 GLN ** 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 337 ASN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 437 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 80192 Z= 0.174 Angle : 0.551 10.738 108416 Z= 0.277 Chirality : 0.039 0.207 12416 Planarity : 0.004 0.048 14064 Dihedral : 4.330 18.396 10960 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.01 % Allowed : 1.50 % Favored : 98.49 % 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: 0.15 (0.09), residues: 10000 helix: 0.54 (0.06), residues: 6992 sheet: -0.99 (0.27), residues: 304 loop : -0.66 (0.13), residues: 2704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 420 HIS 0.007 0.001 HIS P 583 PHE 0.015 0.001 PHE M 603 TYR 0.024 0.001 TYR E 429 ARG 0.008 0.000 ARG D 465 *********************** 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 1332 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1331 time to evaluate : 6.821 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: A 94 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8954 (pt0) REVERT: A 159 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8312 (mmm160) REVERT: A 245 MET cc_start: 0.8920 (mtp) cc_final: 0.8498 (mtp) REVERT: A 420 TRP cc_start: 0.8395 (t60) cc_final: 0.8092 (t60) REVERT: A 594 ASP cc_start: 0.8108 (t0) cc_final: 0.7901 (t70) REVERT: B 94 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8924 (pt0) REVERT: B 150 GLN cc_start: 0.7914 (mm110) cc_final: 0.7531 (tp-100) REVERT: B 159 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8322 (mmm160) REVERT: B 193 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8863 (mtmm) REVERT: B 245 MET cc_start: 0.8884 (mtp) cc_final: 0.8518 (mtp) REVERT: B 420 TRP cc_start: 0.8512 (t60) cc_final: 0.8115 (t60) REVERT: C 94 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8969 (pt0) REVERT: C 245 MET cc_start: 0.8750 (mtt) cc_final: 0.8546 (mtp) REVERT: D 94 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8855 (pt0) REVERT: D 162 ARG cc_start: 0.8616 (mtm180) cc_final: 0.8095 (mtm180) REVERT: D 245 MET cc_start: 0.8891 (mtp) cc_final: 0.8360 (mtp) REVERT: D 395 ARG cc_start: 0.8009 (ptt90) cc_final: 0.7768 (ptt90) REVERT: D 447 THR cc_start: 0.9309 (p) cc_final: 0.9011 (p) REVERT: D 511 ASP cc_start: 0.8623 (p0) cc_final: 0.8416 (p0) REVERT: E 167 VAL cc_start: 0.9041 (t) cc_final: 0.8732 (p) REVERT: E 386 LYS cc_start: 0.8420 (ptmm) cc_final: 0.8206 (pttt) REVERT: E 683 TRP cc_start: 0.8430 (t-100) cc_final: 0.8160 (t-100) REVERT: F 94 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8843 (pt0) REVERT: F 150 GLN cc_start: 0.7750 (mm110) cc_final: 0.7398 (tp40) REVERT: F 245 MET cc_start: 0.8698 (mtm) cc_final: 0.8481 (mtp) REVERT: F 609 GLN cc_start: 0.9106 (mt0) cc_final: 0.8799 (mt0) REVERT: G 66 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8226 (mt-10) REVERT: G 159 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8439 (mmm160) REVERT: G 171 LEU cc_start: 0.9169 (mt) cc_final: 0.8867 (mt) REVERT: G 214 TRP cc_start: 0.8322 (m-10) cc_final: 0.8105 (m-10) REVERT: G 245 MET cc_start: 0.8890 (mtt) cc_final: 0.8580 (mtp) REVERT: G 522 GLN cc_start: 0.8486 (mt0) cc_final: 0.8284 (mm-40) REVERT: G 565 PHE cc_start: 0.8231 (t80) cc_final: 0.7221 (t80) REVERT: G 683 TRP cc_start: 0.8278 (t-100) cc_final: 0.7906 (t-100) REVERT: H 94 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8877 (pt0) REVERT: H 150 GLN cc_start: 0.7757 (mm110) cc_final: 0.7386 (tp40) REVERT: H 189 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8406 (pt0) REVERT: H 395 ARG cc_start: 0.8049 (ptt90) cc_final: 0.7824 (ptt90) REVERT: H 420 TRP cc_start: 0.8487 (t60) cc_final: 0.8070 (t60) REVERT: H 609 GLN cc_start: 0.9140 (mt0) cc_final: 0.8855 (mt0) REVERT: I 94 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8830 (pt0) REVERT: I 420 TRP cc_start: 0.8472 (t60) cc_final: 0.8131 (t60) REVERT: I 545 MET cc_start: 0.8644 (tpp) cc_final: 0.8423 (tpp) REVERT: I 609 GLN cc_start: 0.9124 (mt0) cc_final: 0.8872 (mp10) REVERT: J 94 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8861 (pt0) REVERT: J 98 LEU cc_start: 0.9137 (mt) cc_final: 0.8790 (mt) REVERT: J 157 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.7091 (mtt180) REVERT: J 193 LYS cc_start: 0.9134 (ttmt) cc_final: 0.8729 (mtpp) REVERT: J 245 MET cc_start: 0.8862 (mtt) cc_final: 0.8458 (mtp) REVERT: J 420 TRP cc_start: 0.8322 (t60) cc_final: 0.8060 (t60) REVERT: K 94 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8991 (pt0) REVERT: K 150 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7406 (tp-100) REVERT: K 162 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8192 (mtm180) REVERT: K 245 MET cc_start: 0.8543 (mtm) cc_final: 0.8163 (mtp) REVERT: K 395 ARG cc_start: 0.8303 (ptt90) cc_final: 0.8002 (ptt90) REVERT: K 420 TRP cc_start: 0.8451 (t60) cc_final: 0.8089 (t60) REVERT: K 522 GLN cc_start: 0.8434 (mt0) cc_final: 0.8200 (mm-40) REVERT: K 545 MET cc_start: 0.8662 (tpp) cc_final: 0.8440 (tpp) REVERT: L 94 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8951 (pt0) REVERT: L 245 MET cc_start: 0.8849 (mtt) cc_final: 0.8612 (mtp) REVERT: L 420 TRP cc_start: 0.8373 (t60) cc_final: 0.8083 (t60) REVERT: L 683 TRP cc_start: 0.8003 (t-100) cc_final: 0.7769 (t-100) REVERT: M 62 GLN cc_start: 0.8206 (mt0) cc_final: 0.7796 (tp40) REVERT: M 66 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8063 (mt-10) REVERT: M 110 ARG cc_start: 0.5737 (ttt90) cc_final: 0.5401 (ttm-80) REVERT: M 150 GLN cc_start: 0.7668 (tp-100) cc_final: 0.7384 (tp-100) REVERT: M 159 ARG cc_start: 0.9060 (tpt170) cc_final: 0.8195 (tpp-160) REVERT: M 163 ILE cc_start: 0.8354 (pt) cc_final: 0.7771 (pt) REVERT: M 167 VAL cc_start: 0.9095 (t) cc_final: 0.8741 (p) REVERT: M 293 LEU cc_start: 0.8639 (mt) cc_final: 0.8432 (mt) REVERT: M 420 TRP cc_start: 0.8359 (t60) cc_final: 0.7896 (t60) REVERT: M 424 ILE cc_start: 0.8148 (pt) cc_final: 0.7601 (pt) REVERT: M 511 ASP cc_start: 0.8610 (p0) cc_final: 0.8351 (p0) REVERT: M 522 GLN cc_start: 0.8455 (mt0) cc_final: 0.8220 (mm-40) REVERT: M 609 GLN cc_start: 0.9060 (mt0) cc_final: 0.8760 (mt0) REVERT: N 66 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8316 (mp0) REVERT: N 245 MET cc_start: 0.8836 (mtp) cc_final: 0.8365 (mtp) REVERT: O 86 ARG cc_start: 0.9011 (mpp-170) cc_final: 0.8586 (mtm-85) REVERT: O 94 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8833 (pt0) REVERT: O 395 ARG cc_start: 0.8043 (ptt90) cc_final: 0.7810 (ptt90) REVERT: O 420 TRP cc_start: 0.8502 (t60) cc_final: 0.7866 (t60) REVERT: O 522 GLN cc_start: 0.8455 (mt0) cc_final: 0.8232 (mm-40) REVERT: O 609 GLN cc_start: 0.9081 (mt0) cc_final: 0.8717 (mt0) REVERT: P 94 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8906 (pt0) REVERT: P 157 ARG cc_start: 0.7140 (mtm-85) cc_final: 0.6740 (mtm110) REVERT: P 167 VAL cc_start: 0.9022 (t) cc_final: 0.8722 (p) REVERT: P 214 TRP cc_start: 0.8450 (m-10) cc_final: 0.8148 (m-10) REVERT: P 245 MET cc_start: 0.8641 (mtm) cc_final: 0.8320 (mtp) REVERT: P 420 TRP cc_start: 0.8402 (t60) cc_final: 0.8189 (t60) outliers start: 1 outliers final: 0 residues processed: 1332 average time/residue: 0.7344 time to fit residues: 1667.5706 Evaluate side-chains 945 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 945 time to evaluate : 6.695 ------------------------------------------------------------------------------- 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: 10.0000 chunk 555 optimal weight: 9.9990 chunk 712 optimal weight: 0.0970 chunk 551 optimal weight: 1.9990 chunk 820 optimal weight: 0.6980 chunk 544 optimal weight: 9.9990 chunk 971 optimal weight: 10.0000 chunk 608 optimal weight: 4.9990 chunk 592 optimal weight: 8.9990 chunk 448 optimal weight: 9.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** D 534 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** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 170 ASN G 337 ASN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 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 328 GLN ** J 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 337 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 685 HIS ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 80192 Z= 0.235 Angle : 0.592 10.779 108416 Z= 0.300 Chirality : 0.040 0.228 12416 Planarity : 0.004 0.098 14064 Dihedral : 4.384 18.333 10960 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % 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: 0.15 (0.09), residues: 10000 helix: 0.55 (0.06), residues: 6928 sheet: -0.92 (0.27), residues: 304 loop : -0.68 (0.13), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 420 HIS 0.007 0.001 HIS A 583 PHE 0.018 0.001 PHE F 603 TYR 0.015 0.001 TYR E 429 ARG 0.024 0.000 ARG P 465 *********************** 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 1257 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1256 time to evaluate : 6.787 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: A 66 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8255 (mt-10) REVERT: A 94 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8902 (pt0) REVERT: A 98 LEU cc_start: 0.9099 (mt) cc_final: 0.8767 (mt) REVERT: A 159 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8335 (mmm160) REVERT: A 245 MET cc_start: 0.8892 (mtp) cc_final: 0.8393 (mtp) REVERT: A 420 TRP cc_start: 0.8463 (t60) cc_final: 0.8091 (t60) REVERT: B 94 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8955 (pt0) REVERT: B 150 GLN cc_start: 0.7851 (mm110) cc_final: 0.7537 (tp40) REVERT: B 159 ARG cc_start: 0.8613 (mmm160) cc_final: 0.8392 (mmm160) REVERT: B 245 MET cc_start: 0.8873 (mtp) cc_final: 0.8375 (mtp) REVERT: B 511 ASP cc_start: 0.8610 (p0) cc_final: 0.8341 (p0) REVERT: C 66 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 94 GLU cc_start: 0.9309 (mt-10) cc_final: 0.8952 (pt0) REVERT: C 245 MET cc_start: 0.8802 (mtt) cc_final: 0.8465 (mtp) REVERT: D 86 ARG cc_start: 0.9036 (mpp-170) cc_final: 0.8590 (mtm-85) REVERT: D 94 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8903 (pt0) REVERT: D 245 MET cc_start: 0.8804 (mtp) cc_final: 0.8487 (mtp) REVERT: D 395 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7766 (ptt90) REVERT: D 420 TRP cc_start: 0.8510 (t60) cc_final: 0.7944 (t60) REVERT: D 447 THR cc_start: 0.9350 (p) cc_final: 0.9018 (p) REVERT: D 511 ASP cc_start: 0.8608 (p0) cc_final: 0.8354 (p0) REVERT: E 159 ARG cc_start: 0.8898 (tpt170) cc_final: 0.8091 (tpp-160) REVERT: E 163 ILE cc_start: 0.8260 (pt) cc_final: 0.7612 (pt) REVERT: E 167 VAL cc_start: 0.9064 (t) cc_final: 0.8765 (p) REVERT: E 214 TRP cc_start: 0.8398 (m-10) cc_final: 0.8163 (m-10) REVERT: E 395 ARG cc_start: 0.8248 (ptt90) cc_final: 0.7969 (ptt90) REVERT: E 511 ASP cc_start: 0.8695 (p0) cc_final: 0.8401 (p0) REVERT: E 683 TRP cc_start: 0.8433 (t-100) cc_final: 0.8150 (t-100) REVERT: F 63 ASP cc_start: 0.9272 (m-30) cc_final: 0.8979 (m-30) REVERT: F 94 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8900 (pt0) REVERT: F 150 GLN cc_start: 0.7769 (mm110) cc_final: 0.7430 (tp40) REVERT: F 214 TRP cc_start: 0.8429 (m-10) cc_final: 0.8039 (m-10) REVERT: F 245 MET cc_start: 0.8623 (mtm) cc_final: 0.8417 (mtp) REVERT: F 609 GLN cc_start: 0.9100 (mt0) cc_final: 0.8859 (mp10) REVERT: G 66 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8201 (mt-10) REVERT: G 157 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7100 (mtt90) REVERT: G 245 MET cc_start: 0.9000 (mtt) cc_final: 0.8704 (mtt) REVERT: G 395 ARG cc_start: 0.8231 (ptt90) cc_final: 0.8017 (ptt90) REVERT: G 565 PHE cc_start: 0.8253 (t80) cc_final: 0.7241 (t80) REVERT: G 683 TRP cc_start: 0.8317 (t-100) cc_final: 0.8001 (t-100) REVERT: H 94 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8887 (pt0) REVERT: H 150 GLN cc_start: 0.7798 (mm110) cc_final: 0.7410 (tp40) REVERT: H 157 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6847 (mtt-85) REVERT: H 395 ARG cc_start: 0.8065 (ptt90) cc_final: 0.7818 (ptt90) REVERT: H 420 TRP cc_start: 0.8496 (t60) cc_final: 0.8125 (t60) REVERT: H 609 GLN cc_start: 0.9126 (mt0) cc_final: 0.8876 (mt0) REVERT: I 94 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8815 (pt0) REVERT: I 545 MET cc_start: 0.8719 (tpp) cc_final: 0.8497 (tpp) REVERT: I 609 GLN cc_start: 0.9093 (mt0) cc_final: 0.8858 (mp10) REVERT: J 66 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8274 (mt-10) REVERT: J 94 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8923 (pt0) REVERT: J 157 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7115 (mtt180) REVERT: J 193 LYS cc_start: 0.9150 (ttmt) cc_final: 0.8758 (mtpp) REVERT: J 245 MET cc_start: 0.8865 (mtt) cc_final: 0.8547 (mtp) REVERT: J 420 TRP cc_start: 0.8456 (t60) cc_final: 0.8133 (t60) REVERT: K 66 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8450 (mt-10) REVERT: K 94 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8998 (pt0) REVERT: K 150 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7427 (tp-100) REVERT: K 159 ARG cc_start: 0.8593 (mmm160) cc_final: 0.7705 (mmm160) REVERT: K 162 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8218 (mtm180) REVERT: K 420 TRP cc_start: 0.8505 (t60) cc_final: 0.8081 (t60) REVERT: K 545 MET cc_start: 0.8712 (tpp) cc_final: 0.8478 (tpp) REVERT: L 66 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8166 (mt-10) REVERT: L 94 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8935 (pt0) REVERT: L 157 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.6864 (mtt90) REVERT: L 420 TRP cc_start: 0.8466 (t60) cc_final: 0.8136 (t60) REVERT: L 683 TRP cc_start: 0.8048 (t-100) cc_final: 0.7807 (t-100) REVERT: M 62 GLN cc_start: 0.8190 (mt0) cc_final: 0.7781 (tp40) REVERT: M 66 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8081 (mt-10) REVERT: M 110 ARG cc_start: 0.5823 (ttt90) cc_final: 0.5465 (ttm-80) REVERT: M 159 ARG cc_start: 0.9063 (tpt170) cc_final: 0.8183 (tpp-160) REVERT: M 163 ILE cc_start: 0.8400 (pt) cc_final: 0.7747 (pt) REVERT: M 245 MET cc_start: 0.8834 (mtp) cc_final: 0.8594 (mtp) REVERT: M 420 TRP cc_start: 0.8428 (t60) cc_final: 0.7981 (t60) REVERT: M 424 ILE cc_start: 0.8180 (pt) cc_final: 0.7909 (pt) REVERT: M 609 GLN cc_start: 0.9078 (mt0) cc_final: 0.8772 (mt0) REVERT: M 683 TRP cc_start: 0.8302 (t-100) cc_final: 0.8085 (t-100) REVERT: N 66 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8328 (mp0) REVERT: N 94 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8870 (pt0) REVERT: N 245 MET cc_start: 0.8772 (mtp) cc_final: 0.8271 (mtp) REVERT: N 672 MET cc_start: 0.1628 (ppp) cc_final: 0.1407 (ptt) REVERT: O 86 ARG cc_start: 0.9005 (mpp-170) cc_final: 0.8582 (mtm-85) REVERT: O 94 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8842 (pt0) REVERT: O 420 TRP cc_start: 0.8564 (t60) cc_final: 0.7801 (t60) REVERT: O 522 GLN cc_start: 0.8546 (mt0) cc_final: 0.8289 (mm-40) REVERT: O 609 GLN cc_start: 0.9095 (mt0) cc_final: 0.8780 (mt0) REVERT: P 94 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8904 (pt0) REVERT: P 157 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6576 (mtm110) REVERT: P 167 VAL cc_start: 0.9034 (t) cc_final: 0.8747 (p) REVERT: P 245 MET cc_start: 0.8715 (mtm) cc_final: 0.8441 (mtp) REVERT: P 420 TRP cc_start: 0.8499 (t60) cc_final: 0.8278 (t60) REVERT: P 457 MET cc_start: 0.7000 (tpp) cc_final: 0.6314 (mmt) REVERT: P 462 THR cc_start: 0.8883 (p) cc_final: 0.8451 (p) outliers start: 1 outliers final: 0 residues processed: 1257 average time/residue: 0.7289 time to fit residues: 1563.7578 Evaluate side-chains 917 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 917 time to evaluate : 6.805 ------------------------------------------------------------------------------- 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: 0.8980 chunk 387 optimal weight: 6.9990 chunk 580 optimal weight: 9.9990 chunk 292 optimal weight: 1.9990 chunk 190 optimal weight: 0.3980 chunk 188 optimal weight: 6.9990 chunk 617 optimal weight: 6.9990 chunk 661 optimal weight: 10.0000 chunk 480 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 763 optimal weight: 20.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 583 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 679 ASN ** I 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 80192 Z= 0.181 Angle : 0.563 8.206 108416 Z= 0.284 Chirality : 0.039 0.210 12416 Planarity : 0.004 0.055 14064 Dihedral : 4.242 17.281 10960 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.96 % 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: 0.43 (0.09), residues: 10000 helix: 0.74 (0.07), residues: 6832 sheet: -0.81 (0.27), residues: 304 loop : -0.47 (0.13), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 420 HIS 0.007 0.001 HIS A 583 PHE 0.017 0.001 PHE G 603 TYR 0.015 0.001 TYR G 348 ARG 0.010 0.000 ARG E 465 *********************** 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 1304 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1301 time to evaluate : 6.953 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: A 66 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 94 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8919 (pt0) REVERT: A 157 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6811 (mtm110) REVERT: A 159 ARG cc_start: 0.8547 (mmm160) cc_final: 0.8314 (mmm160) REVERT: A 245 MET cc_start: 0.8852 (mtp) cc_final: 0.8388 (mtp) REVERT: A 420 TRP cc_start: 0.8406 (t60) cc_final: 0.8045 (t60) REVERT: B 150 GLN cc_start: 0.7770 (mm110) cc_final: 0.7450 (tp40) REVERT: B 157 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6961 (mtt180) REVERT: B 159 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8347 (mmm160) REVERT: B 245 MET cc_start: 0.8822 (mtp) cc_final: 0.8444 (mtp) REVERT: B 297 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 420 TRP cc_start: 0.8480 (t60) cc_final: 0.8060 (t60) REVERT: B 462 THR cc_start: 0.8369 (m) cc_final: 0.8150 (m) REVERT: B 511 ASP cc_start: 0.8559 (p0) cc_final: 0.8310 (p0) REVERT: C 94 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8975 (pt0) REVERT: C 157 ARG cc_start: 0.7410 (mtm-85) cc_final: 0.7168 (mtt180) REVERT: C 193 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8801 (mtpp) REVERT: C 245 MET cc_start: 0.8652 (mtt) cc_final: 0.8340 (mtp) REVERT: C 297 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8504 (tm-30) REVERT: C 683 TRP cc_start: 0.8236 (t-100) cc_final: 0.8027 (t-100) REVERT: D 86 ARG cc_start: 0.8999 (mpp-170) cc_final: 0.8573 (mtm-85) REVERT: D 94 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8909 (pt0) REVERT: D 245 MET cc_start: 0.8774 (mtp) cc_final: 0.8395 (mtp) REVERT: D 420 TRP cc_start: 0.8463 (t60) cc_final: 0.8075 (t60) REVERT: D 457 MET cc_start: 0.5596 (tmm) cc_final: 0.4912 (ppp) REVERT: D 511 ASP cc_start: 0.8583 (p0) cc_final: 0.8342 (p0) REVERT: E 214 TRP cc_start: 0.8357 (m-10) cc_final: 0.8136 (m-10) REVERT: E 511 ASP cc_start: 0.8654 (p0) cc_final: 0.8409 (p0) REVERT: E 683 TRP cc_start: 0.8405 (t-100) cc_final: 0.8107 (t-100) REVERT: F 63 ASP cc_start: 0.9304 (m-30) cc_final: 0.8998 (m-30) REVERT: F 94 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8867 (pt0) REVERT: F 214 TRP cc_start: 0.8393 (m-10) cc_final: 0.8076 (m-10) REVERT: F 420 TRP cc_start: 0.8326 (t60) cc_final: 0.7824 (t60) REVERT: F 609 GLN cc_start: 0.9072 (mt0) cc_final: 0.8834 (mp10) REVERT: G 66 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8181 (mt-10) REVERT: G 214 TRP cc_start: 0.8390 (m-10) cc_final: 0.8143 (m-10) REVERT: G 395 ARG cc_start: 0.8277 (ptt90) cc_final: 0.8073 (ptt90) REVERT: G 511 ASP cc_start: 0.8613 (p0) cc_final: 0.8406 (p0) REVERT: G 683 TRP cc_start: 0.8275 (t-100) cc_final: 0.7923 (t-100) REVERT: H 94 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8853 (pt0) REVERT: H 157 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6717 (mtt90) REVERT: H 297 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8391 (tm-30) REVERT: H 395 ARG cc_start: 0.7970 (ptt90) cc_final: 0.7724 (ptt90) REVERT: H 420 TRP cc_start: 0.8480 (t60) cc_final: 0.8044 (t60) REVERT: H 609 GLN cc_start: 0.9111 (mt0) cc_final: 0.8858 (mt0) REVERT: I 94 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8824 (pt0) REVERT: I 245 MET cc_start: 0.8903 (mtp) cc_final: 0.8576 (mtp) REVERT: I 297 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8425 (tm-30) REVERT: I 420 TRP cc_start: 0.8451 (t60) cc_final: 0.8156 (t60) REVERT: I 545 MET cc_start: 0.8723 (tpp) cc_final: 0.8519 (tpp) REVERT: I 609 GLN cc_start: 0.9089 (mt0) cc_final: 0.8860 (mp10) REVERT: J 66 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8247 (mt-10) REVERT: J 94 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8904 (pt0) REVERT: J 157 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7146 (mtt180) REVERT: J 193 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8692 (mtpp) REVERT: J 245 MET cc_start: 0.8763 (mtt) cc_final: 0.8527 (mtp) REVERT: J 420 TRP cc_start: 0.8391 (t60) cc_final: 0.8108 (t60) REVERT: K 66 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8425 (mt-10) REVERT: K 94 GLU cc_start: 0.9230 (mt-10) cc_final: 0.9025 (pt0) REVERT: K 150 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7361 (tp-100) REVERT: K 159 ARG cc_start: 0.8566 (mmm160) cc_final: 0.7655 (mmm160) REVERT: K 162 ARG cc_start: 0.8661 (mtm180) cc_final: 0.8224 (mtm180) REVERT: K 167 VAL cc_start: 0.9063 (t) cc_final: 0.8791 (p) REVERT: K 245 MET cc_start: 0.8782 (mtp) cc_final: 0.8582 (mtp) REVERT: K 395 ARG cc_start: 0.8292 (ptt90) cc_final: 0.7994 (ptt90) REVERT: K 420 TRP cc_start: 0.8508 (t60) cc_final: 0.8133 (t60) REVERT: K 545 MET cc_start: 0.8654 (tpp) cc_final: 0.8446 (tpp) REVERT: L 94 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8951 (pt0) REVERT: L 157 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6907 (mtt90) REVERT: L 297 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8469 (tm-30) REVERT: L 420 TRP cc_start: 0.8381 (t60) cc_final: 0.8082 (t60) REVERT: L 683 TRP cc_start: 0.8005 (t-100) cc_final: 0.7485 (t-100) REVERT: M 62 GLN cc_start: 0.8215 (mt0) cc_final: 0.7775 (tp40) REVERT: M 66 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8025 (mt-10) REVERT: M 110 ARG cc_start: 0.5757 (ttt90) cc_final: 0.5420 (ttm-80) REVERT: M 159 ARG cc_start: 0.9044 (tpt170) cc_final: 0.8162 (tpp-160) REVERT: M 163 ILE cc_start: 0.8406 (pt) cc_final: 0.7818 (pt) REVERT: M 233 CYS cc_start: 0.8178 (t) cc_final: 0.7960 (t) REVERT: M 245 MET cc_start: 0.8764 (mtp) cc_final: 0.8431 (mtp) REVERT: M 420 TRP cc_start: 0.8377 (t60) cc_final: 0.8005 (t60) REVERT: M 522 GLN cc_start: 0.8419 (mt0) cc_final: 0.8171 (mm-40) REVERT: M 609 GLN cc_start: 0.9072 (mt0) cc_final: 0.8717 (mt0) REVERT: N 66 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8296 (mp0) REVERT: N 157 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7046 (mtt180) REVERT: N 245 MET cc_start: 0.8683 (mtp) cc_final: 0.8196 (mtp) REVERT: O 86 ARG cc_start: 0.8956 (mpp-170) cc_final: 0.8521 (mtm-85) REVERT: O 94 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8870 (pt0) REVERT: O 157 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.7077 (mtt180) REVERT: O 245 MET cc_start: 0.8890 (mtp) cc_final: 0.8688 (mtp) REVERT: O 420 TRP cc_start: 0.8461 (t60) cc_final: 0.7970 (t60) REVERT: O 522 GLN cc_start: 0.8414 (mt0) cc_final: 0.8171 (mm-40) REVERT: O 609 GLN cc_start: 0.9080 (mt0) cc_final: 0.8825 (mp10) REVERT: P 94 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8919 (pt0) REVERT: P 97 GLN cc_start: 0.8645 (pp30) cc_final: 0.8434 (pp30) REVERT: P 157 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6650 (mtm110) REVERT: P 167 VAL cc_start: 0.8997 (t) cc_final: 0.8703 (p) REVERT: P 214 TRP cc_start: 0.8468 (m-10) cc_final: 0.8232 (m-10) REVERT: P 245 MET cc_start: 0.8595 (mtm) cc_final: 0.8330 (mtp) REVERT: P 297 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8467 (tm-30) REVERT: P 457 MET cc_start: 0.6894 (tpp) cc_final: 0.6226 (mmt) REVERT: P 462 THR cc_start: 0.8833 (p) cc_final: 0.8370 (p) outliers start: 3 outliers final: 0 residues processed: 1304 average time/residue: 0.7403 time to fit residues: 1637.2807 Evaluate side-chains 930 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 930 time to evaluate : 6.770 ------------------------------------------------------------------------------- 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: 6.9990 chunk 849 optimal weight: 7.9990 chunk 905 optimal weight: 0.9980 chunk 544 optimal weight: 0.8980 chunk 394 optimal weight: 7.9990 chunk 710 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 818 optimal weight: 9.9990 chunk 856 optimal weight: 4.9990 chunk 902 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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 583 HIS A 609 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** 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 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 685 HIS G 383 ASN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 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 642 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN N 232 ASN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 80192 Z= 0.265 Angle : 0.620 7.183 108416 Z= 0.314 Chirality : 0.041 0.207 12416 Planarity : 0.004 0.054 14064 Dihedral : 4.431 18.942 10960 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.01 % Allowed : 0.56 % Favored : 99.43 % 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: 0.07 (0.09), residues: 10000 helix: 0.50 (0.06), residues: 6976 sheet: -0.85 (0.28), residues: 304 loop : -0.76 (0.13), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 420 HIS 0.007 0.001 HIS A 583 PHE 0.019 0.001 PHE B 603 TYR 0.012 0.001 TYR A 429 ARG 0.019 0.001 ARG G 307 *********************** 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 1241 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1240 time to evaluate : 6.822 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: A 66 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 94 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8926 (pt0) REVERT: A 157 ARG cc_start: 0.7273 (mtm-85) cc_final: 0.6729 (mtm110) REVERT: A 159 ARG cc_start: 0.8592 (mmm160) cc_final: 0.8360 (mmm160) REVERT: A 245 MET cc_start: 0.8791 (mtp) cc_final: 0.8254 (mtp) REVERT: B 150 GLN cc_start: 0.7776 (mm110) cc_final: 0.7532 (tp-100) REVERT: B 159 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8408 (mmm160) REVERT: B 245 MET cc_start: 0.8803 (mtp) cc_final: 0.8275 (mtp) REVERT: B 297 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 66 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 94 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8971 (pt0) REVERT: C 157 ARG cc_start: 0.7358 (mtm-85) cc_final: 0.7128 (mtt180) REVERT: C 193 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8738 (mtpp) REVERT: C 245 MET cc_start: 0.8686 (mtt) cc_final: 0.8399 (mtp) REVERT: C 297 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 683 TRP cc_start: 0.8451 (t-100) cc_final: 0.7932 (t-100) REVERT: D 86 ARG cc_start: 0.9005 (mpp-170) cc_final: 0.8736 (mtm-85) REVERT: D 94 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8913 (pt0) REVERT: D 245 MET cc_start: 0.8794 (mtp) cc_final: 0.8480 (mtp) REVERT: D 457 MET cc_start: 0.5868 (tmm) cc_final: 0.4990 (ppp) REVERT: E 159 ARG cc_start: 0.8979 (tpt170) cc_final: 0.8187 (tpp-160) REVERT: E 163 ILE cc_start: 0.8323 (pt) cc_final: 0.7675 (pt) REVERT: E 245 MET cc_start: 0.8934 (mtt) cc_final: 0.8715 (mtt) REVERT: E 565 PHE cc_start: 0.8345 (t80) cc_final: 0.7458 (t80) REVERT: E 683 TRP cc_start: 0.8425 (t-100) cc_final: 0.8138 (t-100) REVERT: F 63 ASP cc_start: 0.9266 (m-30) cc_final: 0.8972 (m-30) REVERT: F 94 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8861 (pt0) REVERT: F 609 GLN cc_start: 0.9082 (mt0) cc_final: 0.8739 (mt0) REVERT: G 66 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8195 (mt-10) REVERT: G 395 ARG cc_start: 0.8306 (ptt90) cc_final: 0.8092 (ptt90) REVERT: G 511 ASP cc_start: 0.8645 (p0) cc_final: 0.8412 (p0) REVERT: G 565 PHE cc_start: 0.8457 (t80) cc_final: 0.7527 (t80) REVERT: G 683 TRP cc_start: 0.8312 (t-100) cc_final: 0.8016 (t-100) REVERT: H 94 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8843 (pt0) REVERT: H 157 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: H 609 GLN cc_start: 0.9101 (mt0) cc_final: 0.8788 (mt0) REVERT: I 94 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8818 (pt0) REVERT: I 233 CYS cc_start: 0.8242 (t) cc_final: 0.8028 (t) REVERT: I 245 MET cc_start: 0.8888 (mtp) cc_final: 0.8347 (mtp) REVERT: I 420 TRP cc_start: 0.8556 (t60) cc_final: 0.8140 (t60) REVERT: I 545 MET cc_start: 0.8763 (tpp) cc_final: 0.8535 (tpp) REVERT: I 609 GLN cc_start: 0.9069 (mt0) cc_final: 0.8721 (mt0) REVERT: J 66 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8248 (mt-10) REVERT: J 94 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8902 (pt0) REVERT: J 193 LYS cc_start: 0.9158 (ttmt) cc_final: 0.8738 (mtpp) REVERT: J 297 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8449 (tm-30) REVERT: J 420 TRP cc_start: 0.8496 (t60) cc_final: 0.8101 (t60) REVERT: J 683 TRP cc_start: 0.8624 (t-100) cc_final: 0.8168 (t-100) REVERT: K 66 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8427 (mt-10) REVERT: K 94 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8993 (pt0) REVERT: K 167 VAL cc_start: 0.9113 (t) cc_final: 0.8844 (p) REVERT: K 245 MET cc_start: 0.8871 (mtp) cc_final: 0.8547 (mtp) REVERT: K 297 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8544 (tm-30) REVERT: K 395 ARG cc_start: 0.8291 (ptt90) cc_final: 0.7989 (ptt90) REVERT: K 545 MET cc_start: 0.8761 (tpp) cc_final: 0.8509 (tpp) REVERT: L 66 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8117 (mt-10) REVERT: L 94 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8946 (pt0) REVERT: L 157 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6788 (mtt90) REVERT: L 297 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8512 (tm-30) REVERT: L 420 TRP cc_start: 0.8497 (t60) cc_final: 0.8148 (t60) REVERT: L 683 TRP cc_start: 0.7931 (t-100) cc_final: 0.7613 (t-100) REVERT: M 62 GLN cc_start: 0.8204 (mt0) cc_final: 0.7746 (tp40) REVERT: M 66 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8057 (mt-10) REVERT: M 159 ARG cc_start: 0.9081 (tpt170) cc_final: 0.8221 (tpp-160) REVERT: M 163 ILE cc_start: 0.8431 (pt) cc_final: 0.7677 (pt) REVERT: M 245 MET cc_start: 0.8784 (mtp) cc_final: 0.8492 (mtp) REVERT: M 420 TRP cc_start: 0.8416 (t60) cc_final: 0.7908 (t60) REVERT: M 424 ILE cc_start: 0.8130 (pt) cc_final: 0.7922 (pt) REVERT: M 609 GLN cc_start: 0.9055 (mt0) cc_final: 0.8703 (mt0) REVERT: N 66 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8292 (mp0) REVERT: N 157 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7248 (mtt180) REVERT: N 167 VAL cc_start: 0.9057 (t) cc_final: 0.8762 (p) REVERT: N 245 MET cc_start: 0.8754 (mtp) cc_final: 0.8226 (mtp) REVERT: O 86 ARG cc_start: 0.8977 (mpp-170) cc_final: 0.8533 (mtm-85) REVERT: O 94 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8887 (pt0) REVERT: O 233 CYS cc_start: 0.8593 (t) cc_final: 0.8328 (t) REVERT: O 245 MET cc_start: 0.8906 (mtp) cc_final: 0.8478 (mtp) REVERT: O 522 GLN cc_start: 0.8545 (mt0) cc_final: 0.8279 (mm-40) REVERT: O 609 GLN cc_start: 0.9080 (mt0) cc_final: 0.8802 (mp10) REVERT: P 94 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8952 (pt0) REVERT: P 157 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6576 (mtm110) REVERT: P 167 VAL cc_start: 0.9025 (t) cc_final: 0.8736 (p) REVERT: P 297 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8491 (tm-30) REVERT: P 457 MET cc_start: 0.7113 (tpp) cc_final: 0.6436 (mmt) REVERT: P 462 THR cc_start: 0.8846 (p) cc_final: 0.8452 (p) outliers start: 1 outliers final: 0 residues processed: 1240 average time/residue: 0.7467 time to fit residues: 1567.8918 Evaluate side-chains 901 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 901 time to evaluate : 6.748 ------------------------------------------------------------------------------- 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: 6.9990 chunk 957 optimal weight: 1.9990 chunk 584 optimal weight: 6.9990 chunk 454 optimal weight: 1.9990 chunk 665 optimal weight: 9.9990 chunk 1004 optimal weight: 0.4980 chunk 924 optimal weight: 0.9990 chunk 799 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 617 optimal weight: 10.0000 chunk 490 optimal weight: 0.0030 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 583 HIS ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 ASN ** 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 437 GLN ** 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 383 ASN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 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 170 ASN J 437 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 437 GLN ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 232 ASN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 80192 Z= 0.173 Angle : 0.581 9.420 108416 Z= 0.291 Chirality : 0.039 0.183 12416 Planarity : 0.004 0.065 14064 Dihedral : 4.233 19.491 10960 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: 0.51 (0.09), residues: 10000 helix: 0.80 (0.07), residues: 6832 sheet: -0.72 (0.28), residues: 304 loop : -0.44 (0.13), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP P 420 HIS 0.008 0.001 HIS A 583 PHE 0.021 0.001 PHE P 426 TYR 0.016 0.001 TYR E 348 ARG 0.009 0.000 ARG B 244 ********************** 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 1296 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1292 time to evaluate : 6.848 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: A 66 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 94 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8912 (pt0) REVERT: A 151 ILE cc_start: 0.9030 (pt) cc_final: 0.8827 (pt) REVERT: A 157 ARG cc_start: 0.7149 (mtm-85) cc_final: 0.6601 (mtm110) REVERT: A 159 ARG cc_start: 0.8529 (mmm160) cc_final: 0.8282 (mmm160) REVERT: A 245 MET cc_start: 0.8734 (mtp) cc_final: 0.8271 (mtp) REVERT: A 297 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8475 (tm-30) REVERT: A 473 LEU cc_start: 0.9031 (tp) cc_final: 0.8826 (tp) REVERT: B 94 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8744 (pt0) REVERT: B 98 LEU cc_start: 0.9005 (mt) cc_final: 0.8687 (mt) REVERT: B 157 ARG cc_start: 0.7552 (mtt180) cc_final: 0.7245 (mtt180) REVERT: B 159 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8338 (mmm160) REVERT: B 245 MET cc_start: 0.8785 (mtp) cc_final: 0.8416 (mtp) REVERT: B 297 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 420 TRP cc_start: 0.8474 (t60) cc_final: 0.7956 (t60) REVERT: C 94 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8982 (pt0) REVERT: C 157 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.7173 (mtt180) REVERT: C 193 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8681 (mtpp) REVERT: C 245 MET cc_start: 0.8630 (mtt) cc_final: 0.8315 (mtp) REVERT: C 297 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8482 (tm-30) REVERT: D 86 ARG cc_start: 0.8996 (mpp-170) cc_final: 0.8716 (mtm-85) REVERT: D 94 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8889 (pt0) REVERT: D 233 CYS cc_start: 0.8288 (t) cc_final: 0.8053 (t) REVERT: D 245 MET cc_start: 0.8763 (mtp) cc_final: 0.8384 (mtp) REVERT: D 420 TRP cc_start: 0.8436 (t60) cc_final: 0.8064 (t60) REVERT: E 167 VAL cc_start: 0.9015 (t) cc_final: 0.8809 (t) REVERT: E 565 PHE cc_start: 0.8322 (t80) cc_final: 0.7400 (t80) REVERT: E 683 TRP cc_start: 0.8385 (t-100) cc_final: 0.8090 (t-100) REVERT: F 63 ASP cc_start: 0.9291 (m-30) cc_final: 0.8981 (m-30) REVERT: F 94 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8829 (pt0) REVERT: F 151 ILE cc_start: 0.8841 (pt) cc_final: 0.8622 (pt) REVERT: F 157 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7266 (mtt180) REVERT: F 214 TRP cc_start: 0.8351 (m-10) cc_final: 0.8074 (m-10) REVERT: F 386 LYS cc_start: 0.7975 (ptmm) cc_final: 0.7605 (pttp) REVERT: F 420 TRP cc_start: 0.8370 (t60) cc_final: 0.7876 (t60) REVERT: G 66 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8146 (mt-10) REVERT: G 76 LEU cc_start: 0.9396 (tp) cc_final: 0.9074 (tp) REVERT: G 245 MET cc_start: 0.8922 (mtt) cc_final: 0.8693 (mtt) REVERT: G 395 ARG cc_start: 0.8291 (ptt90) cc_final: 0.8085 (ptt90) REVERT: G 565 PHE cc_start: 0.8421 (t80) cc_final: 0.7456 (t80) REVERT: G 683 TRP cc_start: 0.8241 (t-100) cc_final: 0.7885 (t-100) REVERT: H 94 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8742 (pt0) REVERT: H 98 LEU cc_start: 0.9082 (mt) cc_final: 0.8752 (mt) REVERT: H 151 ILE cc_start: 0.8777 (pt) cc_final: 0.8562 (pt) REVERT: H 157 ARG cc_start: 0.7107 (mtm-85) cc_final: 0.6809 (mtt90) REVERT: H 420 TRP cc_start: 0.8473 (t60) cc_final: 0.7999 (t60) REVERT: H 447 THR cc_start: 0.9345 (p) cc_final: 0.8940 (p) REVERT: I 94 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8828 (pt0) REVERT: I 245 MET cc_start: 0.8884 (mtp) cc_final: 0.8538 (mtp) REVERT: I 420 TRP cc_start: 0.8468 (t60) cc_final: 0.8160 (t60) REVERT: I 545 MET cc_start: 0.8724 (tpp) cc_final: 0.8520 (tpp) REVERT: J 66 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8210 (mt-10) REVERT: J 94 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8896 (pt0) REVERT: J 193 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8720 (mtpp) REVERT: J 297 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8476 (tm-30) REVERT: J 420 TRP cc_start: 0.8402 (t60) cc_final: 0.7980 (t60) REVERT: J 683 TRP cc_start: 0.8510 (t-100) cc_final: 0.8291 (t-100) REVERT: K 66 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8400 (mt-10) REVERT: K 94 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8978 (pt0) REVERT: K 162 ARG cc_start: 0.8674 (mtm180) cc_final: 0.8238 (mtm180) REVERT: K 167 VAL cc_start: 0.9014 (t) cc_final: 0.8541 (p) REVERT: K 245 MET cc_start: 0.8755 (mtp) cc_final: 0.8479 (mtp) REVERT: K 297 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8469 (tm-30) REVERT: K 395 ARG cc_start: 0.8253 (ptt90) cc_final: 0.7959 (ptt90) REVERT: K 420 TRP cc_start: 0.8375 (t60) cc_final: 0.8041 (t60) REVERT: K 447 THR cc_start: 0.9237 (p) cc_final: 0.8937 (p) REVERT: K 545 MET cc_start: 0.8681 (tpp) cc_final: 0.8471 (tpp) REVERT: L 94 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8936 (pt0) REVERT: L 157 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6740 (mtt90) REVERT: L 297 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8480 (tm-30) REVERT: L 420 TRP cc_start: 0.8415 (t60) cc_final: 0.8127 (t60) REVERT: M 62 GLN cc_start: 0.8192 (mt0) cc_final: 0.7739 (tp40) REVERT: M 66 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8026 (mt-10) REVERT: M 110 ARG cc_start: 0.6149 (ttt90) cc_final: 0.5786 (ttm-80) REVERT: M 159 ARG cc_start: 0.9055 (tpt170) cc_final: 0.8174 (tpp-160) REVERT: M 163 ILE cc_start: 0.8365 (pt) cc_final: 0.7647 (pt) REVERT: M 245 MET cc_start: 0.8707 (mtp) cc_final: 0.8415 (mtp) REVERT: M 325 ASP cc_start: 0.8655 (m-30) cc_final: 0.8359 (p0) REVERT: M 420 TRP cc_start: 0.8372 (t60) cc_final: 0.8014 (t60) REVERT: M 609 GLN cc_start: 0.9049 (mt0) cc_final: 0.8713 (mt0) REVERT: N 66 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8267 (mt-10) REVERT: N 167 VAL cc_start: 0.8984 (t) cc_final: 0.8682 (p) REVERT: N 233 CYS cc_start: 0.8048 (t) cc_final: 0.7813 (t) REVERT: N 245 MET cc_start: 0.8714 (mtp) cc_final: 0.8268 (mtp) REVERT: O 86 ARG cc_start: 0.8938 (mpp-170) cc_final: 0.8723 (mpp-170) REVERT: O 94 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8846 (pt0) REVERT: O 157 ARG cc_start: 0.7550 (mtt180) cc_final: 0.7276 (mtt180) REVERT: O 245 MET cc_start: 0.8839 (mtp) cc_final: 0.8618 (mtp) REVERT: O 420 TRP cc_start: 0.8401 (t60) cc_final: 0.7912 (t60) REVERT: P 94 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8974 (pt0) REVERT: P 157 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6624 (mtm110) REVERT: P 214 TRP cc_start: 0.8412 (m-10) cc_final: 0.8208 (m-10) REVERT: P 297 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8439 (tm-30) REVERT: P 457 MET cc_start: 0.6906 (tpp) cc_final: 0.6328 (mmt) REVERT: P 462 THR cc_start: 0.8768 (p) cc_final: 0.8319 (p) REVERT: P 683 TRP cc_start: 0.8091 (t-100) cc_final: 0.7799 (t-100) outliers start: 4 outliers final: 0 residues processed: 1296 average time/residue: 0.7387 time to fit residues: 1618.8425 Evaluate side-chains 927 residues out of total 8400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 927 time to evaluate : 6.750 ------------------------------------------------------------------------------- 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: 1.9990 chunk 851 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 737 optimal weight: 0.0870 chunk 118 optimal weight: 30.0000 chunk 222 optimal weight: 0.0010 chunk 800 optimal weight: 7.9990 chunk 335 optimal weight: 7.9990 chunk 822 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 437 GLN ** 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN ** G 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 170 ASN ** H 437 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** ** K 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 685 HIS N 150 GLN ** N 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093954 restraints weight = 264812.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096761 restraints weight = 153009.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098565 restraints weight = 106329.098| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4650 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= 0.188 Angle : 0.587 9.838 108416 Z= 0.294 Chirality : 0.040 0.183 12416 Planarity : 0.004 0.107 14064 Dihedral : 4.187 20.287 10960 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.53 (0.09), residues: 10000 helix: 0.82 (0.07), residues: 6832 sheet: -0.73 (0.28), residues: 304 loop : -0.44 (0.13), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 420 HIS 0.008 0.001 HIS J 190 PHE 0.018 0.001 PHE B 603 TYR 0.012 0.001 TYR G 348 ARG 0.017 0.000 ARG N 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22847.58 seconds wall clock time: 399 minutes 53.05 seconds (23993.05 seconds total)