Starting phenix.real_space_refine on Thu Dec 14 02:13:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/12_2023/6qym_4679.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 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 84 5.16 5 C 17148 2.51 5 N 4512 2.21 5 O 5136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 26880 Number of models: 1 Model: "" Number of chains: 12 Chain: "0a" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0b" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0c" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0d" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0e" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0f" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0g" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0h" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0i" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0j" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0k" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "0l" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2240 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 13.80, per 1000 atoms: 0.51 Number of scatterers: 26880 At special positions: 0 Unit cell: (150.96, 150.96, 107.44, 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 84 16.00 O 5136 8.00 N 4512 7.00 C 17148 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: 10.35 Conformation dependent library (CDL) restraints added in 4.8 seconds 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6480 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 48 sheets defined 50.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain '0a' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0a 22 " --> pdb=" O GLN0a 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0a 25 " --> pdb=" O ASN0a 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0a 26 " --> pdb=" O ARG0a 22 " (cutoff:3.500A) Processing helix chain '0a' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0a 56 " --> pdb=" O PHE0a 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0a 58 " --> pdb=" O GLU0a 54 " (cutoff:3.500A) Processing helix chain '0a' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0a 135 " --> pdb=" O THR0a 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0a 136 " --> pdb=" O PRO0a 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0a 137 " --> pdb=" O THR0a 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0a 140 " --> pdb=" O LEU0a 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0a 142 " --> pdb=" O ALA0a 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0a 143 " --> pdb=" O ALA0a 139 " (cutoff:3.500A) Processing helix chain '0a' and resid 164 through 166 No H-bonds generated for 'chain '0a' and resid 164 through 166' Processing helix chain '0a' and resid 167 through 180 Processing helix chain '0a' and resid 192 through 194 No H-bonds generated for 'chain '0a' and resid 192 through 194' Processing helix chain '0a' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0a 211 " --> pdb=" O VAL0a 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0a 212 " --> pdb=" O ASP0a 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0a 213 " --> pdb=" O LYS0a 209 " (cutoff:3.500A) Processing helix chain '0a' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0a 251 " --> pdb=" O ASP0a 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0a 256 " --> pdb=" O SER0a 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0a 257 " --> pdb=" O SER0a 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0a 258 " --> pdb=" O GLY0a 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0a 259 " --> pdb=" O THR0a 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0a 260 " --> pdb=" O VAL0a 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0a 264 " --> pdb=" O SER0a 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0a 267 " --> pdb=" O GLU0a 263 " (cutoff:3.500A) Processing helix chain '0a' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0a 295 " --> pdb=" O GLU0a 291 " (cutoff:3.500A) Processing helix chain '0b' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0b 22 " --> pdb=" O GLN0b 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0b 25 " --> pdb=" O ASN0b 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0b 26 " --> pdb=" O ARG0b 22 " (cutoff:3.500A) Processing helix chain '0b' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0b 56 " --> pdb=" O PHE0b 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0b 58 " --> pdb=" O GLU0b 54 " (cutoff:3.500A) Processing helix chain '0b' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0b 135 " --> pdb=" O THR0b 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0b 136 " --> pdb=" O PRO0b 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0b 137 " --> pdb=" O THR0b 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0b 140 " --> pdb=" O LEU0b 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0b 142 " --> pdb=" O ALA0b 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0b 143 " --> pdb=" O ALA0b 139 " (cutoff:3.500A) Processing helix chain '0b' and resid 164 through 166 No H-bonds generated for 'chain '0b' and resid 164 through 166' Processing helix chain '0b' and resid 167 through 180 Processing helix chain '0b' and resid 192 through 194 No H-bonds generated for 'chain '0b' and resid 192 through 194' Processing helix chain '0b' and resid 206 through 226 removed outlier: 3.626A pdb=" N ASN0b 211 " --> pdb=" O VAL0b 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0b 212 " --> pdb=" O ASP0b 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0b 213 " --> pdb=" O LYS0b 209 " (cutoff:3.500A) Processing helix chain '0b' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0b 251 " --> pdb=" O ASP0b 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0b 256 " --> pdb=" O SER0b 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0b 257 " --> pdb=" O SER0b 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0b 258 " --> pdb=" O GLY0b 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0b 259 " --> pdb=" O THR0b 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0b 260 " --> pdb=" O VAL0b 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0b 264 " --> pdb=" O SER0b 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0b 267 " --> pdb=" O GLU0b 263 " (cutoff:3.500A) Processing helix chain '0b' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0b 295 " --> pdb=" O GLU0b 291 " (cutoff:3.500A) Processing helix chain '0c' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0c 22 " --> pdb=" O GLN0c 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0c 25 " --> pdb=" O ASN0c 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0c 26 " --> pdb=" O ARG0c 22 " (cutoff:3.500A) Processing helix chain '0c' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0c 56 " --> pdb=" O PHE0c 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0c 58 " --> pdb=" O GLU0c 54 " (cutoff:3.500A) Processing helix chain '0c' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0c 135 " --> pdb=" O THR0c 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0c 136 " --> pdb=" O PRO0c 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0c 137 " --> pdb=" O THR0c 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0c 140 " --> pdb=" O LEU0c 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0c 142 " --> pdb=" O ALA0c 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0c 143 " --> pdb=" O ALA0c 139 " (cutoff:3.500A) Processing helix chain '0c' and resid 164 through 166 No H-bonds generated for 'chain '0c' and resid 164 through 166' Processing helix chain '0c' and resid 167 through 180 Processing helix chain '0c' and resid 192 through 194 No H-bonds generated for 'chain '0c' and resid 192 through 194' Processing helix chain '0c' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0c 211 " --> pdb=" O VAL0c 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0c 212 " --> pdb=" O ASP0c 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN0c 213 " --> pdb=" O LYS0c 209 " (cutoff:3.500A) Processing helix chain '0c' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0c 251 " --> pdb=" O ASP0c 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL0c 256 " --> pdb=" O SER0c 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0c 257 " --> pdb=" O SER0c 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0c 258 " --> pdb=" O GLY0c 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0c 259 " --> pdb=" O THR0c 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0c 260 " --> pdb=" O VAL0c 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0c 264 " --> pdb=" O SER0c 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0c 267 " --> pdb=" O GLU0c 263 " (cutoff:3.500A) Processing helix chain '0c' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0c 295 " --> pdb=" O GLU0c 291 " (cutoff:3.500A) Processing helix chain '0d' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0d 22 " --> pdb=" O GLN0d 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0d 25 " --> pdb=" O ASN0d 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0d 26 " --> pdb=" O ARG0d 22 " (cutoff:3.500A) Processing helix chain '0d' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0d 56 " --> pdb=" O PHE0d 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0d 58 " --> pdb=" O GLU0d 54 " (cutoff:3.500A) Processing helix chain '0d' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0d 135 " --> pdb=" O THR0d 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU0d 136 " --> pdb=" O PRO0d 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0d 137 " --> pdb=" O THR0d 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0d 140 " --> pdb=" O LEU0d 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0d 142 " --> pdb=" O ALA0d 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0d 143 " --> pdb=" O ALA0d 139 " (cutoff:3.500A) Processing helix chain '0d' and resid 164 through 166 No H-bonds generated for 'chain '0d' and resid 164 through 166' Processing helix chain '0d' and resid 167 through 180 Processing helix chain '0d' and resid 192 through 194 No H-bonds generated for 'chain '0d' and resid 192 through 194' Processing helix chain '0d' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0d 211 " --> pdb=" O VAL0d 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0d 212 " --> pdb=" O ASP0d 208 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN0d 213 " --> pdb=" O LYS0d 209 " (cutoff:3.500A) Processing helix chain '0d' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0d 251 " --> pdb=" O ASP0d 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0d 256 " --> pdb=" O SER0d 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0d 257 " --> pdb=" O SER0d 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU0d 258 " --> pdb=" O GLY0d 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0d 259 " --> pdb=" O THR0d 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0d 260 " --> pdb=" O VAL0d 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0d 264 " --> pdb=" O SER0d 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0d 267 " --> pdb=" O GLU0d 263 " (cutoff:3.500A) Processing helix chain '0d' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0d 295 " --> pdb=" O GLU0d 291 " (cutoff:3.500A) Processing helix chain '0e' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0e 22 " --> pdb=" O GLN0e 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0e 25 " --> pdb=" O ASN0e 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0e 26 " --> pdb=" O ARG0e 22 " (cutoff:3.500A) Processing helix chain '0e' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0e 56 " --> pdb=" O PHE0e 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0e 58 " --> pdb=" O GLU0e 54 " (cutoff:3.500A) Processing helix chain '0e' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0e 135 " --> pdb=" O THR0e 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0e 136 " --> pdb=" O PRO0e 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0e 137 " --> pdb=" O THR0e 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0e 140 " --> pdb=" O LEU0e 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0e 142 " --> pdb=" O ALA0e 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0e 143 " --> pdb=" O ALA0e 139 " (cutoff:3.500A) Processing helix chain '0e' and resid 164 through 166 No H-bonds generated for 'chain '0e' and resid 164 through 166' Processing helix chain '0e' and resid 167 through 180 Processing helix chain '0e' and resid 192 through 194 No H-bonds generated for 'chain '0e' and resid 192 through 194' Processing helix chain '0e' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0e 211 " --> pdb=" O VAL0e 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0e 212 " --> pdb=" O ASP0e 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0e 213 " --> pdb=" O LYS0e 209 " (cutoff:3.500A) Processing helix chain '0e' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0e 251 " --> pdb=" O ASP0e 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0e 256 " --> pdb=" O SER0e 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0e 257 " --> pdb=" O SER0e 253 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU0e 258 " --> pdb=" O GLY0e 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0e 259 " --> pdb=" O THR0e 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0e 260 " --> pdb=" O VAL0e 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0e 264 " --> pdb=" O SER0e 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0e 267 " --> pdb=" O GLU0e 263 " (cutoff:3.500A) Processing helix chain '0e' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0e 295 " --> pdb=" O GLU0e 291 " (cutoff:3.500A) Processing helix chain '0f' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0f 22 " --> pdb=" O GLN0f 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0f 25 " --> pdb=" O ASN0f 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0f 26 " --> pdb=" O ARG0f 22 " (cutoff:3.500A) Processing helix chain '0f' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0f 56 " --> pdb=" O PHE0f 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0f 58 " --> pdb=" O GLU0f 54 " (cutoff:3.500A) Processing helix chain '0f' and resid 130 through 154 removed outlier: 3.539A pdb=" N GLU0f 135 " --> pdb=" O THR0f 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0f 136 " --> pdb=" O PRO0f 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0f 137 " --> pdb=" O THR0f 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0f 140 " --> pdb=" O LEU0f 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0f 142 " --> pdb=" O ALA0f 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0f 143 " --> pdb=" O ALA0f 139 " (cutoff:3.500A) Processing helix chain '0f' and resid 164 through 166 No H-bonds generated for 'chain '0f' and resid 164 through 166' Processing helix chain '0f' and resid 167 through 180 Processing helix chain '0f' and resid 192 through 194 No H-bonds generated for 'chain '0f' and resid 192 through 194' Processing helix chain '0f' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0f 211 " --> pdb=" O VAL0f 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0f 212 " --> pdb=" O ASP0f 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0f 213 " --> pdb=" O LYS0f 209 " (cutoff:3.500A) Processing helix chain '0f' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0f 251 " --> pdb=" O ASP0f 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0f 256 " --> pdb=" O SER0f 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE0f 257 " --> pdb=" O SER0f 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0f 258 " --> pdb=" O GLY0f 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS0f 259 " --> pdb=" O THR0f 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0f 260 " --> pdb=" O VAL0f 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0f 264 " --> pdb=" O SER0f 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0f 267 " --> pdb=" O GLU0f 263 " (cutoff:3.500A) Processing helix chain '0f' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0f 295 " --> pdb=" O GLU0f 291 " (cutoff:3.500A) Processing helix chain '0g' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0g 22 " --> pdb=" O GLN0g 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0g 25 " --> pdb=" O ASN0g 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0g 26 " --> pdb=" O ARG0g 22 " (cutoff:3.500A) Processing helix chain '0g' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0g 56 " --> pdb=" O PHE0g 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0g 58 " --> pdb=" O GLU0g 54 " (cutoff:3.500A) Processing helix chain '0g' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0g 135 " --> pdb=" O THR0g 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0g 136 " --> pdb=" O PRO0g 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0g 137 " --> pdb=" O THR0g 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0g 140 " --> pdb=" O LEU0g 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0g 142 " --> pdb=" O ALA0g 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0g 143 " --> pdb=" O ALA0g 139 " (cutoff:3.500A) Processing helix chain '0g' and resid 164 through 166 No H-bonds generated for 'chain '0g' and resid 164 through 166' Processing helix chain '0g' and resid 167 through 180 Processing helix chain '0g' and resid 192 through 194 No H-bonds generated for 'chain '0g' and resid 192 through 194' Processing helix chain '0g' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0g 211 " --> pdb=" O VAL0g 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0g 212 " --> pdb=" O ASP0g 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0g 213 " --> pdb=" O LYS0g 209 " (cutoff:3.500A) Processing helix chain '0g' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0g 251 " --> pdb=" O ASP0g 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0g 256 " --> pdb=" O SER0g 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0g 257 " --> pdb=" O SER0g 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0g 258 " --> pdb=" O GLY0g 254 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS0g 259 " --> pdb=" O THR0g 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0g 260 " --> pdb=" O VAL0g 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0g 264 " --> pdb=" O SER0g 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0g 267 " --> pdb=" O GLU0g 263 " (cutoff:3.500A) Processing helix chain '0g' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0g 295 " --> pdb=" O GLU0g 291 " (cutoff:3.500A) Processing helix chain '0h' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0h 22 " --> pdb=" O GLN0h 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0h 25 " --> pdb=" O ASN0h 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0h 26 " --> pdb=" O ARG0h 22 " (cutoff:3.500A) Processing helix chain '0h' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0h 56 " --> pdb=" O PHE0h 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0h 58 " --> pdb=" O GLU0h 54 " (cutoff:3.500A) Processing helix chain '0h' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0h 135 " --> pdb=" O THR0h 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0h 136 " --> pdb=" O PRO0h 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE0h 137 " --> pdb=" O THR0h 133 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU0h 140 " --> pdb=" O LEU0h 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0h 142 " --> pdb=" O ALA0h 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0h 143 " --> pdb=" O ALA0h 139 " (cutoff:3.500A) Processing helix chain '0h' and resid 164 through 166 No H-bonds generated for 'chain '0h' and resid 164 through 166' Processing helix chain '0h' and resid 167 through 180 Processing helix chain '0h' and resid 192 through 194 No H-bonds generated for 'chain '0h' and resid 192 through 194' Processing helix chain '0h' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0h 211 " --> pdb=" O VAL0h 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0h 212 " --> pdb=" O ASP0h 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0h 213 " --> pdb=" O LYS0h 209 " (cutoff:3.500A) Processing helix chain '0h' and resid 247 through 269 removed outlier: 3.652A pdb=" N GLU0h 251 " --> pdb=" O ASP0h 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL0h 256 " --> pdb=" O SER0h 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0h 257 " --> pdb=" O SER0h 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0h 258 " --> pdb=" O GLY0h 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0h 259 " --> pdb=" O THR0h 255 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER0h 260 " --> pdb=" O VAL0h 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0h 264 " --> pdb=" O SER0h 260 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS0h 267 " --> pdb=" O GLU0h 263 " (cutoff:3.500A) Processing helix chain '0h' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0h 295 " --> pdb=" O GLU0h 291 " (cutoff:3.500A) Processing helix chain '0i' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0i 22 " --> pdb=" O GLN0i 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0i 25 " --> pdb=" O ASN0i 21 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS0i 26 " --> pdb=" O ARG0i 22 " (cutoff:3.500A) Processing helix chain '0i' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0i 56 " --> pdb=" O PHE0i 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0i 58 " --> pdb=" O GLU0i 54 " (cutoff:3.500A) Processing helix chain '0i' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0i 135 " --> pdb=" O THR0i 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0i 136 " --> pdb=" O PRO0i 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0i 137 " --> pdb=" O THR0i 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0i 140 " --> pdb=" O LEU0i 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA0i 142 " --> pdb=" O ALA0i 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0i 143 " --> pdb=" O ALA0i 139 " (cutoff:3.500A) Processing helix chain '0i' and resid 164 through 166 No H-bonds generated for 'chain '0i' and resid 164 through 166' Processing helix chain '0i' and resid 167 through 180 Processing helix chain '0i' and resid 192 through 194 No H-bonds generated for 'chain '0i' and resid 192 through 194' Processing helix chain '0i' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0i 211 " --> pdb=" O VAL0i 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0i 212 " --> pdb=" O ASP0i 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0i 213 " --> pdb=" O LYS0i 209 " (cutoff:3.500A) Processing helix chain '0i' and resid 247 through 269 removed outlier: 3.652A pdb=" N GLU0i 251 " --> pdb=" O ASP0i 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0i 256 " --> pdb=" O SER0i 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0i 257 " --> pdb=" O SER0i 253 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU0i 258 " --> pdb=" O GLY0i 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0i 259 " --> pdb=" O THR0i 255 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER0i 260 " --> pdb=" O VAL0i 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0i 264 " --> pdb=" O SER0i 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0i 267 " --> pdb=" O GLU0i 263 " (cutoff:3.500A) Processing helix chain '0i' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0i 295 " --> pdb=" O GLU0i 291 " (cutoff:3.500A) Processing helix chain '0j' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0j 22 " --> pdb=" O GLN0j 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0j 25 " --> pdb=" O ASN0j 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0j 26 " --> pdb=" O ARG0j 22 " (cutoff:3.500A) Processing helix chain '0j' and resid 49 through 60 removed outlier: 3.825A pdb=" N SER0j 56 " --> pdb=" O PHE0j 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0j 58 " --> pdb=" O GLU0j 54 " (cutoff:3.500A) Processing helix chain '0j' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0j 135 " --> pdb=" O THR0j 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU0j 136 " --> pdb=" O PRO0j 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0j 137 " --> pdb=" O THR0j 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0j 140 " --> pdb=" O LEU0j 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0j 142 " --> pdb=" O ALA0j 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0j 143 " --> pdb=" O ALA0j 139 " (cutoff:3.500A) Processing helix chain '0j' and resid 164 through 166 No H-bonds generated for 'chain '0j' and resid 164 through 166' Processing helix chain '0j' and resid 167 through 180 Processing helix chain '0j' and resid 192 through 194 No H-bonds generated for 'chain '0j' and resid 192 through 194' Processing helix chain '0j' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0j 211 " --> pdb=" O VAL0j 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0j 212 " --> pdb=" O ASP0j 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0j 213 " --> pdb=" O LYS0j 209 " (cutoff:3.500A) Processing helix chain '0j' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0j 251 " --> pdb=" O ASP0j 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL0j 256 " --> pdb=" O SER0j 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0j 257 " --> pdb=" O SER0j 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0j 258 " --> pdb=" O GLY0j 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0j 259 " --> pdb=" O THR0j 255 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER0j 260 " --> pdb=" O VAL0j 256 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA0j 264 " --> pdb=" O SER0j 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0j 267 " --> pdb=" O GLU0j 263 " (cutoff:3.500A) Processing helix chain '0j' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0j 295 " --> pdb=" O GLU0j 291 " (cutoff:3.500A) Processing helix chain '0k' and resid 11 through 36 removed outlier: 3.510A pdb=" N ARG0k 22 " --> pdb=" O GLN0k 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0k 25 " --> pdb=" O ASN0k 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0k 26 " --> pdb=" O ARG0k 22 " (cutoff:3.500A) Processing helix chain '0k' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0k 56 " --> pdb=" O PHE0k 52 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS0k 58 " --> pdb=" O GLU0k 54 " (cutoff:3.500A) Processing helix chain '0k' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0k 135 " --> pdb=" O THR0k 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0k 136 " --> pdb=" O PRO0k 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0k 137 " --> pdb=" O THR0k 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0k 140 " --> pdb=" O LEU0k 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0k 142 " --> pdb=" O ALA0k 138 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU0k 143 " --> pdb=" O ALA0k 139 " (cutoff:3.500A) Processing helix chain '0k' and resid 164 through 166 No H-bonds generated for 'chain '0k' and resid 164 through 166' Processing helix chain '0k' and resid 167 through 180 Processing helix chain '0k' and resid 192 through 194 No H-bonds generated for 'chain '0k' and resid 192 through 194' Processing helix chain '0k' and resid 206 through 226 removed outlier: 3.627A pdb=" N ASN0k 211 " --> pdb=" O VAL0k 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA0k 212 " --> pdb=" O ASP0k 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0k 213 " --> pdb=" O LYS0k 209 " (cutoff:3.500A) Processing helix chain '0k' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0k 251 " --> pdb=" O ASP0k 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0k 256 " --> pdb=" O SER0k 252 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE0k 257 " --> pdb=" O SER0k 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0k 258 " --> pdb=" O GLY0k 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0k 259 " --> pdb=" O THR0k 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0k 260 " --> pdb=" O VAL0k 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0k 264 " --> pdb=" O SER0k 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0k 267 " --> pdb=" O GLU0k 263 " (cutoff:3.500A) Processing helix chain '0k' and resid 284 through 297 removed outlier: 4.096A pdb=" N ILE0k 295 " --> pdb=" O GLU0k 291 " (cutoff:3.500A) Processing helix chain '0l' and resid 11 through 36 removed outlier: 3.509A pdb=" N ARG0l 22 " --> pdb=" O GLN0l 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0l 25 " --> pdb=" O ASN0l 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS0l 26 " --> pdb=" O ARG0l 22 " (cutoff:3.500A) Processing helix chain '0l' and resid 49 through 60 removed outlier: 3.826A pdb=" N SER0l 56 " --> pdb=" O PHE0l 52 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS0l 58 " --> pdb=" O GLU0l 54 " (cutoff:3.500A) Processing helix chain '0l' and resid 130 through 154 removed outlier: 3.540A pdb=" N GLU0l 135 " --> pdb=" O THR0l 131 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU0l 136 " --> pdb=" O PRO0l 132 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE0l 137 " --> pdb=" O THR0l 133 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU0l 140 " --> pdb=" O LEU0l 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA0l 142 " --> pdb=" O ALA0l 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU0l 143 " --> pdb=" O ALA0l 139 " (cutoff:3.500A) Processing helix chain '0l' and resid 164 through 166 No H-bonds generated for 'chain '0l' and resid 164 through 166' Processing helix chain '0l' and resid 167 through 180 Processing helix chain '0l' and resid 192 through 194 No H-bonds generated for 'chain '0l' and resid 192 through 194' Processing helix chain '0l' and resid 206 through 226 removed outlier: 3.628A pdb=" N ASN0l 211 " --> pdb=" O VAL0l 207 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA0l 212 " --> pdb=" O ASP0l 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN0l 213 " --> pdb=" O LYS0l 209 " (cutoff:3.500A) Processing helix chain '0l' and resid 247 through 269 removed outlier: 3.653A pdb=" N GLU0l 251 " --> pdb=" O ASP0l 247 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL0l 256 " --> pdb=" O SER0l 252 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE0l 257 " --> pdb=" O SER0l 253 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU0l 258 " --> pdb=" O GLY0l 254 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS0l 259 " --> pdb=" O THR0l 255 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER0l 260 " --> pdb=" O VAL0l 256 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA0l 264 " --> pdb=" O SER0l 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS0l 267 " --> pdb=" O GLU0l 263 " (cutoff:3.500A) Processing helix chain '0l' and resid 284 through 297 removed outlier: 4.097A pdb=" N ILE0l 295 " --> pdb=" O GLU0l 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0a' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain '0a' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0a 63 " --> pdb=" O ILE0a 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0a 121 " --> pdb=" O VAL0a 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0a' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0a 93 " --> pdb=" O PHE0a 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '0a' and resid 196 through 198 removed outlier: 5.697A pdb=" N VAL0a 159 " --> pdb=" O ILE0b 185 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA0b 187 " --> pdb=" O VAL0a 159 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE0a 161 " --> pdb=" O ALA0b 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0a' and resid 184 through 188 Processing sheet with id=AA6, first strand: chain '0b' and resid 39 through 42 Processing sheet with id=AA7, first strand: chain '0b' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0b 63 " --> pdb=" O ILE0b 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0b 121 " --> pdb=" O VAL0b 63 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0b' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0b 93 " --> pdb=" O PHE0b 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '0b' and resid 196 through 198 removed outlier: 5.553A pdb=" N VAL0b 159 " --> pdb=" O ILE0c 185 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA0c 187 " --> pdb=" O VAL0b 159 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE0b 161 " --> pdb=" O ALA0c 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '0c' and resid 39 through 42 Processing sheet with id=AB2, first strand: chain '0c' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0c 63 " --> pdb=" O ILE0c 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0c 121 " --> pdb=" O VAL0c 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0c' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0c 93 " --> pdb=" O PHE0c 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '0c' and resid 196 through 198 removed outlier: 5.843A pdb=" N VAL0c 159 " --> pdb=" O ILE0d 185 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA0d 187 " --> pdb=" O VAL0c 159 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE0c 161 " --> pdb=" O ALA0d 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '0d' and resid 39 through 42 Processing sheet with id=AB6, first strand: chain '0d' and resid 73 through 76 removed outlier: 3.526A pdb=" N VAL0d 63 " --> pdb=" O ILE0d 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0d 121 " --> pdb=" O VAL0d 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '0d' and resid 78 through 81 removed outlier: 3.541A pdb=" N PHE0d 93 " --> pdb=" O PHE0d 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '0d' and resid 196 through 198 removed outlier: 5.694A pdb=" N VAL0d 159 " --> pdb=" O ILE0e 185 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA0e 187 " --> pdb=" O VAL0d 159 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE0d 161 " --> pdb=" O ALA0e 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '0e' and resid 39 through 42 Processing sheet with id=AC1, first strand: chain '0e' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0e 63 " --> pdb=" O ILE0e 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0e 121 " --> pdb=" O VAL0e 63 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '0e' and resid 78 through 81 removed outlier: 3.541A pdb=" N PHE0e 93 " --> pdb=" O PHE0e 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '0e' and resid 196 through 198 removed outlier: 5.843A pdb=" N VAL0e 159 " --> pdb=" O ILE0f 185 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA0f 187 " --> pdb=" O VAL0e 159 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE0e 161 " --> pdb=" O ALA0f 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0f' and resid 39 through 42 Processing sheet with id=AC5, first strand: chain '0f' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0f 63 " --> pdb=" O ILE0f 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0f 121 " --> pdb=" O VAL0f 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '0f' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0f 93 " --> pdb=" O PHE0f 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '0f' and resid 196 through 198 removed outlier: 5.778A pdb=" N VAL0f 159 " --> pdb=" O ILE0g 185 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA0g 187 " --> pdb=" O VAL0f 159 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE0f 161 " --> pdb=" O ALA0g 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '0g' and resid 39 through 42 Processing sheet with id=AC9, first strand: chain '0g' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0g 63 " --> pdb=" O ILE0g 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0g 121 " --> pdb=" O VAL0g 63 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '0g' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0g 93 " --> pdb=" O PHE0g 104 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '0g' and resid 196 through 198 removed outlier: 5.595A pdb=" N VAL0g 159 " --> pdb=" O ILE0h 185 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA0h 187 " --> pdb=" O VAL0g 159 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE0g 161 " --> pdb=" O ALA0h 187 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '0h' and resid 39 through 42 Processing sheet with id=AD4, first strand: chain '0h' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0h 63 " --> pdb=" O ILE0h 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0h 121 " --> pdb=" O VAL0h 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '0h' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0h 93 " --> pdb=" O PHE0h 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '0h' and resid 196 through 198 removed outlier: 5.667A pdb=" N VAL0h 159 " --> pdb=" O ILE0i 185 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA0i 187 " --> pdb=" O VAL0h 159 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE0h 161 " --> pdb=" O ALA0i 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '0i' and resid 39 through 42 Processing sheet with id=AD8, first strand: chain '0i' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0i 63 " --> pdb=" O ILE0i 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0i 121 " --> pdb=" O VAL0i 63 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '0i' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0i 93 " --> pdb=" O PHE0i 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '0i' and resid 196 through 198 removed outlier: 5.690A pdb=" N VAL0i 159 " --> pdb=" O ILE0l 185 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA0l 187 " --> pdb=" O VAL0i 159 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE0i 161 " --> pdb=" O ALA0l 187 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '0j' and resid 39 through 42 Processing sheet with id=AE3, first strand: chain '0j' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0j 63 " --> pdb=" O ILE0j 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0j 121 " --> pdb=" O VAL0j 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0j' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0j 93 " --> pdb=" O PHE0j 104 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '0j' and resid 184 through 188 Processing sheet with id=AE6, first strand: chain '0k' and resid 39 through 42 Processing sheet with id=AE7, first strand: chain '0k' and resid 73 through 76 removed outlier: 3.525A pdb=" N VAL0k 63 " --> pdb=" O ILE0k 121 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE0k 121 " --> pdb=" O VAL0k 63 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '0k' and resid 78 through 81 removed outlier: 3.543A pdb=" N PHE0k 93 " --> pdb=" O PHE0k 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '0k' and resid 184 through 188 Processing sheet with id=AF1, first strand: chain '0l' and resid 39 through 42 Processing sheet with id=AF2, first strand: chain '0l' and resid 73 through 76 removed outlier: 3.524A pdb=" N VAL0l 63 " --> pdb=" O ILE0l 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE0l 121 " --> pdb=" O VAL0l 63 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '0l' and resid 78 through 81 removed outlier: 3.542A pdb=" N PHE0l 93 " --> pdb=" O PHE0l 104 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3672 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: 8.72 Time building geometry restraints manager: 11.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8187 1.33 - 1.45: 4795 1.45 - 1.57: 14330 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 27456 Sorted by residual: bond pdb=" CB PHE0k 24 " pdb=" CG PHE0k 24 " ideal model delta sigma weight residual 1.502 1.431 0.071 2.30e-02 1.89e+03 9.49e+00 bond pdb=" CB PHE0b 24 " pdb=" CG PHE0b 24 " ideal model delta sigma weight residual 1.502 1.431 0.071 2.30e-02 1.89e+03 9.49e+00 bond pdb=" CB PHE0d 24 " pdb=" CG PHE0d 24 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.39e+00 bond pdb=" CB PHE0l 24 " pdb=" CG PHE0l 24 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.34e+00 bond pdb=" CB PHE0j 24 " pdb=" CG PHE0j 24 " ideal model delta sigma weight residual 1.502 1.432 0.070 2.30e-02 1.89e+03 9.33e+00 ... (remaining 27451 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 565 106.42 - 113.31: 14626 113.31 - 120.20: 10660 120.20 - 127.09: 11165 127.09 - 133.97: 220 Bond angle restraints: 37236 Sorted by residual: angle pdb=" CA THR0f 131 " pdb=" C THR0f 131 " pdb=" N PRO0f 132 " ideal model delta sigma weight residual 118.44 122.47 -4.03 1.59e+00 3.96e-01 6.44e+00 angle pdb=" CA THR0e 131 " pdb=" C THR0e 131 " pdb=" N PRO0e 132 " ideal model delta sigma weight residual 118.44 122.47 -4.03 1.59e+00 3.96e-01 6.43e+00 angle pdb=" CA THR0h 131 " pdb=" C THR0h 131 " pdb=" N PRO0h 132 " ideal model delta sigma weight residual 118.44 122.47 -4.03 1.59e+00 3.96e-01 6.43e+00 angle pdb=" NE ARG0b 17 " pdb=" CZ ARG0b 17 " pdb=" NH2 ARG0b 17 " ideal model delta sigma weight residual 119.20 121.48 -2.28 9.00e-01 1.23e+00 6.41e+00 angle pdb=" CA THR0a 131 " pdb=" C THR0a 131 " pdb=" N PRO0a 132 " ideal model delta sigma weight residual 118.44 122.46 -4.02 1.59e+00 3.96e-01 6.40e+00 ... (remaining 37231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.41: 14419 10.41 - 20.81: 1733 20.81 - 31.22: 180 31.22 - 41.62: 120 41.62 - 52.03: 48 Dihedral angle restraints: 16500 sinusoidal: 6480 harmonic: 10020 Sorted by residual: dihedral pdb=" CA TRP0j 23 " pdb=" C TRP0j 23 " pdb=" N PHE0j 24 " pdb=" CA PHE0j 24 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TRP0k 23 " pdb=" C TRP0k 23 " pdb=" N PHE0k 24 " pdb=" CA PHE0k 24 " ideal model delta harmonic sigma weight residual -180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TRP0d 23 " pdb=" C TRP0d 23 " pdb=" N PHE0d 24 " pdb=" CA PHE0d 24 " ideal model delta harmonic sigma weight residual 180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 16497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1891 0.035 - 0.070: 1355 0.070 - 0.104: 583 0.104 - 0.139: 167 0.139 - 0.174: 36 Chirality restraints: 4032 Sorted by residual: chirality pdb=" CB VAL0l 278 " pdb=" CA VAL0l 278 " pdb=" CG1 VAL0l 278 " pdb=" CG2 VAL0l 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB VAL0h 278 " pdb=" CA VAL0h 278 " pdb=" CG1 VAL0h 278 " pdb=" CG2 VAL0h 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CB VAL0c 278 " pdb=" CA VAL0c 278 " pdb=" CG1 VAL0c 278 " pdb=" CG2 VAL0c 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 4029 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO0h 45 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO0h 46 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO0h 46 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO0h 46 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO0f 45 " 0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO0f 46 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO0f 46 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO0f 46 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO0k 45 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO0k 46 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO0k 46 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO0k 46 " -0.024 5.00e-02 4.00e+02 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3208 2.74 - 3.28: 26814 3.28 - 3.82: 44996 3.82 - 4.36: 56239 4.36 - 4.90: 89289 Nonbonded interactions: 220546 Sorted by model distance: nonbonded pdb=" OH TYR0f 87 " pdb=" O THR0g 47 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR0e 66 " pdb=" OD1 ASP0e 116 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR0b 66 " pdb=" OD1 ASP0b 116 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR0j 66 " pdb=" OD1 ASP0j 116 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR0i 66 " pdb=" OD1 ASP0i 116 " model vdw 2.225 2.440 ... (remaining 220541 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 '0a' selection = chain '0b' selection = chain '0c' selection = chain '0d' selection = chain '0e' selection = chain '0f' selection = chain '0g' selection = chain '0h' selection = chain '0i' selection = chain '0j' selection = chain '0k' selection = chain '0l' } 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: 10.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 29.020 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 68.010 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 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 : 0.007 0.071 27456 Z= 0.471 Angle : 0.885 8.531 37236 Z= 0.490 Chirality : 0.053 0.174 4032 Planarity : 0.006 0.043 4896 Dihedral : 9.658 52.028 10020 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: -4.63 (0.11), residues: 3312 helix: -3.36 (0.09), residues: 1440 sheet: -4.28 (0.18), residues: 312 loop : -2.36 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP0d 23 HIS 0.006 0.002 HIS0l 188 PHE 0.015 0.003 PHE0f 24 TYR 0.022 0.004 TYR0b 109 ARG 0.006 0.002 ARG0j 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1669 time to evaluate : 2.703 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 outliers start: 0 outliers final: 0 residues processed: 1669 average time/residue: 0.4195 time to fit residues: 1067.1692 Evaluate side-chains 1322 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1322 time to evaluate : 3.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 0.4980 chunk 136 optimal weight: 0.5980 chunk 263 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 160 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 305 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 16 GLN 0a 21 ASN 0a 58 HIS ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 211 ASN 0a 213 GLN 0a 269 ASN ** 0b 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 58 HIS ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 101 GLN 0b 124 ASN 0b 151 ASN 0b 213 GLN ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 269 ASN 0c 16 GLN 0c 21 ASN 0c 58 HIS ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN 0c 211 ASN 0c 269 ASN 0d 16 GLN 0d 21 ASN 0d 58 HIS ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 211 ASN 0d 213 GLN 0d 269 ASN ** 0e 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 58 HIS ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 124 ASN 0e 151 ASN 0e 213 GLN 0e 269 ASN 0f 16 GLN 0f 58 HIS ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 213 GLN 0f 269 ASN 0g 16 GLN 0g 21 ASN 0g 58 HIS ** 0g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 213 GLN 0g 269 ASN ** 0h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 58 HIS ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 101 GLN 0h 124 ASN ** 0h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 213 GLN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 269 ASN 0i 16 GLN 0i 58 HIS ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 213 GLN 0i 269 ASN 0j 16 GLN 0j 58 HIS ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 213 GLN 0j 269 ASN 0k 58 HIS ** 0k 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 124 ASN 0k 151 ASN 0k 181 ASN 0k 213 GLN 0k 219 ASN 0k 269 ASN 0l 16 GLN 0l 21 ASN 0l 58 HIS ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 211 ASN ** 0l 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 269 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27456 Z= 0.275 Angle : 0.752 9.333 37236 Z= 0.404 Chirality : 0.047 0.320 4032 Planarity : 0.005 0.041 4896 Dihedral : 5.545 22.232 3660 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.32 % Allowed : 18.62 % Favored : 76.06 % 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: -2.73 (0.13), residues: 3312 helix: -1.32 (0.11), residues: 1656 sheet: -3.43 (0.20), residues: 360 loop : -1.72 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP0c 23 HIS 0.012 0.003 HIS0c 26 PHE 0.027 0.002 PHE0l 39 TYR 0.034 0.003 TYR0a 66 ARG 0.007 0.001 ARG0i 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1442 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 83 residues processed: 1491 average time/residue: 0.3956 time to fit residues: 906.9639 Evaluate side-chains 1392 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1309 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.2376 time to fit residues: 39.2809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.0470 chunk 253 optimal weight: 0.2980 chunk 207 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 0.1980 chunk 330 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 303 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 16 GLN ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 176 ASN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 16 GLN ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 21 ASN ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 16 GLN 0f 21 ASN ** 0f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 249 GLN 0g 16 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 16 GLN ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 59 GLN ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN 0h 181 ASN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 249 GLN 0i 16 GLN 0i 21 ASN ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN ** 0i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 16 GLN 0j 21 ASN ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 249 GLN ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN 0l 16 GLN ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27456 Z= 0.247 Angle : 0.678 9.458 37236 Z= 0.364 Chirality : 0.046 0.216 4032 Planarity : 0.004 0.031 4896 Dihedral : 5.323 24.100 3660 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.18 % Allowed : 22.84 % Favored : 71.99 % 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: -1.78 (0.14), residues: 3312 helix: -0.46 (0.12), residues: 1716 sheet: -3.51 (0.19), residues: 384 loop : -1.18 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP0h 218 HIS 0.007 0.001 HIS0a 26 PHE 0.022 0.002 PHE0h 280 TYR 0.032 0.002 TYR0a 205 ARG 0.010 0.001 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1373 time to evaluate : 3.012 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 outliers start: 146 outliers final: 73 residues processed: 1415 average time/residue: 0.3973 time to fit residues: 863.5907 Evaluate side-chains 1376 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1303 time to evaluate : 2.793 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.2579 time to fit residues: 37.9025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.0370 chunk 229 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 145 optimal weight: 0.0370 chunk 205 optimal weight: 0.8980 chunk 306 optimal weight: 0.6980 chunk 324 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 290 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 16 GLN ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN 0b 152 GLN ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 152 GLN 0c 176 ASN ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 152 GLN 0e 181 ASN 0f 16 GLN ** 0f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 16 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN 0h 152 GLN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 249 GLN 0i 16 GLN ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN 0i 152 GLN 0j 16 GLN ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 152 GLN ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 16 GLN ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.7223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27456 Z= 0.217 Angle : 0.664 10.261 37236 Z= 0.352 Chirality : 0.046 0.232 4032 Planarity : 0.004 0.038 4896 Dihedral : 5.295 23.327 3660 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.66 % Allowed : 27.20 % Favored : 70.14 % 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: -1.18 (0.15), residues: 3312 helix: 0.07 (0.13), residues: 1692 sheet: -3.46 (0.20), residues: 384 loop : -0.86 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP0j 218 HIS 0.003 0.001 HIS0l 26 PHE 0.032 0.002 PHE0d 280 TYR 0.033 0.002 TYR0k 205 ARG 0.007 0.000 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1368 time to evaluate : 2.783 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 outliers start: 75 outliers final: 37 residues processed: 1380 average time/residue: 0.4011 time to fit residues: 847.0321 Evaluate side-chains 1363 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1326 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2584 time to fit residues: 21.1990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 291 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 151 ASN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN 0d 13 ASN ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN 0f 16 GLN ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 16 GLN ** 0g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 151 ASN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 16 GLN ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 13 ASN 0j 16 GLN ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 176 ASN 0k 32 GLN ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 211 ASN 0k 269 ASN ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN 0l 213 GLN 0l 249 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 27456 Z= 0.343 Angle : 0.751 10.699 37236 Z= 0.405 Chirality : 0.049 0.230 4032 Planarity : 0.004 0.053 4896 Dihedral : 5.718 25.230 3660 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.91 % Allowed : 28.09 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3312 helix: -0.03 (0.12), residues: 1704 sheet: -3.24 (0.21), residues: 384 loop : -0.91 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP0h 23 HIS 0.005 0.001 HIS0j 188 PHE 0.038 0.003 PHE0d 280 TYR 0.035 0.003 TYR0b 205 ARG 0.008 0.001 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1389 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 52 residues processed: 1414 average time/residue: 0.4157 time to fit residues: 901.3752 Evaluate side-chains 1385 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1333 time to evaluate : 2.915 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2826 time to fit residues: 30.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.7980 chunk 292 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 325 optimal weight: 0.5980 chunk 269 optimal weight: 0.5980 chunk 150 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 153 ASN ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 151 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN ** 0f 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 13 ASN ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.8589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 27456 Z= 0.311 Angle : 0.760 10.517 37236 Z= 0.407 Chirality : 0.049 0.271 4032 Planarity : 0.004 0.036 4896 Dihedral : 5.743 24.638 3660 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 26.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.59 % Allowed : 30.25 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3312 helix: 0.14 (0.12), residues: 1680 sheet: -3.12 (0.22), residues: 384 loop : -0.59 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP0k 41 HIS 0.004 0.001 HIS0j 188 PHE 0.036 0.003 PHE0a 280 TYR 0.048 0.002 TYR0k 205 ARG 0.007 0.001 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1390 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 40 residues processed: 1405 average time/residue: 0.4127 time to fit residues: 888.4539 Evaluate side-chains 1374 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1334 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2740 time to fit residues: 23.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 181 optimal weight: 0.5980 chunk 323 optimal weight: 2.9990 chunk 202 optimal weight: 0.0170 chunk 197 optimal weight: 0.0470 chunk 149 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 32 GLN ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0b 151 ASN ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 151 ASN ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 49 ASN ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 49 ASN ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.8874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 27456 Z= 0.275 Angle : 0.747 9.960 37236 Z= 0.396 Chirality : 0.049 0.240 4032 Planarity : 0.004 0.041 4896 Dihedral : 5.630 24.837 3660 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.81 % Allowed : 31.31 % Favored : 66.88 % 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: -0.63 (0.15), residues: 3312 helix: 0.34 (0.13), residues: 1656 sheet: -2.83 (0.23), residues: 360 loop : -0.47 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.005 TRP0k 41 HIS 0.004 0.001 HIS0l 58 PHE 0.034 0.002 PHE0h 280 TYR 0.048 0.002 TYR0h 205 ARG 0.005 0.000 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1355 time to evaluate : 2.928 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 outliers start: 51 outliers final: 29 residues processed: 1364 average time/residue: 0.4071 time to fit residues: 854.5564 Evaluate side-chains 1348 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1319 time to evaluate : 2.776 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2739 time to fit residues: 18.0075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 205 optimal weight: 0.6980 chunk 220 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 211 ASN ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 151 ASN ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.9119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 27456 Z= 0.298 Angle : 0.772 10.280 37236 Z= 0.412 Chirality : 0.050 0.267 4032 Planarity : 0.004 0.037 4896 Dihedral : 5.677 25.808 3660 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 28.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.91 % Allowed : 32.06 % Favored : 66.03 % 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: -0.70 (0.15), residues: 3312 helix: 0.25 (0.13), residues: 1656 sheet: -2.73 (0.23), residues: 360 loop : -0.51 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP0h 41 HIS 0.005 0.001 HIS0g 188 PHE 0.037 0.003 PHE0h 280 TYR 0.035 0.002 TYR0d 205 ARG 0.005 0.000 ARG0d 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1345 time to evaluate : 2.872 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 outliers start: 54 outliers final: 31 residues processed: 1353 average time/residue: 0.4073 time to fit residues: 847.5009 Evaluate side-chains 1329 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1298 time to evaluate : 2.894 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2480 time to fit residues: 18.2999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 283 optimal weight: 0.3980 chunk 301 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 0.3980 chunk 236 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 151 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 89 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 188 HIS ** 0g 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 151 ASN ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 151 ASN ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.9326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 27456 Z= 0.310 Angle : 0.809 10.633 37236 Z= 0.431 Chirality : 0.051 0.294 4032 Planarity : 0.004 0.037 4896 Dihedral : 5.781 29.150 3660 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 29.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.60 % Allowed : 32.84 % Favored : 65.57 % 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: -0.78 (0.15), residues: 3312 helix: 0.17 (0.13), residues: 1656 sheet: -2.70 (0.24), residues: 360 loop : -0.56 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP0c 41 HIS 0.003 0.001 HIS0e 26 PHE 0.040 0.003 PHE0i 104 TYR 0.033 0.002 TYR0b 205 ARG 0.007 0.000 ARG0l 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1330 time to evaluate : 3.204 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 outliers start: 45 outliers final: 22 residues processed: 1339 average time/residue: 0.4173 time to fit residues: 861.6889 Evaluate side-chains 1314 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1292 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2717 time to fit residues: 15.0555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.6980 chunk 319 optimal weight: 0.0270 chunk 194 optimal weight: 0.6980 chunk 151 optimal weight: 0.2980 chunk 221 optimal weight: 0.0000 chunk 334 optimal weight: 0.5980 chunk 308 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 176 ASN ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0e 37 GLN 0e 151 ASN ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 89 GLN ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.9457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27456 Z= 0.266 Angle : 0.809 10.665 37236 Z= 0.427 Chirality : 0.050 0.368 4032 Planarity : 0.004 0.036 4896 Dihedral : 5.690 33.494 3660 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 27.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.03 % Allowed : 34.65 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.76 (0.15), residues: 3312 helix: 0.13 (0.13), residues: 1692 sheet: -2.72 (0.24), residues: 360 loop : -0.44 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.006 TRP0f 41 HIS 0.004 0.001 HIS0l 58 PHE 0.050 0.003 PHE0h 280 TYR 0.038 0.002 TYR0i 27 ARG 0.006 0.000 ARG0g 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6624 Ramachandran restraints generated. 3312 Oldfield, 0 Emsley, 3312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1329 time to evaluate : 3.213 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 outliers start: 29 outliers final: 18 residues processed: 1334 average time/residue: 0.4416 time to fit residues: 916.0334 Evaluate side-chains 1306 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1288 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2913 time to fit residues: 13.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 266 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 274 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0b 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 16 GLN ** 0f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 211 ASN ** 0g 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 16 GLN 0i 49 ASN ** 0i 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0j 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0k 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.152118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.133621 restraints weight = 67219.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136581 restraints weight = 43098.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.138584 restraints weight = 31482.814| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.9625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27456 Z= 0.293 Angle : 0.867 19.820 37236 Z= 0.449 Chirality : 0.051 0.278 4032 Planarity : 0.004 0.058 4896 Dihedral : 5.773 32.686 3660 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.28 % Allowed : 35.50 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.66 (0.15), residues: 3312 helix: 0.26 (0.13), residues: 1620 sheet: -2.69 (0.24), residues: 360 loop : -0.45 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.007 TRP0i 41 HIS 0.004 0.001 HIS0a 58 PHE 0.052 0.003 PHE0h 280 TYR 0.060 0.002 TYR0l 205 ARG 0.015 0.001 ARG0b 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12060.52 seconds wall clock time: 218 minutes 6.23 seconds (13086.23 seconds total)