Starting phenix.real_space_refine on Sun Nov 19 14:05:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/11_2023/6qym_4679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/11_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_4679/11_2023/6qym_4679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/11_2023/6qym_4679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/11_2023/6qym_4679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qym_4679/11_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-1.21rc1-5144/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: 13.99, per 1000 atoms: 0.52 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: 10.66 Conformation dependent library (CDL) restraints added in 5.1 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: 2.87 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: 8.74 Time building geometry restraints manager: 11.52 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: 15.290 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: 0.000 Extract box with map and model: 36.310 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 68.030 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.180 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.360 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.126 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: 0.4256 time to fit residues: 1081.4743 Evaluate side-chains 1322 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1322 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9335 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.261 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: 0.4291 time to fit residues: 994.1707 Evaluate side-chains 1392 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1309 time to evaluate : 2.998 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.2742 time to fit residues: 45.2954 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.056 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: 0.4121 time to fit residues: 895.1680 Evaluate side-chains 1376 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1303 time to evaluate : 3.542 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3019 time to fit residues: 44.5973 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.296 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: 0.4148 time to fit residues: 874.0445 Evaluate side-chains 1363 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1326 time to evaluate : 3.115 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2764 time to fit residues: 22.5950 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.556 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: 0.4131 time to fit residues: 894.0483 Evaluate side-chains 1385 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1333 time to evaluate : 2.934 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2575 time to fit residues: 28.5007 ------------------------------------------------------------------------------- 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 *********************** 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 : 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: 73 outliers final: 40 residues processed: 1405 average time/residue: 0.4174 time to fit residues: 896.7715 Evaluate side-chains 1374 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1334 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2720 time to fit residues: 23.6604 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.845 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: 0.4144 time to fit residues: 873.3406 Evaluate side-chains 1348 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1319 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3202 time to fit residues: 20.7611 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.858 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: 0.4069 time to fit residues: 845.5052 Evaluate side-chains 1329 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1298 time to evaluate : 3.071 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2575 time to fit residues: 18.9844 ------------------------------------------------------------------------------- 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 *********************** 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 : 3.278 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: 0.4353 time to fit residues: 898.0530 Evaluate side-chains 1314 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1292 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2658 time to fit residues: 14.6270 ------------------------------------------------------------------------------- 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 ********************** 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 : 2.997 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: 0.4346 time to fit residues: 894.6433 Evaluate side-chains 1306 residues out of total 3012 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1288 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2854 time to fit residues: 13.9805 ------------------------------------------------------------------------------- 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12294.75 seconds wall clock time: 219 minutes 55.58 seconds (13195.58 seconds total)