Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 18:49:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qyj_4678/04_2023/6qyj_4678.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.271 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 16608 2.51 5 N 4320 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 25956 Number of models: 1 Model: "" Number of chains: 12 Chain: "0a" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0b" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0c" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0d" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0e" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0f" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0g" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0h" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0i" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0j" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0k" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Chain: "0l" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Time building chain proxies: 12.93, per 1000 atoms: 0.50 Number of scatterers: 25956 At special positions: 0 Unit cell: (152.1, 152.1, 93.6, 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 4944 8.00 N 4320 7.00 C 16608 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: 10.74 Conformation dependent library (CDL) restraints added in 3.8 seconds 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6120 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 48 sheets defined 50.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain '0a' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0a 21 " --> pdb=" O ARG0a 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0a 35 " --> pdb=" O LEU0a 31 " (cutoff:3.500A) Processing helix chain '0a' and resid 49 through 61 Processing helix chain '0a' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0a 72 " --> pdb=" O PRO0a 69 " (cutoff:3.500A) Processing helix chain '0a' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0a 136 " --> pdb=" O PRO0a 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU0a 140 " --> pdb=" O LEU0a 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0a 146 " --> pdb=" O ALA0a 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0a 151 " --> pdb=" O ILE0a 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0a 155 " --> pdb=" O ASN0a 151 " (cutoff:3.500A) Processing helix chain '0a' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0a 174 " --> pdb=" O SER0a 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0a 212 " --> pdb=" O ASP0a 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0a 213 " --> pdb=" O LYS0a 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0a 224 " --> pdb=" O GLU0a 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0a 225 " --> pdb=" O MET0a 221 " (cutoff:3.500A) Processing helix chain '0a' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0a 257 " --> pdb=" O SER0a 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0a 260 " --> pdb=" O VAL0a 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0a 261 " --> pdb=" O PHE0a 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0a 264 " --> pdb=" O SER0a 260 " (cutoff:3.500A) Processing helix chain '0b' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0b 21 " --> pdb=" O ARG0b 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0b 35 " --> pdb=" O LEU0b 31 " (cutoff:3.500A) Processing helix chain '0b' and resid 49 through 61 Processing helix chain '0b' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0b 72 " --> pdb=" O PRO0b 69 " (cutoff:3.500A) Processing helix chain '0b' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0b 136 " --> pdb=" O PRO0b 132 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU0b 140 " --> pdb=" O LEU0b 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU0b 146 " --> pdb=" O ALA0b 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0b 151 " --> pdb=" O ILE0b 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0b 155 " --> pdb=" O ASN0b 151 " (cutoff:3.500A) Processing helix chain '0b' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0b 174 " --> pdb=" O SER0b 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0b 212 " --> pdb=" O ASP0b 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0b 213 " --> pdb=" O LYS0b 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0b 224 " --> pdb=" O GLU0b 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0b 225 " --> pdb=" O MET0b 221 " (cutoff:3.500A) Processing helix chain '0b' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0b 257 " --> pdb=" O SER0b 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0b 260 " --> pdb=" O VAL0b 256 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG0b 261 " --> pdb=" O PHE0b 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0b 264 " --> pdb=" O SER0b 260 " (cutoff:3.500A) Processing helix chain '0c' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0c 21 " --> pdb=" O ARG0c 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0c 35 " --> pdb=" O LEU0c 31 " (cutoff:3.500A) Processing helix chain '0c' and resid 49 through 61 Processing helix chain '0c' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0c 72 " --> pdb=" O PRO0c 69 " (cutoff:3.500A) Processing helix chain '0c' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0c 136 " --> pdb=" O PRO0c 132 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU0c 140 " --> pdb=" O LEU0c 136 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU0c 146 " --> pdb=" O ALA0c 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0c 151 " --> pdb=" O ILE0c 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0c 155 " --> pdb=" O ASN0c 151 " (cutoff:3.500A) Processing helix chain '0c' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0c 174 " --> pdb=" O SER0c 170 " (cutoff:3.500A) 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 225 removed outlier: 3.584A pdb=" N ALA0c 212 " --> pdb=" O ASP0c 208 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN0c 213 " --> pdb=" O LYS0c 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0c 224 " --> pdb=" O GLU0c 220 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU0c 225 " --> pdb=" O MET0c 221 " (cutoff:3.500A) Processing helix chain '0c' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0c 257 " --> pdb=" O SER0c 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER0c 260 " --> pdb=" O VAL0c 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0c 261 " --> pdb=" O PHE0c 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0c 264 " --> pdb=" O SER0c 260 " (cutoff:3.500A) Processing helix chain '0d' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0d 21 " --> pdb=" O ARG0d 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0d 35 " --> pdb=" O LEU0d 31 " (cutoff:3.500A) Processing helix chain '0d' and resid 49 through 61 Processing helix chain '0d' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0d 72 " --> pdb=" O PRO0d 69 " (cutoff:3.500A) Processing helix chain '0d' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0d 136 " --> pdb=" O PRO0d 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU0d 140 " --> pdb=" O LEU0d 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0d 146 " --> pdb=" O ALA0d 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0d 151 " --> pdb=" O ILE0d 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0d 155 " --> pdb=" O ASN0d 151 " (cutoff:3.500A) Processing helix chain '0d' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0d 174 " --> pdb=" O SER0d 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0d 212 " --> pdb=" O ASP0d 208 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN0d 213 " --> pdb=" O LYS0d 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0d 224 " --> pdb=" O GLU0d 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0d 225 " --> pdb=" O MET0d 221 " (cutoff:3.500A) Processing helix chain '0d' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0d 257 " --> pdb=" O SER0d 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0d 260 " --> pdb=" O VAL0d 256 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG0d 261 " --> pdb=" O PHE0d 257 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA0d 264 " --> pdb=" O SER0d 260 " (cutoff:3.500A) Processing helix chain '0e' and resid 11 through 37 removed outlier: 3.527A pdb=" N ASN0e 21 " --> pdb=" O ARG0e 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0e 35 " --> pdb=" O LEU0e 31 " (cutoff:3.500A) Processing helix chain '0e' and resid 49 through 61 Processing helix chain '0e' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0e 72 " --> pdb=" O PRO0e 69 " (cutoff:3.500A) Processing helix chain '0e' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0e 136 " --> pdb=" O PRO0e 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU0e 140 " --> pdb=" O LEU0e 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU0e 146 " --> pdb=" O ALA0e 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0e 151 " --> pdb=" O ILE0e 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0e 155 " --> pdb=" O ASN0e 151 " (cutoff:3.500A) Processing helix chain '0e' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0e 174 " --> pdb=" O SER0e 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0e 212 " --> pdb=" O ASP0e 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0e 213 " --> pdb=" O LYS0e 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0e 224 " --> pdb=" O GLU0e 220 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU0e 225 " --> pdb=" O MET0e 221 " (cutoff:3.500A) Processing helix chain '0e' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0e 257 " --> pdb=" O SER0e 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0e 260 " --> pdb=" O VAL0e 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0e 261 " --> pdb=" O PHE0e 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0e 264 " --> pdb=" O SER0e 260 " (cutoff:3.500A) Processing helix chain '0f' and resid 11 through 37 removed outlier: 3.527A pdb=" N ASN0f 21 " --> pdb=" O ARG0f 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0f 35 " --> pdb=" O LEU0f 31 " (cutoff:3.500A) Processing helix chain '0f' and resid 49 through 61 Processing helix chain '0f' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0f 72 " --> pdb=" O PRO0f 69 " (cutoff:3.500A) Processing helix chain '0f' and resid 130 through 155 removed outlier: 3.626A pdb=" N LEU0f 136 " --> pdb=" O PRO0f 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU0f 140 " --> pdb=" O LEU0f 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU0f 146 " --> pdb=" O ALA0f 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0f 151 " --> pdb=" O ILE0f 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0f 155 " --> pdb=" O ASN0f 151 " (cutoff:3.500A) Processing helix chain '0f' and resid 167 through 181 removed outlier: 3.516A pdb=" N VAL0f 174 " --> pdb=" O SER0f 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0f 212 " --> pdb=" O ASP0f 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0f 213 " --> pdb=" O LYS0f 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE0f 224 " --> pdb=" O GLU0f 220 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU0f 225 " --> pdb=" O MET0f 221 " (cutoff:3.500A) Processing helix chain '0f' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0f 257 " --> pdb=" O SER0f 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0f 260 " --> pdb=" O VAL0f 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0f 261 " --> pdb=" O PHE0f 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0f 264 " --> pdb=" O SER0f 260 " (cutoff:3.500A) Processing helix chain '0g' and resid 11 through 37 removed outlier: 3.527A pdb=" N ASN0g 21 " --> pdb=" O ARG0g 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0g 35 " --> pdb=" O LEU0g 31 " (cutoff:3.500A) Processing helix chain '0g' and resid 49 through 61 Processing helix chain '0g' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0g 72 " --> pdb=" O PRO0g 69 " (cutoff:3.500A) Processing helix chain '0g' and resid 130 through 155 removed outlier: 3.626A pdb=" N LEU0g 136 " --> pdb=" O PRO0g 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU0g 140 " --> pdb=" O LEU0g 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU0g 146 " --> pdb=" O ALA0g 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0g 151 " --> pdb=" O ILE0g 147 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN0g 155 " --> pdb=" O ASN0g 151 " (cutoff:3.500A) Processing helix chain '0g' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0g 174 " --> pdb=" O SER0g 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0g 212 " --> pdb=" O ASP0g 208 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN0g 213 " --> pdb=" O LYS0g 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0g 224 " --> pdb=" O GLU0g 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0g 225 " --> pdb=" O MET0g 221 " (cutoff:3.500A) Processing helix chain '0g' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0g 257 " --> pdb=" O SER0g 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER0g 260 " --> pdb=" O VAL0g 256 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG0g 261 " --> pdb=" O PHE0g 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0g 264 " --> pdb=" O SER0g 260 " (cutoff:3.500A) Processing helix chain '0h' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0h 21 " --> pdb=" O ARG0h 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0h 35 " --> pdb=" O LEU0h 31 " (cutoff:3.500A) Processing helix chain '0h' and resid 49 through 61 Processing helix chain '0h' and resid 68 through 72 removed outlier: 4.190A pdb=" N SER0h 72 " --> pdb=" O PRO0h 69 " (cutoff:3.500A) Processing helix chain '0h' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0h 136 " --> pdb=" O PRO0h 132 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU0h 140 " --> pdb=" O LEU0h 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0h 146 " --> pdb=" O ALA0h 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0h 151 " --> pdb=" O ILE0h 147 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN0h 155 " --> pdb=" O ASN0h 151 " (cutoff:3.500A) Processing helix chain '0h' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0h 174 " --> pdb=" O SER0h 170 " (cutoff:3.500A) 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 225 removed outlier: 3.584A pdb=" N ALA0h 212 " --> pdb=" O ASP0h 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0h 213 " --> pdb=" O LYS0h 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0h 224 " --> pdb=" O GLU0h 220 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU0h 225 " --> pdb=" O MET0h 221 " (cutoff:3.500A) Processing helix chain '0h' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0h 257 " --> pdb=" O SER0h 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER0h 260 " --> pdb=" O VAL0h 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0h 261 " --> pdb=" O PHE0h 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0h 264 " --> pdb=" O SER0h 260 " (cutoff:3.500A) Processing helix chain '0i' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0i 21 " --> pdb=" O ARG0i 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0i 35 " --> pdb=" O LEU0i 31 " (cutoff:3.500A) Processing helix chain '0i' and resid 49 through 61 Processing helix chain '0i' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0i 72 " --> pdb=" O PRO0i 69 " (cutoff:3.500A) Processing helix chain '0i' and resid 130 through 155 removed outlier: 3.626A pdb=" N LEU0i 136 " --> pdb=" O PRO0i 132 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU0i 140 " --> pdb=" O LEU0i 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0i 146 " --> pdb=" O ALA0i 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0i 151 " --> pdb=" O ILE0i 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0i 155 " --> pdb=" O ASN0i 151 " (cutoff:3.500A) Processing helix chain '0i' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0i 174 " --> pdb=" O SER0i 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0i 212 " --> pdb=" O ASP0i 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0i 213 " --> pdb=" O LYS0i 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0i 224 " --> pdb=" O GLU0i 220 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU0i 225 " --> pdb=" O MET0i 221 " (cutoff:3.500A) Processing helix chain '0i' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0i 257 " --> pdb=" O SER0i 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0i 260 " --> pdb=" O VAL0i 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0i 261 " --> pdb=" O PHE0i 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0i 264 " --> pdb=" O SER0i 260 " (cutoff:3.500A) Processing helix chain '0j' and resid 11 through 37 removed outlier: 3.529A pdb=" N ASN0j 21 " --> pdb=" O ARG0j 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0j 35 " --> pdb=" O LEU0j 31 " (cutoff:3.500A) Processing helix chain '0j' and resid 49 through 61 Processing helix chain '0j' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0j 72 " --> pdb=" O PRO0j 69 " (cutoff:3.500A) Processing helix chain '0j' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0j 136 " --> pdb=" O PRO0j 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU0j 140 " --> pdb=" O LEU0j 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0j 146 " --> pdb=" O ALA0j 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0j 151 " --> pdb=" O ILE0j 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0j 155 " --> pdb=" O ASN0j 151 " (cutoff:3.500A) Processing helix chain '0j' and resid 167 through 181 removed outlier: 3.516A pdb=" N VAL0j 174 " --> pdb=" O SER0j 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0j 212 " --> pdb=" O ASP0j 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0j 213 " --> pdb=" O LYS0j 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0j 224 " --> pdb=" O GLU0j 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0j 225 " --> pdb=" O MET0j 221 " (cutoff:3.500A) Processing helix chain '0j' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0j 257 " --> pdb=" O SER0j 253 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER0j 260 " --> pdb=" O VAL0j 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0j 261 " --> pdb=" O PHE0j 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0j 264 " --> pdb=" O SER0j 260 " (cutoff:3.500A) Processing helix chain '0k' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0k 21 " --> pdb=" O ARG0k 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA0k 35 " --> pdb=" O LEU0k 31 " (cutoff:3.500A) Processing helix chain '0k' and resid 49 through 61 Processing helix chain '0k' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0k 72 " --> pdb=" O PRO0k 69 " (cutoff:3.500A) Processing helix chain '0k' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0k 136 " --> pdb=" O PRO0k 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU0k 140 " --> pdb=" O LEU0k 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU0k 146 " --> pdb=" O ALA0k 142 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN0k 151 " --> pdb=" O ILE0k 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0k 155 " --> pdb=" O ASN0k 151 " (cutoff:3.500A) Processing helix chain '0k' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0k 174 " --> pdb=" O SER0k 170 " (cutoff:3.500A) 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 225 removed outlier: 3.584A pdb=" N ALA0k 212 " --> pdb=" O ASP0k 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0k 213 " --> pdb=" O LYS0k 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0k 224 " --> pdb=" O GLU0k 220 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU0k 225 " --> pdb=" O MET0k 221 " (cutoff:3.500A) Processing helix chain '0k' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0k 257 " --> pdb=" O SER0k 253 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER0k 260 " --> pdb=" O VAL0k 256 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG0k 261 " --> pdb=" O PHE0k 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0k 264 " --> pdb=" O SER0k 260 " (cutoff:3.500A) Processing helix chain '0l' and resid 11 through 37 removed outlier: 3.528A pdb=" N ASN0l 21 " --> pdb=" O ARG0l 17 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA0l 35 " --> pdb=" O LEU0l 31 " (cutoff:3.500A) Processing helix chain '0l' and resid 49 through 61 Processing helix chain '0l' and resid 68 through 72 removed outlier: 4.189A pdb=" N SER0l 72 " --> pdb=" O PRO0l 69 " (cutoff:3.500A) Processing helix chain '0l' and resid 130 through 155 removed outlier: 3.625A pdb=" N LEU0l 136 " --> pdb=" O PRO0l 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU0l 140 " --> pdb=" O LEU0l 136 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU0l 146 " --> pdb=" O ALA0l 142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN0l 151 " --> pdb=" O ILE0l 147 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN0l 155 " --> pdb=" O ASN0l 151 " (cutoff:3.500A) Processing helix chain '0l' and resid 167 through 181 removed outlier: 3.517A pdb=" N VAL0l 174 " --> pdb=" O SER0l 170 " (cutoff:3.500A) 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 225 removed outlier: 3.583A pdb=" N ALA0l 212 " --> pdb=" O ASP0l 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN0l 213 " --> pdb=" O LYS0l 209 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE0l 224 " --> pdb=" O GLU0l 220 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU0l 225 " --> pdb=" O MET0l 221 " (cutoff:3.500A) Processing helix chain '0l' and resid 247 through 270 removed outlier: 4.114A pdb=" N PHE0l 257 " --> pdb=" O SER0l 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER0l 260 " --> pdb=" O VAL0l 256 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG0l 261 " --> pdb=" O PHE0l 257 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA0l 264 " --> pdb=" O SER0l 260 " (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 74 through 76 removed outlier: 3.737A pdb=" N ILE0a 74 " --> pdb=" O TYR0a 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0a 66 " --> pdb=" O ILE0a 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0a' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain '0a' and resid 196 through 198 Processing sheet with id=AA5, first strand: chain '0a' and resid 184 through 188 removed outlier: 6.821A pdb=" N ILE0a 185 " --> pdb=" O ILE0l 161 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ALA0l 163 " --> pdb=" O ILE0a 185 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA0a 187 " --> pdb=" O ALA0l 163 " (cutoff:3.500A) 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0b 74 " --> pdb=" O TYR0b 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0b 66 " --> pdb=" O ILE0b 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0b' and resid 78 through 81 Processing sheet with id=AA9, first strand: chain '0b' and resid 196 through 198 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 74 through 76 removed outlier: 3.738A pdb=" N ILE0c 74 " --> pdb=" O TYR0c 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0c 66 " --> pdb=" O ILE0c 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0c' and resid 78 through 81 Processing sheet with id=AB4, first strand: chain '0c' and resid 196 through 198 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 74 through 76 removed outlier: 3.738A pdb=" N ILE0d 74 " --> pdb=" O TYR0d 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR0d 66 " --> pdb=" O ILE0d 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '0d' and resid 78 through 81 Processing sheet with id=AB8, first strand: chain '0d' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0e 74 " --> pdb=" O TYR0e 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0e 66 " --> pdb=" O ILE0e 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '0e' and resid 78 through 81 Processing sheet with id=AC3, first strand: chain '0e' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0f 74 " --> pdb=" O TYR0f 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0f 66 " --> pdb=" O ILE0f 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '0f' and resid 78 through 81 Processing sheet with id=AC7, first strand: chain '0f' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0g 74 " --> pdb=" O TYR0g 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR0g 66 " --> pdb=" O ILE0g 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '0g' and resid 78 through 81 Processing sheet with id=AD2, first strand: chain '0g' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0h 74 " --> pdb=" O TYR0h 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0h 66 " --> pdb=" O ILE0h 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '0h' and resid 78 through 81 Processing sheet with id=AD6, first strand: chain '0h' and resid 196 through 198 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 74 through 76 removed outlier: 3.738A pdb=" N ILE0i 74 " --> pdb=" O TYR0i 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0i 66 " --> pdb=" O ILE0i 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '0i' and resid 78 through 81 Processing sheet with id=AE1, first strand: chain '0i' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0j 74 " --> pdb=" O TYR0j 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR0j 66 " --> pdb=" O ILE0j 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0j' and resid 78 through 81 Processing sheet with id=AE5, first strand: chain '0j' and resid 196 through 198 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 74 through 76 removed outlier: 3.738A pdb=" N ILE0k 74 " --> pdb=" O TYR0k 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0k 66 " --> pdb=" O ILE0k 74 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '0k' and resid 78 through 81 Processing sheet with id=AE9, first strand: chain '0k' and resid 196 through 198 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 74 through 76 removed outlier: 3.737A pdb=" N ILE0l 74 " --> pdb=" O TYR0l 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR0l 66 " --> pdb=" O ILE0l 74 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '0l' and resid 78 through 81 1316 hydrogen bonds defined for protein. 3804 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: 8.28 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8426 1.34 - 1.46: 5682 1.46 - 1.58: 12280 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 26532 Sorted by residual: bond pdb=" C THR0i 131 " pdb=" N PRO0i 132 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.54e+00 bond pdb=" C THR0c 131 " pdb=" N PRO0c 132 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.23e-02 6.61e+03 2.54e+00 bond pdb=" C THR0e 131 " pdb=" N PRO0e 132 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.51e+00 bond pdb=" C THR0j 131 " pdb=" N PRO0j 132 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.38e+00 bond pdb=" C THR0d 131 " pdb=" N PRO0d 132 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.23e-02 6.61e+03 2.38e+00 ... (remaining 26527 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.03: 660 107.03 - 113.75: 14139 113.75 - 120.47: 10772 120.47 - 127.18: 10153 127.18 - 133.90: 228 Bond angle restraints: 35952 Sorted by residual: angle pdb=" N SER0e 72 " pdb=" CA SER0e 72 " pdb=" C SER0e 72 " ideal model delta sigma weight residual 109.60 118.61 -9.01 1.53e+00 4.27e-01 3.47e+01 angle pdb=" N SER0d 72 " pdb=" CA SER0d 72 " pdb=" C SER0d 72 " ideal model delta sigma weight residual 109.60 118.61 -9.01 1.53e+00 4.27e-01 3.46e+01 angle pdb=" N SER0k 72 " pdb=" CA SER0k 72 " pdb=" C SER0k 72 " ideal model delta sigma weight residual 109.60 118.60 -9.00 1.53e+00 4.27e-01 3.46e+01 angle pdb=" N SER0b 72 " pdb=" CA SER0b 72 " pdb=" C SER0b 72 " ideal model delta sigma weight residual 109.60 118.60 -9.00 1.53e+00 4.27e-01 3.46e+01 angle pdb=" N SER0i 72 " pdb=" CA SER0i 72 " pdb=" C SER0i 72 " ideal model delta sigma weight residual 109.60 118.59 -8.99 1.53e+00 4.27e-01 3.45e+01 ... (remaining 35947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 15086 14.03 - 28.06: 634 28.06 - 42.08: 192 42.08 - 56.11: 36 56.11 - 70.14: 12 Dihedral angle restraints: 15960 sinusoidal: 6492 harmonic: 9468 Sorted by residual: dihedral pdb=" CA SER0i 72 " pdb=" C SER0i 72 " pdb=" N TYR0i 73 " pdb=" CA TYR0i 73 " ideal model delta harmonic sigma weight residual -180.00 -139.65 -40.35 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA SER0c 72 " pdb=" C SER0c 72 " pdb=" N TYR0c 73 " pdb=" CA TYR0c 73 " ideal model delta harmonic sigma weight residual 180.00 -139.67 -40.33 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA SER0f 72 " pdb=" C SER0f 72 " pdb=" N TYR0f 73 " pdb=" CA TYR0f 73 " ideal model delta harmonic sigma weight residual -180.00 -139.67 -40.33 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 15957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2069 0.033 - 0.066: 1148 0.066 - 0.100: 392 0.100 - 0.133: 158 0.133 - 0.166: 97 Chirality restraints: 3864 Sorted by residual: chirality pdb=" CB ILE0k 74 " pdb=" CA ILE0k 74 " pdb=" CG1 ILE0k 74 " pdb=" CG2 ILE0k 74 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CB ILE0g 74 " pdb=" CA ILE0g 74 " pdb=" CG1 ILE0g 74 " pdb=" CG2 ILE0g 74 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CB ILE0l 74 " pdb=" CA ILE0l 74 " pdb=" CG1 ILE0l 74 " pdb=" CG2 ILE0l 74 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 3861 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER0i 72 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C SER0i 72 " -0.048 2.00e-02 2.50e+03 pdb=" O SER0i 72 " 0.019 2.00e-02 2.50e+03 pdb=" N TYR0i 73 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER0j 72 " 0.013 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C SER0j 72 " -0.048 2.00e-02 2.50e+03 pdb=" O SER0j 72 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR0j 73 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER0e 72 " 0.013 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C SER0e 72 " -0.048 2.00e-02 2.50e+03 pdb=" O SER0e 72 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR0e 73 " 0.016 2.00e-02 2.50e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6130 2.78 - 3.31: 23160 3.31 - 3.84: 43218 3.84 - 4.37: 52127 4.37 - 4.90: 88111 Nonbonded interactions: 212746 Sorted by model distance: nonbonded pdb=" OH TYR0h 107 " pdb=" O GLU0h 114 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR0k 107 " pdb=" O GLU0k 114 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR0g 107 " pdb=" O GLU0g 114 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR0j 107 " pdb=" O GLU0j 114 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR0a 107 " pdb=" O GLU0a 114 " model vdw 2.247 2.440 ... (remaining 212741 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.850 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: 0.020 Extract box with map and model: 39.610 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 62.500 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 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 : 0.004 0.042 26532 Z= 0.281 Angle : 0.870 9.366 35952 Z= 0.525 Chirality : 0.051 0.166 3864 Planarity : 0.006 0.042 4704 Dihedral : 9.701 70.139 9840 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.69 (0.11), residues: 3120 helix: -3.88 (0.07), residues: 1488 sheet: -2.86 (0.42), residues: 120 loop : -2.18 (0.14), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1399 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1399 time to evaluate : 3.280 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 outliers start: 0 outliers final: 0 residues processed: 1399 average time/residue: 0.4296 time to fit residues: 910.6299 Evaluate side-chains 979 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 979 time to evaluate : 3.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.7980 chunk 236 optimal weight: 0.4980 chunk 131 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 283 optimal weight: 0.4980 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 77 ASN 0a 89 GLN 0a 124 ASN 0a 153 ASN 0b 59 GLN 0b 89 GLN 0b 155 GLN 0b 249 GLN ** 0c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 152 GLN 0c 155 GLN 0c 211 ASN ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 77 ASN 0d 89 GLN 0d 124 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN 0e 59 GLN 0e 155 GLN 0e 249 GLN ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 152 GLN 0f 155 GLN ** 0f 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 77 ASN 0g 89 GLN 0g 124 ASN 0g 153 ASN 0h 89 GLN 0h 155 GLN 0h 249 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 152 GLN 0i 155 GLN 0i 211 ASN ** 0i 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 77 ASN 0j 89 GLN 0j 124 ASN 0j 153 ASN 0k 59 GLN 0k 89 GLN 0k 155 GLN 0k 249 GLN 0l 108 ASN 0l 152 GLN 0l 155 GLN 0l 211 ASN 0l 249 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 26532 Z= 0.341 Angle : 0.734 9.941 35952 Z= 0.400 Chirality : 0.050 0.165 3864 Planarity : 0.006 0.048 4704 Dihedral : 6.063 40.581 3468 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.07 % Favored : 95.64 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.16 (0.13), residues: 3120 helix: -0.97 (0.12), residues: 1488 sheet: -2.81 (0.34), residues: 120 loop : -1.73 (0.14), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1060 time to evaluate : 3.328 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: 93 outliers final: 54 residues processed: 1093 average time/residue: 0.4441 time to fit residues: 714.5910 Evaluate side-chains 1028 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 974 time to evaluate : 3.260 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.2872 time to fit residues: 31.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 235 optimal weight: 0.0870 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 306 optimal weight: 0.7980 chunk 252 optimal weight: 0.6980 chunk 281 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 227 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 89 GLN ** 0a 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0a 153 ASN 0b 58 HIS 0c 89 GLN ** 0c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0c 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 153 ASN ** 0e 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 89 GLN ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 152 GLN ** 0f 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 89 GLN ** 0g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 153 ASN 0i 89 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 89 GLN ** 0j 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 153 ASN 0l 89 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 26532 Z= 0.291 Angle : 0.661 10.143 35952 Z= 0.355 Chirality : 0.049 0.256 3864 Planarity : 0.005 0.045 4704 Dihedral : 5.811 43.102 3468 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.04 % Favored : 95.58 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -1.27 (0.14), residues: 3120 helix: 0.10 (0.13), residues: 1488 sheet: -2.18 (0.25), residues: 360 loop : -1.47 (0.16), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 994 time to evaluate : 3.066 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 outliers start: 78 outliers final: 37 residues processed: 1009 average time/residue: 0.4802 time to fit residues: 701.0494 Evaluate side-chains 950 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 913 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3269 time to fit residues: 24.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 147 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 0.5980 chunk 301 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 269 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 152 GLN 0a 181 ASN 0c 32 GLN ** 0c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN 0d 89 GLN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0e 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 32 GLN ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN 0i 32 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 153 ASN 0j 89 GLN 0j 152 GLN ** 0j 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 32 GLN 0l 89 GLN 0l 108 ASN 0l 153 ASN 0l 249 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 26532 Z= 0.333 Angle : 0.659 6.883 35952 Z= 0.355 Chirality : 0.049 0.154 3864 Planarity : 0.005 0.050 4704 Dihedral : 5.806 43.504 3468 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.04 % Favored : 95.64 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.96 (0.14), residues: 3120 helix: 0.44 (0.13), residues: 1488 sheet: -2.36 (0.22), residues: 432 loop : -1.20 (0.17), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1015 time to evaluate : 3.022 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 outliers start: 66 outliers final: 39 residues processed: 1042 average time/residue: 0.4375 time to fit residues: 673.9303 Evaluate side-chains 993 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 954 time to evaluate : 3.209 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2601 time to fit residues: 22.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 224 optimal weight: 0.6980 chunk 124 optimal weight: 0.3980 chunk 257 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 270 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 89 GLN ** 0c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 89 GLN 0g 152 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 89 GLN ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 26532 Z= 0.302 Angle : 0.660 9.702 35952 Z= 0.355 Chirality : 0.048 0.164 3864 Planarity : 0.005 0.051 4704 Dihedral : 5.778 44.937 3468 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.85 % Favored : 95.90 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.62 (0.14), residues: 3120 helix: 0.79 (0.13), residues: 1476 sheet: -2.09 (0.25), residues: 360 loop : -1.26 (0.16), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1018 time to evaluate : 3.033 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 outliers start: 80 outliers final: 46 residues processed: 1044 average time/residue: 0.4591 time to fit residues: 716.0282 Evaluate side-chains 1029 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 983 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2584 time to fit residues: 26.4253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.5980 chunk 271 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 177 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 250 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 88 ASN ** 0a 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 16 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0j 89 GLN ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 26532 Z= 0.384 Angle : 0.700 8.022 35952 Z= 0.375 Chirality : 0.049 0.171 3864 Planarity : 0.005 0.044 4704 Dihedral : 5.922 45.023 3468 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.33 % Favored : 95.35 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3120 helix: 0.96 (0.13), residues: 1476 sheet: -2.34 (0.23), residues: 372 loop : -1.22 (0.16), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1022 time to evaluate : 3.307 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 outliers start: 67 outliers final: 36 residues processed: 1033 average time/residue: 0.4230 time to fit residues: 653.0922 Evaluate side-chains 1024 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 988 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2463 time to fit residues: 20.1083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 0.0570 chunk 300 optimal weight: 0.3980 chunk 188 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0a 181 ASN 0c 83 GLN 0c 108 ASN ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0d 89 GLN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 89 GLN 0h 16 GLN 0h 59 GLN ** 0h 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 168 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 108 ASN 0l 89 GLN 0l 153 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 26532 Z= 0.290 Angle : 0.676 9.066 35952 Z= 0.359 Chirality : 0.048 0.168 3864 Planarity : 0.005 0.044 4704 Dihedral : 5.909 47.618 3468 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.24 (0.15), residues: 3120 helix: 1.25 (0.13), residues: 1476 sheet: -2.31 (0.23), residues: 372 loop : -1.10 (0.16), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1009 time to evaluate : 3.187 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 outliers start: 69 outliers final: 33 residues processed: 1016 average time/residue: 0.4238 time to fit residues: 647.8736 Evaluate side-chains 993 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 960 time to evaluate : 3.087 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2566 time to fit residues: 19.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 58 optimal weight: 0.2980 chunk 191 optimal weight: 0.4980 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 236 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0b 16 GLN ** 0c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0c 153 ASN ** 0c 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0i 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 83 GLN ** 0l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 26532 Z= 0.271 Angle : 0.690 8.699 35952 Z= 0.366 Chirality : 0.047 0.187 3864 Planarity : 0.004 0.042 4704 Dihedral : 5.870 47.829 3468 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -0.06 (0.15), residues: 3120 helix: 1.41 (0.13), residues: 1476 sheet: -2.31 (0.23), residues: 372 loop : -1.01 (0.17), residues: 1272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 972 time to evaluate : 3.048 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: 34 outliers final: 17 residues processed: 978 average time/residue: 0.4353 time to fit residues: 640.8726 Evaluate side-chains 977 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 960 time to evaluate : 3.160 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2913 time to fit residues: 12.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 262 optimal weight: 0.2980 chunk 280 optimal weight: 0.8980 chunk 168 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 265 optimal weight: 0.8980 chunk 279 optimal weight: 0.1980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0c 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0g 88 ASN 0g 89 GLN 0h 168 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 16 GLN 0l 58 HIS ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 26532 Z= 0.267 Angle : 0.696 8.696 35952 Z= 0.372 Chirality : 0.047 0.209 3864 Planarity : 0.004 0.042 4704 Dihedral : 5.813 47.297 3468 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.13 % Favored : 95.67 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3120 helix: 1.53 (0.13), residues: 1476 sheet: -2.14 (0.24), residues: 360 loop : -0.98 (0.17), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 978 time to evaluate : 3.192 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 outliers start: 42 outliers final: 20 residues processed: 987 average time/residue: 0.4332 time to fit residues: 647.7473 Evaluate side-chains 957 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 937 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2742 time to fit residues: 14.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9990 chunk 296 optimal weight: 0.2980 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 chunk 205 optimal weight: 0.5980 chunk 310 optimal weight: 0.5980 chunk 286 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0c 152 GLN 0c 153 ASN ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0f 153 ASN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0i 153 ASN ** 0l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 26532 Z= 0.321 Angle : 0.732 8.821 35952 Z= 0.391 Chirality : 0.049 0.202 3864 Planarity : 0.004 0.041 4704 Dihedral : 5.886 48.371 3468 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.55 % Favored : 95.22 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3120 helix: 1.49 (0.13), residues: 1476 sheet: -2.16 (0.24), residues: 360 loop : -0.94 (0.17), residues: 1284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6240 Ramachandran restraints generated. 3120 Oldfield, 0 Emsley, 3120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 967 time to evaluate : 3.136 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 outliers start: 28 outliers final: 15 residues processed: 970 average time/residue: 0.4206 time to fit residues: 618.7574 Evaluate side-chains 961 residues out of total 2832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 946 time to evaluate : 3.200 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2585 time to fit residues: 11.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.6980 chunk 263 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 228 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 247 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 254 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0f 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0h 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0h 168 GLN ** 0i 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 16 GLN 0k 59 GLN ** 0k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0k 155 GLN ** 0l 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0l 153 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104899 restraints weight = 45407.894| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.40 r_work: 0.3222 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 26532 Z= 0.293 Angle : 0.734 8.929 35952 Z= 0.392 Chirality : 0.048 0.208 3864 Planarity : 0.005 0.041 4704 Dihedral : 5.890 47.796 3468 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.26 % Favored : 95.51 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: 0.11 (0.15), residues: 3120 helix: 1.50 (0.13), residues: 1476 sheet: -2.16 (0.24), residues: 360 loop : -0.90 (0.17), residues: 1284 =============================================================================== Job complete usr+sys time: 10023.15 seconds wall clock time: 180 minutes 20.42 seconds (10820.42 seconds total)