Starting phenix.real_space_refine on Fri Mar 6 15:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.map" model { file = "/net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u32_26322/03_2026/7u32_26322.cif" } resolution = 3.46 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 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= 0.020 sd= 0.098 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 12 6.06 5 P 64 5.49 5 S 118 5.16 5 C 20266 2.51 5 N 5626 2.21 5 O 6062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32150 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "B" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1645 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Chain: "C" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2128 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "E" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "F" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "G" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1651 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "X" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "W" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "J" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1645 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Chain: "K" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2128 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "M" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "N" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "O" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1651 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "Y" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "Z" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 311 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 40 55.071 99.097 31.591 1.00129.86 S ATOM 350 SG CYS A 43 57.581 100.643 32.491 1.00134.18 S ATOM 2550 SG CYS B 40 145.419 78.026 48.508 1.00242.49 S ATOM 2571 SG CYS B 43 143.686 76.582 46.111 1.00236.15 S ATOM 4209 SG CYS C 40 113.075 54.441 22.076 1.00197.32 S ATOM 4230 SG CYS C 43 115.325 55.530 23.590 1.00195.44 S ATOM 8098 SG CYS E 40 35.830 91.067 56.836 1.00336.83 S ATOM 8119 SG CYS E 43 37.110 88.953 58.543 1.00337.56 S ATOM 10183 SG CYS F 40 54.256 59.664 22.570 1.00507.97 S ATOM 10204 SG CYS F 43 52.113 57.535 23.480 1.00486.18 S ATOM 12329 SG CYS G 40 25.140 33.457 54.454 1.00410.89 S ATOM 12350 SG CYS G 43 25.536 35.590 52.063 1.00401.77 S ATOM 16397 SG CYS I 40 114.247 110.733 31.515 1.00129.86 S ATOM 16418 SG CYS I 43 111.736 109.185 32.412 1.00134.18 S ATOM 18618 SG CYS J 40 23.896 131.765 48.470 1.00242.49 S ATOM 18639 SG CYS J 43 25.629 133.213 46.075 1.00236.15 S ATOM 20277 SG CYS K 40 56.236 155.396 22.074 1.00197.32 S ATOM 20298 SG CYS K 43 53.986 154.304 23.586 1.00195.44 S ATOM 24166 SG CYS M 40 133.487 118.725 56.772 1.00336.83 S ATOM 24187 SG CYS M 43 132.208 120.836 58.482 1.00337.56 S ATOM 26251 SG CYS N 40 115.056 150.180 22.557 1.00507.97 S ATOM 26272 SG CYS N 43 117.198 152.308 23.470 1.00486.18 S ATOM 28397 SG CYS O 40 144.170 176.341 54.481 1.00410.89 S ATOM 28418 SG CYS O 43 143.774 174.211 52.086 1.00401.77 S Time building chain proxies: 7.50, per 1000 atoms: 0.23 Number of scatterers: 32150 At special positions: 0 Unit cell: (170.2, 210.68, 93.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 Ca 2 19.99 S 118 16.00 P 64 15.00 O 6062 8.00 N 5626 7.00 C 20266 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 - 3.00 Amino acid : True - 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 43 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 16 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 12 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 43 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 40 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 43 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" ND1 HIS N 16 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 12 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 43 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" ND1 HIS O 16 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 12 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 40 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 43 " Number of angles added : 22 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7072 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 48 sheets defined 48.3% alpha, 16.1% beta 26 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 125 through 136 removed outlier: 3.769A pdb=" N GLN A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.526A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.259A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 148 through 168 Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 95 through 110 removed outlier: 4.048A pdb=" N MET C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 136 removed outlier: 3.570A pdb=" N LEU C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 163 removed outlier: 3.588A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 removed outlier: 3.840A pdb=" N ALA C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 216 removed outlier: 3.592A pdb=" N GLN C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN C 212 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.837A pdb=" N PHE D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 146 through 167 Processing helix chain 'D' and resid 168 through 171 removed outlier: 3.513A pdb=" N PHE D 171 " --> pdb=" O ILE D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 171' Processing helix chain 'D' and resid 174 through 189 removed outlier: 3.760A pdb=" N ARG D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 214 Processing helix chain 'D' and resid 214 through 219 removed outlier: 3.958A pdb=" N GLN D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.529A pdb=" N ASN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 109 removed outlier: 3.661A pdb=" N VAL E 101 " --> pdb=" O GLN E 97 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR E 107 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 136 removed outlier: 4.084A pdb=" N LEU E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET E 132 " --> pdb=" O THR E 128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.483A pdb=" N GLN E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS E 161 " --> pdb=" O HIS E 157 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN E 162 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 187 removed outlier: 3.867A pdb=" N ILE E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR E 184 " --> pdb=" O GLY E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 215 removed outlier: 3.913A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 removed outlier: 3.846A pdb=" N GLU E 219 " --> pdb=" O SER E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.953A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 109 removed outlier: 3.576A pdb=" N ARG F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET F 104 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.667A pdb=" N LEU F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 163 removed outlier: 3.875A pdb=" N HIS F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 174 through 186 removed outlier: 3.581A pdb=" N ALA F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 215 removed outlier: 3.524A pdb=" N ILE F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE F 201 " --> pdb=" O PRO F 197 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN F 207 " --> pdb=" O PHE F 203 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE F 210 " --> pdb=" O GLU F 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 27 removed outlier: 3.690A pdb=" N LEU G 22 " --> pdb=" O ASP G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 129 through 134 removed outlier: 4.201A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.553A pdb=" N GLN G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU G 154 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS G 157 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 removed outlier: 3.740A pdb=" N LEU G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR G 184 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 215 removed outlier: 4.273A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN G 213 " --> pdb=" O ARG G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 removed outlier: 4.199A pdb=" N MET H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 136 Processing helix chain 'H' and resid 146 through 165 removed outlier: 3.866A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 189 Processing helix chain 'H' and resid 196 through 207 removed outlier: 3.508A pdb=" N ILE H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 214 removed outlier: 4.151A pdb=" N GLN H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 209 through 214' Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 125 through 136 removed outlier: 3.769A pdb=" N GLN I 129 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 removed outlier: 3.526A pdb=" N GLN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS I 166 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 167 " --> pdb=" O THR I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 208 Processing helix chain 'I' and resid 209 through 214 removed outlier: 4.258A pdb=" N GLN I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 95 through 110 Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 148 through 168 Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 198 through 216 Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 95 through 110 removed outlier: 4.049A pdb=" N MET K 109 " --> pdb=" O LYS K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 136 removed outlier: 3.571A pdb=" N LEU K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 removed outlier: 3.588A pdb=" N ARG K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS K 157 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 removed outlier: 3.840A pdb=" N ALA K 179 " --> pdb=" O GLU K 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU K 182 " --> pdb=" O LEU K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 216 removed outlier: 3.591A pdb=" N GLN K 207 " --> pdb=" O PHE K 203 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN K 211 " --> pdb=" O GLN K 207 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN K 212 " --> pdb=" O GLN K 208 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN K 213 " --> pdb=" O ARG K 209 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER K 214 " --> pdb=" O ILE K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'L' and resid 95 through 110 removed outlier: 3.840A pdb=" N PHE L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 135 Processing helix chain 'L' and resid 146 through 167 Processing helix chain 'L' and resid 168 through 171 removed outlier: 3.513A pdb=" N PHE L 171 " --> pdb=" O ILE L 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 168 through 171' Processing helix chain 'L' and resid 174 through 189 removed outlier: 3.764A pdb=" N ARG L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 214 Processing helix chain 'L' and resid 214 through 219 removed outlier: 3.960A pdb=" N GLN L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 40 through 46 removed outlier: 3.528A pdb=" N ASN M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 109 removed outlier: 3.661A pdb=" N VAL M 101 " --> pdb=" O GLN M 97 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR M 103 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET M 104 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR M 107 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET M 109 " --> pdb=" O LYS M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 136 removed outlier: 4.084A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET M 132 " --> pdb=" O THR M 128 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS M 133 " --> pdb=" O GLN M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 166 removed outlier: 4.483A pdb=" N GLN M 150 " --> pdb=" O ASN M 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN M 158 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR M 159 " --> pdb=" O ARG M 155 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU M 160 " --> pdb=" O THR M 156 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS M 161 " --> pdb=" O HIS M 157 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN M 162 " --> pdb=" O GLN M 158 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS M 166 " --> pdb=" O ASN M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 187 removed outlier: 3.866A pdb=" N ILE M 183 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR M 184 " --> pdb=" O GLY M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 215 removed outlier: 3.913A pdb=" N GLN M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN M 212 " --> pdb=" O GLN M 208 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 removed outlier: 3.846A pdb=" N GLU M 219 " --> pdb=" O SER M 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 216 through 219' Processing helix chain 'N' and resid 5 through 16 Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 removed outlier: 3.954A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 109 removed outlier: 3.576A pdb=" N ARG N 100 " --> pdb=" O GLY N 96 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET N 104 " --> pdb=" O ARG N 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS N 105 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR N 107 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 135 removed outlier: 3.667A pdb=" N LEU N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 163 removed outlier: 3.875A pdb=" N HIS N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN N 158 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR N 159 " --> pdb=" O ARG N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 167 Processing helix chain 'N' and resid 174 through 186 removed outlier: 3.581A pdb=" N ALA N 179 " --> pdb=" O GLU N 175 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN N 186 " --> pdb=" O LEU N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 215 removed outlier: 3.524A pdb=" N ILE N 200 " --> pdb=" O SER N 196 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE N 201 " --> pdb=" O PRO N 197 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN N 207 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG N 209 " --> pdb=" O LYS N 205 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE N 210 " --> pdb=" O GLU N 206 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS N 215 " --> pdb=" O GLN N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 18 through 27 removed outlier: 3.690A pdb=" N LEU O 22 " --> pdb=" O ASP O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'O' and resid 95 through 107 Processing helix chain 'O' and resid 129 through 134 removed outlier: 4.202A pdb=" N TYR O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 168 removed outlier: 3.553A pdb=" N GLN O 150 " --> pdb=" O ASN O 146 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU O 154 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS O 157 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN O 158 " --> pdb=" O GLU O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 removed outlier: 3.740A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR O 184 " --> pdb=" O GLY O 180 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU O 185 " --> pdb=" O THR O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 215 removed outlier: 4.273A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN O 212 " --> pdb=" O GLN O 208 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN O 213 " --> pdb=" O ARG O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 removed outlier: 4.199A pdb=" N MET P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 136 Processing helix chain 'P' and resid 146 through 165 removed outlier: 3.866A pdb=" N GLU P 165 " --> pdb=" O LYS P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 Processing helix chain 'P' and resid 196 through 207 removed outlier: 3.508A pdb=" N ILE P 200 " --> pdb=" O SER P 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 214 removed outlier: 4.151A pdb=" N GLN P 213 " --> pdb=" O ARG P 209 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER P 214 " --> pdb=" O ILE P 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 209 through 214' Processing helix chain 'P' and resid 267 through 269 No H-bonds generated for 'chain 'P' and resid 267 through 269' Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 90 removed outlier: 6.443A pdb=" N TRP A 63 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 242 removed outlier: 6.173A pdb=" N THR A 228 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 237 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR A 226 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 239 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A 224 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 250 through 255 Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 90 removed outlier: 6.118A pdb=" N TRP B 63 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.723A pdb=" N ILE C 75 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 68 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 115 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 226 removed outlier: 6.619A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 250 through 254 Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 91 removed outlier: 4.203A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU D 115 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 261 through 265 removed outlier: 3.582A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS D 254 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL D 243 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY D 239 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TYR D 226 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 270 " --> pdb=" O TYR D 225 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 229 through 230 Processing sheet with id=AB2, first strand: chain 'E' and resid 69 through 70 removed outlier: 4.528A pdb=" N ILE E 74 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL E 91 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 69 through 70 removed outlier: 5.032A pdb=" N VAL E 77 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP E 66 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 79 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP E 63 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN E 116 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 65 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU E 115 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 238 through 241 removed outlier: 6.215A pdb=" N GLY E 239 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N TYR E 226 " --> pdb=" O GLY E 239 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR E 241 " --> pdb=" O CYS E 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 245 through 246 removed outlier: 3.813A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 64 through 70 removed outlier: 4.177A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 76 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 89 " --> pdb=" O LEU F 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.721A pdb=" N LEU F 115 " --> pdb=" O THR F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 238 through 242 removed outlier: 6.558A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE F 223 " --> pdb=" O ILE F 272 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC1, first strand: chain 'F' and resid 245 through 246 removed outlier: 3.648A pdb=" N TRP F 245 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 63 through 70 Processing sheet with id=AC3, first strand: chain 'G' and resid 114 through 116 removed outlier: 3.538A pdb=" N THR G 140 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 86 through 91 removed outlier: 4.282A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 115 " --> pdb=" O THR H 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 223 through 224 removed outlier: 3.852A pdb=" N CYS H 224 " --> pdb=" O THR H 241 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL H 243 " --> pdb=" O LYS H 254 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS H 254 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL H 252 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AC7, first strand: chain 'I' and resid 86 through 90 removed outlier: 6.444A pdb=" N TRP I 63 " --> pdb=" O GLN I 116 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 233 through 242 removed outlier: 6.172A pdb=" N THR I 228 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP I 237 " --> pdb=" O TYR I 226 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR I 226 " --> pdb=" O TRP I 237 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY I 239 " --> pdb=" O CYS I 224 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS I 224 " --> pdb=" O GLY I 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 250 through 255 Processing sheet with id=AD1, first strand: chain 'J' and resid 86 through 90 removed outlier: 6.117A pdb=" N TRP J 63 " --> pdb=" O GLN J 116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 86 through 87 removed outlier: 3.722A pdb=" N ILE K 75 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR K 68 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU K 115 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 223 through 226 removed outlier: 6.620A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 250 through 254 Processing sheet with id=AD5, first strand: chain 'L' and resid 86 through 91 removed outlier: 4.204A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N LEU L 115 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 261 through 265 removed outlier: 3.581A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LYS L 254 " --> pdb=" O VAL L 243 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL L 243 " --> pdb=" O LYS L 254 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY L 239 " --> pdb=" O TYR L 226 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR L 226 " --> pdb=" O GLY L 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS L 270 " --> pdb=" O TYR L 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 229 through 230 Processing sheet with id=AD8, first strand: chain 'M' and resid 69 through 70 removed outlier: 4.528A pdb=" N ILE M 74 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 91 " --> pdb=" O ILE M 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 69 through 70 removed outlier: 5.032A pdb=" N VAL M 77 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP M 66 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M 79 " --> pdb=" O GLN M 64 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP M 63 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN M 116 " --> pdb=" O TRP M 63 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL M 65 " --> pdb=" O GLN M 116 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU M 115 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 238 through 241 removed outlier: 6.215A pdb=" N GLY M 239 " --> pdb=" O TYR M 226 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N TYR M 226 " --> pdb=" O GLY M 239 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR M 241 " --> pdb=" O CYS M 224 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 245 through 246 removed outlier: 3.812A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 64 through 70 removed outlier: 4.177A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU N 76 " --> pdb=" O GLU N 89 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU N 89 " --> pdb=" O LEU N 76 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 114 through 117 removed outlier: 6.721A pdb=" N LEU N 115 " --> pdb=" O THR N 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 238 through 242 removed outlier: 6.557A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE N 223 " --> pdb=" O ILE N 272 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AE7, first strand: chain 'N' and resid 245 through 246 removed outlier: 3.648A pdb=" N TRP N 245 " --> pdb=" O VAL N 252 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 63 through 70 Processing sheet with id=AE9, first strand: chain 'O' and resid 114 through 116 removed outlier: 3.539A pdb=" N THR O 140 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 86 through 91 removed outlier: 4.282A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU P 115 " --> pdb=" O THR P 140 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 223 through 224 removed outlier: 3.852A pdb=" N CYS P 224 " --> pdb=" O THR P 241 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL P 243 " --> pdb=" O LYS P 254 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS P 254 " --> pdb=" O VAL P 243 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL P 252 " --> pdb=" O TRP P 245 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 229 through 230 1380 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.13 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: 9888 1.34 - 1.46: 5308 1.46 - 1.57: 17512 1.57 - 1.69: 124 1.69 - 1.81: 200 Bond restraints: 33032 Sorted by residual: bond pdb=" N ASP B 72 " pdb=" CA ASP B 72 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.06e+01 bond pdb=" N ASP J 72 " pdb=" CA ASP J 72 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" C ILE F 168 " pdb=" N PRO F 169 " ideal model delta sigma weight residual 1.336 1.366 -0.030 1.20e-02 6.94e+03 6.07e+00 bond pdb=" C ILE N 168 " pdb=" N PRO N 169 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.69e+00 bond pdb=" C ILE M 5 " pdb=" N PRO M 6 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 1.98e+00 ... (remaining 33027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 44794 2.97 - 5.94: 158 5.94 - 8.91: 16 8.91 - 11.88: 0 11.88 - 14.85: 2 Bond angle restraints: 44970 Sorted by residual: angle pdb=" C GLU B 71 " pdb=" N ASP B 72 " pdb=" CA ASP B 72 " ideal model delta sigma weight residual 121.54 136.39 -14.85 1.91e+00 2.74e-01 6.05e+01 angle pdb=" C GLU J 71 " pdb=" N ASP J 72 " pdb=" CA ASP J 72 " ideal model delta sigma weight residual 121.54 136.36 -14.82 1.91e+00 2.74e-01 6.02e+01 angle pdb=" N ASP J 72 " pdb=" CA ASP J 72 " pdb=" CB ASP J 72 " ideal model delta sigma weight residual 110.49 117.99 -7.50 1.69e+00 3.50e-01 1.97e+01 angle pdb=" N ASP B 72 " pdb=" CA ASP B 72 " pdb=" CB ASP B 72 " ideal model delta sigma weight residual 110.49 117.92 -7.43 1.69e+00 3.50e-01 1.93e+01 angle pdb=" C ASP J 72 " pdb=" CA ASP J 72 " pdb=" CB ASP J 72 " ideal model delta sigma weight residual 110.42 104.81 5.61 1.99e+00 2.53e-01 7.94e+00 ... (remaining 44965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.17: 18731 30.17 - 60.35: 741 60.35 - 90.52: 40 90.52 - 120.70: 0 120.70 - 150.87: 2 Dihedral angle restraints: 19514 sinusoidal: 8550 harmonic: 10964 Sorted by residual: dihedral pdb=" C4' DG W 6 " pdb=" C3' DG W 6 " pdb=" O3' DG W 6 " pdb=" P DA W 7 " ideal model delta sinusoidal sigma weight residual 220.00 69.13 150.87 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" C4' DG Z 6 " pdb=" C3' DG Z 6 " pdb=" O3' DG Z 6 " pdb=" P DA Z 7 " ideal model delta sinusoidal sigma weight residual 220.00 69.18 150.82 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA MET M 170 " pdb=" C MET M 170 " pdb=" N PHE M 171 " pdb=" CA PHE M 171 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 19511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3439 0.038 - 0.075: 988 0.075 - 0.113: 330 0.113 - 0.151: 69 0.151 - 0.188: 4 Chirality restraints: 4830 Sorted by residual: chirality pdb=" CB ILE D 221 " pdb=" CA ILE D 221 " pdb=" CG1 ILE D 221 " pdb=" CG2 ILE D 221 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CB ILE B 200 " pdb=" CA ILE B 200 " pdb=" CG1 ILE B 200 " pdb=" CG2 ILE B 200 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CB ILE L 221 " pdb=" CA ILE L 221 " pdb=" CG1 ILE L 221 " pdb=" CG2 ILE L 221 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 4827 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 71 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C GLU B 71 " 0.025 2.00e-02 2.50e+03 pdb=" O GLU B 71 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP B 72 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 71 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C GLU J 71 " 0.025 2.00e-02 2.50e+03 pdb=" O GLU J 71 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP J 72 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 28 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO E 29 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.019 5.00e-02 4.00e+02 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1063 2.72 - 3.26: 31371 3.26 - 3.81: 51621 3.81 - 4.35: 61453 4.35 - 4.90: 102633 Nonbonded interactions: 248141 Sorted by model distance: nonbonded pdb=" O ALA K 173 " pdb=" OG SER K 176 " model vdw 2.170 3.040 nonbonded pdb=" O ALA C 173 " pdb=" OG SER C 176 " model vdw 2.170 3.040 nonbonded pdb=" OG SER N 83 " pdb=" O PRO N 197 " model vdw 2.211 3.040 nonbonded pdb=" OG SER F 83 " pdb=" O PRO F 197 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 261 " pdb=" OD1 ASP H 248 " model vdw 2.237 3.040 ... (remaining 248136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'C' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'E' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'F' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'I' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'K' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'M' and (resid 4 through 45 or resid 60 through 272)) selection = (chain 'N' and (resid 4 through 45 or resid 60 through 272)) } ncs_group { reference = (chain 'B' and (resid 2 through 46 or resid 59 through 215 or resid 301)) selection = (chain 'G' and (resid 2 through 46 or resid 59 through 301)) selection = (chain 'J' and (resid 2 through 46 or resid 59 through 215 or resid 301)) selection = (chain 'O' and (resid 2 through 46 or resid 59 through 301)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 4.550 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.380 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4674 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 : 0.002 0.042 33080 Z= 0.107 Angle : 0.848 46.152 44992 Z= 0.308 Chirality : 0.041 0.188 4830 Planarity : 0.003 0.034 5568 Dihedral : 14.736 150.873 12442 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3750 helix: 1.66 (0.14), residues: 1568 sheet: 0.80 (0.20), residues: 698 loop : -0.92 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 222 TYR 0.013 0.001 TYR B 70 PHE 0.011 0.001 PHE E 203 TRP 0.013 0.001 TRP D 78 HIS 0.003 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00200 (33032) covalent geometry : angle 0.51182 (44970) hydrogen bonds : bond 0.16563 ( 1443) hydrogen bonds : angle 6.31076 ( 4154) metal coordination : bond 0.01368 ( 48) metal coordination : angle 30.56203 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 722 time to evaluate : 0.795 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: A 224 CYS cc_start: 0.6962 (t) cc_final: 0.6642 (t) REVERT: B 9 GLU cc_start: 0.7510 (tp30) cc_final: 0.6926 (pt0) REVERT: B 10 GLU cc_start: 0.8583 (tp30) cc_final: 0.8312 (tt0) REVERT: B 119 ASN cc_start: 0.8423 (t0) cc_final: 0.7937 (m-40) REVERT: B 162 ASN cc_start: 0.6082 (t0) cc_final: 0.5705 (m-40) REVERT: C 90 ARG cc_start: 0.4866 (mmm-85) cc_final: 0.3402 (ppt170) REVERT: C 132 MET cc_start: 0.8183 (ptp) cc_final: 0.7861 (ttm) REVERT: C 139 HIS cc_start: 0.5897 (t70) cc_final: 0.5496 (t-170) REVERT: C 222 ARG cc_start: 0.4446 (mtm110) cc_final: 0.3590 (ptp-170) REVERT: C 237 TRP cc_start: 0.5491 (m100) cc_final: 0.5267 (m100) REVERT: D 82 ASN cc_start: 0.6077 (t0) cc_final: 0.5405 (m-40) REVERT: D 86 ILE cc_start: 0.6614 (pt) cc_final: 0.6288 (mm) REVERT: D 172 ASN cc_start: 0.4372 (p0) cc_final: 0.4031 (m-40) REVERT: D 230 LYS cc_start: 0.7907 (mttt) cc_final: 0.7586 (mttt) REVERT: D 259 ASP cc_start: 0.7713 (m-30) cc_final: 0.7077 (t0) REVERT: E 15 TRP cc_start: 0.4619 (m100) cc_final: 0.4226 (m100) REVERT: E 18 ASP cc_start: 0.6857 (p0) cc_final: 0.6588 (p0) REVERT: E 44 GLN cc_start: 0.5423 (tp40) cc_final: 0.5175 (pt0) REVERT: E 83 SER cc_start: 0.4442 (p) cc_final: 0.3907 (p) REVERT: E 132 MET cc_start: 0.4681 (mpp) cc_final: 0.4436 (mpp) REVERT: E 160 LEU cc_start: 0.8073 (pp) cc_final: 0.7812 (tt) REVERT: E 171 PHE cc_start: 0.4271 (m-10) cc_final: 0.3855 (m-80) REVERT: E 184 THR cc_start: 0.6153 (p) cc_final: 0.5665 (t) REVERT: E 198 MET cc_start: 0.3386 (tpp) cc_final: 0.2958 (ttm) REVERT: F 23 HIS cc_start: 0.6020 (t-90) cc_final: 0.5552 (t-170) REVERT: F 26 PHE cc_start: 0.6280 (m-80) cc_final: 0.6051 (m-80) REVERT: F 106 TRP cc_start: 0.6392 (t60) cc_final: 0.5939 (t60) REVERT: F 157 HIS cc_start: 0.7867 (m90) cc_final: 0.6929 (t-170) REVERT: F 170 MET cc_start: 0.2181 (ptt) cc_final: 0.0374 (pmm) REVERT: F 199 ASP cc_start: 0.8389 (m-30) cc_final: 0.7716 (t0) REVERT: F 204 ASN cc_start: 0.7612 (m110) cc_final: 0.7377 (m110) REVERT: G 15 TRP cc_start: 0.7095 (m100) cc_final: 0.6754 (m100) REVERT: G 66 ASP cc_start: 0.5095 (t0) cc_final: 0.4712 (m-30) REVERT: G 99 PHE cc_start: 0.4615 (t80) cc_final: 0.4305 (m-80) REVERT: G 104 MET cc_start: 0.4475 (mpp) cc_final: 0.4193 (ttm) REVERT: G 109 MET cc_start: 0.6584 (pmm) cc_final: 0.5973 (mtp) REVERT: G 123 PHE cc_start: 0.0425 (m-10) cc_final: 0.0217 (m-80) REVERT: G 167 LEU cc_start: 0.8426 (tp) cc_final: 0.8075 (tp) REVERT: G 203 PHE cc_start: 0.8753 (t80) cc_final: 0.8518 (t80) REVERT: H 110 PHE cc_start: 0.6102 (m-10) cc_final: 0.5770 (m-10) REVERT: H 261 TYR cc_start: 0.7116 (m-80) cc_final: 0.6460 (m-10) REVERT: I 13 ASN cc_start: 0.6794 (m-40) cc_final: 0.6483 (m-40) REVERT: I 92 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8365 (mmtm) REVERT: I 224 CYS cc_start: 0.7091 (t) cc_final: 0.6774 (t) REVERT: J 9 GLU cc_start: 0.7513 (tp30) cc_final: 0.6921 (pt0) REVERT: J 10 GLU cc_start: 0.8670 (tp30) cc_final: 0.8434 (tt0) REVERT: J 162 ASN cc_start: 0.6055 (t0) cc_final: 0.5705 (m-40) REVERT: K 90 ARG cc_start: 0.4735 (mmm-85) cc_final: 0.3129 (ppt170) REVERT: K 132 MET cc_start: 0.8055 (ptp) cc_final: 0.7737 (ttm) REVERT: K 222 ARG cc_start: 0.4463 (mtm110) cc_final: 0.4006 (ptp-170) REVERT: L 82 ASN cc_start: 0.6052 (t0) cc_final: 0.5358 (m-40) REVERT: L 86 ILE cc_start: 0.6618 (pt) cc_final: 0.6272 (mm) REVERT: L 87 TYR cc_start: 0.4286 (t80) cc_final: 0.3841 (t80) REVERT: L 172 ASN cc_start: 0.4167 (p0) cc_final: 0.3878 (m-40) REVERT: L 259 ASP cc_start: 0.7797 (m-30) cc_final: 0.7099 (t0) REVERT: M 15 TRP cc_start: 0.4823 (m100) cc_final: 0.4411 (m100) REVERT: M 18 ASP cc_start: 0.6710 (p0) cc_final: 0.6460 (p0) REVERT: M 83 SER cc_start: 0.4287 (p) cc_final: 0.3704 (p) REVERT: M 132 MET cc_start: 0.4829 (mpp) cc_final: 0.4556 (mpp) REVERT: M 160 LEU cc_start: 0.8143 (pp) cc_final: 0.7874 (tt) REVERT: M 171 PHE cc_start: 0.4188 (m-10) cc_final: 0.3786 (m-80) REVERT: M 184 THR cc_start: 0.6074 (p) cc_final: 0.5576 (t) REVERT: M 198 MET cc_start: 0.3391 (tpp) cc_final: 0.2957 (ttm) REVERT: N 23 HIS cc_start: 0.6075 (t-90) cc_final: 0.5597 (t-170) REVERT: N 26 PHE cc_start: 0.6274 (m-80) cc_final: 0.6012 (m-80) REVERT: N 155 ARG cc_start: 0.6725 (tmm160) cc_final: 0.6111 (tpt-90) REVERT: N 157 HIS cc_start: 0.7879 (m90) cc_final: 0.6905 (t-170) REVERT: N 170 MET cc_start: 0.2118 (ptt) cc_final: 0.0976 (pmm) REVERT: N 199 ASP cc_start: 0.8386 (m-30) cc_final: 0.7689 (t0) REVERT: N 204 ASN cc_start: 0.7640 (m110) cc_final: 0.7367 (m110) REVERT: O 15 TRP cc_start: 0.7206 (m100) cc_final: 0.6908 (m100) REVERT: O 66 ASP cc_start: 0.5127 (t0) cc_final: 0.4810 (m-30) REVERT: O 99 PHE cc_start: 0.4454 (t80) cc_final: 0.4108 (m-80) REVERT: O 109 MET cc_start: 0.6471 (pmm) cc_final: 0.5849 (mtm) REVERT: O 167 LEU cc_start: 0.8495 (tp) cc_final: 0.8176 (tp) REVERT: O 203 PHE cc_start: 0.8726 (t80) cc_final: 0.8487 (t80) REVERT: P 110 PHE cc_start: 0.6193 (m-10) cc_final: 0.5965 (m-10) REVERT: P 256 ARG cc_start: 0.7626 (ptp-170) cc_final: 0.7209 (mmm160) REVERT: P 261 TYR cc_start: 0.7062 (m-80) cc_final: 0.6396 (m-10) outliers start: 0 outliers final: 0 residues processed: 722 average time/residue: 0.2082 time to fit residues: 230.5928 Evaluate side-chains 336 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 212 GLN C 186 ASN D 69 HIS D 102 GLN D 157 HIS E 46 ASN F 44 GLN H 102 GLN I 44 GLN I 148 GLN ** I 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 GLN K 186 ASN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 102 GLN L 157 HIS M 46 ASN N 44 GLN N 102 GLN P 102 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.229137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.200943 restraints weight = 49062.573| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.32 r_work: 0.4261 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 33080 Z= 0.134 Angle : 0.618 34.329 44992 Z= 0.304 Chirality : 0.045 0.482 4830 Planarity : 0.004 0.050 5568 Dihedral : 12.872 149.339 4732 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.51 % Allowed : 8.52 % Favored : 89.97 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3750 helix: 1.57 (0.13), residues: 1588 sheet: 0.70 (0.20), residues: 708 loop : -1.02 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 256 TYR 0.023 0.001 TYR M 87 PHE 0.025 0.001 PHE L 203 TRP 0.018 0.001 TRP A 237 HIS 0.043 0.002 HIS N 12 Details of bonding type rmsd covalent geometry : bond 0.00266 (33032) covalent geometry : angle 0.56367 (44970) hydrogen bonds : bond 0.04347 ( 1443) hydrogen bonds : angle 4.92606 ( 4154) metal coordination : bond 0.05885 ( 48) metal coordination : angle 11.44475 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 1.178 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: D 82 ASN cc_start: 0.4941 (t0) cc_final: 0.4677 (m-40) REVERT: D 114 SER cc_start: 0.5554 (OUTLIER) cc_final: 0.5318 (p) REVERT: D 134 TYR cc_start: 0.6324 (t80) cc_final: 0.6120 (t80) REVERT: D 259 ASP cc_start: 0.7566 (m-30) cc_final: 0.7098 (t0) REVERT: E 18 ASP cc_start: 0.7139 (p0) cc_final: 0.6850 (m-30) REVERT: F 47 LYS cc_start: 0.4417 (OUTLIER) cc_final: 0.3923 (mppt) REVERT: F 170 MET cc_start: -0.0449 (ptt) cc_final: -0.0949 (pmm) REVERT: G 67 TYR cc_start: 0.5283 (p90) cc_final: 0.4832 (p90) REVERT: G 109 MET cc_start: 0.5393 (pmm) cc_final: 0.3586 (ptm) REVERT: G 176 SER cc_start: 0.4546 (p) cc_final: 0.4286 (m) REVERT: I 13 ASN cc_start: 0.8518 (m-40) cc_final: 0.8284 (m110) REVERT: J 164 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8248 (tt) REVERT: L 82 ASN cc_start: 0.5043 (t0) cc_final: 0.4780 (m-40) REVERT: L 114 SER cc_start: 0.5719 (OUTLIER) cc_final: 0.5450 (p) REVERT: L 259 ASP cc_start: 0.7474 (m-30) cc_final: 0.7114 (t0) REVERT: M 7 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7481 (pp) REVERT: M 18 ASP cc_start: 0.6992 (p0) cc_final: 0.6770 (m-30) REVERT: N 170 MET cc_start: -0.0296 (ptt) cc_final: -0.0903 (pmm) REVERT: O 67 TYR cc_start: 0.5401 (p90) cc_final: 0.4972 (p90) REVERT: O 109 MET cc_start: 0.5363 (pmm) cc_final: 0.3356 (ptm) outliers start: 50 outliers final: 29 residues processed: 380 average time/residue: 0.1818 time to fit residues: 113.0607 Evaluate side-chains 289 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 157 HIS Chi-restraints excluded: chain L residue 201 PHE Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 74 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 350 optimal weight: 0.0270 chunk 293 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 242 GLN B 82 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN F 44 GLN G 148 GLN I 238 GLN I 242 GLN J 82 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN K 211 GLN L 146 ASN N 44 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.223584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.192541 restraints weight = 47946.157| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.33 r_work: 0.4164 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4132 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 33080 Z= 0.196 Angle : 0.650 35.356 44992 Z= 0.318 Chirality : 0.046 0.299 4830 Planarity : 0.004 0.044 5568 Dihedral : 13.412 149.654 4732 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.90 % Allowed : 11.93 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3750 helix: 1.41 (0.13), residues: 1614 sheet: 0.51 (0.20), residues: 688 loop : -1.15 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.017 0.002 TYR I 134 PHE 0.027 0.002 PHE C 123 TRP 0.032 0.002 TRP C 145 HIS 0.035 0.002 HIS N 12 Details of bonding type rmsd covalent geometry : bond 0.00452 (33032) covalent geometry : angle 0.59651 (44970) hydrogen bonds : bond 0.04383 ( 1443) hydrogen bonds : angle 4.77275 ( 4154) metal coordination : bond 0.06235 ( 48) metal coordination : angle 11.65306 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 1.016 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: D 82 ASN cc_start: 0.5081 (t0) cc_final: 0.4797 (m-40) REVERT: D 114 SER cc_start: 0.5684 (OUTLIER) cc_final: 0.5272 (p) REVERT: D 259 ASP cc_start: 0.7726 (m-30) cc_final: 0.7180 (t0) REVERT: E 18 ASP cc_start: 0.7058 (p0) cc_final: 0.6840 (m-30) REVERT: F 47 LYS cc_start: 0.4370 (OUTLIER) cc_final: 0.3725 (mppt) REVERT: F 170 MET cc_start: -0.0135 (ptt) cc_final: -0.0784 (pmm) REVERT: G 109 MET cc_start: 0.5425 (pmm) cc_final: 0.3260 (mtp) REVERT: L 82 ASN cc_start: 0.5176 (t0) cc_final: 0.4924 (m-40) REVERT: L 114 SER cc_start: 0.5951 (OUTLIER) cc_final: 0.5465 (p) REVERT: L 259 ASP cc_start: 0.7696 (m-30) cc_final: 0.7196 (t0) REVERT: M 7 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7542 (pp) REVERT: N 47 LYS cc_start: 0.3238 (OUTLIER) cc_final: 0.2933 (mptt) REVERT: N 170 MET cc_start: -0.0304 (ptt) cc_final: -0.0815 (pmm) REVERT: O 109 MET cc_start: 0.5428 (pmm) cc_final: 0.3044 (mtp) REVERT: P 110 PHE cc_start: 0.3403 (m-10) cc_final: 0.3055 (m-80) outliers start: 63 outliers final: 34 residues processed: 336 average time/residue: 0.1761 time to fit residues: 97.6814 Evaluate side-chains 281 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 224 CYS Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 47 LYS Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 176 optimal weight: 0.0470 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 0.0020 chunk 212 optimal weight: 9.9990 chunk 231 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN D 146 ASN F 4 ASN I 13 ASN ** J 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN O 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.226274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.197419 restraints weight = 48787.856| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 2.22 r_work: 0.4205 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 33080 Z= 0.112 Angle : 0.568 30.593 44992 Z= 0.277 Chirality : 0.042 0.296 4830 Planarity : 0.004 0.041 5568 Dihedral : 13.259 149.058 4732 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.54 % Allowed : 13.95 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3750 helix: 1.59 (0.13), residues: 1610 sheet: 0.51 (0.20), residues: 640 loop : -1.07 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 209 TYR 0.015 0.001 TYR M 87 PHE 0.027 0.001 PHE L 203 TRP 0.034 0.001 TRP C 145 HIS 0.031 0.001 HIS N 12 Details of bonding type rmsd covalent geometry : bond 0.00223 (33032) covalent geometry : angle 0.52335 (44970) hydrogen bonds : bond 0.03296 ( 1443) hydrogen bonds : angle 4.56364 ( 4154) metal coordination : bond 0.04763 ( 48) metal coordination : angle 10.02614 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 1.134 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: B 80 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: B 145 TRP cc_start: 0.4131 (m-10) cc_final: 0.3619 (t60) REVERT: D 82 ASN cc_start: 0.4890 (t0) cc_final: 0.4631 (m-40) REVERT: D 114 SER cc_start: 0.5614 (OUTLIER) cc_final: 0.5246 (p) REVERT: D 259 ASP cc_start: 0.7687 (m-30) cc_final: 0.7110 (t0) REVERT: F 170 MET cc_start: -0.0258 (ptt) cc_final: -0.0851 (pmm) REVERT: G 109 MET cc_start: 0.5337 (pmm) cc_final: 0.3193 (mtp) REVERT: J 80 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: L 82 ASN cc_start: 0.4910 (t0) cc_final: 0.4683 (m-40) REVERT: L 114 SER cc_start: 0.5718 (OUTLIER) cc_final: 0.5385 (p) REVERT: L 197 PRO cc_start: 0.3436 (Cg_endo) cc_final: 0.3188 (Cg_exo) REVERT: L 259 ASP cc_start: 0.7610 (m-30) cc_final: 0.7134 (t0) REVERT: M 7 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7471 (pp) REVERT: M 171 PHE cc_start: 0.3015 (m-80) cc_final: 0.2791 (m-80) REVERT: N 170 MET cc_start: -0.0481 (ptt) cc_final: -0.0962 (pmm) REVERT: O 109 MET cc_start: 0.5222 (pmm) cc_final: 0.2977 (mtp) outliers start: 51 outliers final: 30 residues processed: 300 average time/residue: 0.1685 time to fit residues: 85.6328 Evaluate side-chains 257 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 261 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 284 optimal weight: 0.0980 chunk 160 optimal weight: 20.0000 chunk 372 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 242 GLN B 97 GLN C 186 ASN G 62 HIS I 139 HIS J 97 GLN K 186 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.222356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.190390 restraints weight = 47892.360| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 2.49 r_work: 0.4143 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.4110 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 33080 Z= 0.157 Angle : 0.573 21.383 44992 Z= 0.291 Chirality : 0.044 0.250 4830 Planarity : 0.004 0.043 5568 Dihedral : 13.357 150.252 4732 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.11 % Allowed : 15.21 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3750 helix: 1.54 (0.13), residues: 1626 sheet: 0.41 (0.20), residues: 648 loop : -1.16 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.017 0.001 TYR A 134 PHE 0.024 0.002 PHE H 174 TRP 0.038 0.002 TRP E 78 HIS 0.027 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00359 (33032) covalent geometry : angle 0.54935 (44970) hydrogen bonds : bond 0.03785 ( 1443) hydrogen bonds : angle 4.51875 ( 4154) metal coordination : bond 0.04209 ( 48) metal coordination : angle 7.35849 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 246 time to evaluate : 1.230 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: B 80 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: B 145 TRP cc_start: 0.4105 (m-10) cc_final: 0.3607 (t60) REVERT: C 123 PHE cc_start: 0.3009 (OUTLIER) cc_final: 0.2490 (t80) REVERT: C 198 MET cc_start: 0.7496 (ttp) cc_final: 0.7243 (ttp) REVERT: D 82 ASN cc_start: 0.4926 (t0) cc_final: 0.4711 (m-40) REVERT: D 114 SER cc_start: 0.5632 (OUTLIER) cc_final: 0.5201 (p) REVERT: F 63 TRP cc_start: 0.6306 (m100) cc_final: 0.6000 (m100) REVERT: F 170 MET cc_start: -0.0089 (ptt) cc_final: -0.0912 (pmm) REVERT: G 109 MET cc_start: 0.5305 (pmm) cc_final: 0.3300 (mtp) REVERT: H 174 PHE cc_start: 0.4648 (t80) cc_final: 0.4422 (t80) REVERT: J 80 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: J 145 TRP cc_start: 0.4062 (m-10) cc_final: 0.3697 (t60) REVERT: K 24 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7977 (mm) REVERT: K 198 MET cc_start: 0.7417 (ttp) cc_final: 0.7124 (ttp) REVERT: L 114 SER cc_start: 0.5764 (OUTLIER) cc_final: 0.5368 (p) REVERT: M 7 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7506 (pp) REVERT: N 170 MET cc_start: -0.0279 (ptt) cc_final: -0.0906 (pmm) REVERT: O 109 MET cc_start: 0.5276 (pmm) cc_final: 0.3152 (mtp) outliers start: 70 outliers final: 40 residues processed: 298 average time/residue: 0.1839 time to fit residues: 90.6447 Evaluate side-chains 268 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain G residue 62 HIS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 211 GLN Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain N residue 204 ASN Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 344 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 211 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 208 GLN A 242 GLN B 129 GLN C 186 ASN C 211 GLN I 44 GLN I 208 GLN I 242 GLN K 186 ASN O 46 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.221145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.191028 restraints weight = 47435.272| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.33 r_work: 0.4136 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.250 33080 Z= 0.181 Angle : 0.594 28.761 44992 Z= 0.299 Chirality : 0.044 0.197 4830 Planarity : 0.004 0.044 5568 Dihedral : 13.469 150.443 4732 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.56 % Allowed : 15.15 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3750 helix: 1.49 (0.13), residues: 1626 sheet: 0.35 (0.20), residues: 628 loop : -1.18 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 58 TYR 0.018 0.001 TYR I 134 PHE 0.025 0.002 PHE L 203 TRP 0.036 0.002 TRP K 145 HIS 0.027 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00416 (33032) covalent geometry : angle 0.55962 (44970) hydrogen bonds : bond 0.03715 ( 1443) hydrogen bonds : angle 4.65245 ( 4154) metal coordination : bond 0.06681 ( 48) metal coordination : angle 9.06995 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 237 time to evaluate : 1.108 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: A 80 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: A 116 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: B 71 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7914 (tm-30) REVERT: B 80 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: B 145 TRP cc_start: 0.4158 (m-10) cc_final: 0.3638 (t60) REVERT: C 24 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 123 PHE cc_start: 0.3089 (OUTLIER) cc_final: 0.2519 (t80) REVERT: C 198 MET cc_start: 0.7666 (ttp) cc_final: 0.7399 (ttp) REVERT: D 82 ASN cc_start: 0.4981 (t0) cc_final: 0.4739 (m-40) REVERT: D 114 SER cc_start: 0.5503 (OUTLIER) cc_final: 0.5093 (p) REVERT: D 221 ILE cc_start: 0.8023 (mt) cc_final: 0.7803 (mm) REVERT: F 39 GLN cc_start: 0.3365 (OUTLIER) cc_final: 0.3146 (mt0) REVERT: F 47 LYS cc_start: 0.4332 (OUTLIER) cc_final: 0.3457 (mppt) REVERT: F 63 TRP cc_start: 0.6228 (m100) cc_final: 0.5959 (m100) REVERT: F 170 MET cc_start: -0.0064 (ptt) cc_final: -0.0947 (pmm) REVERT: G 109 MET cc_start: 0.5103 (pmm) cc_final: 0.3297 (mtp) REVERT: I 80 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: I 116 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: J 80 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: J 145 TRP cc_start: 0.4164 (m-10) cc_final: 0.3764 (t60) REVERT: K 24 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8045 (mm) REVERT: K 198 MET cc_start: 0.7555 (ttp) cc_final: 0.7281 (ttp) REVERT: L 114 SER cc_start: 0.5828 (OUTLIER) cc_final: 0.5391 (p) REVERT: L 221 ILE cc_start: 0.8061 (mt) cc_final: 0.7809 (mm) REVERT: M 7 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7472 (pp) REVERT: N 170 MET cc_start: -0.0263 (ptt) cc_final: -0.1042 (pmm) REVERT: O 109 MET cc_start: 0.5108 (pmm) cc_final: 0.3095 (mtp) outliers start: 85 outliers final: 48 residues processed: 305 average time/residue: 0.1737 time to fit residues: 88.9706 Evaluate side-chains 288 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 211 GLN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain O residue 209 ARG Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 234 optimal weight: 0.0040 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 178 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 186 ASN I 242 GLN K 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.223080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.192419 restraints weight = 48100.036| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.44 r_work: 0.4157 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.288 33080 Z= 0.117 Angle : 0.556 31.752 44992 Z= 0.271 Chirality : 0.042 0.168 4830 Planarity : 0.004 0.042 5568 Dihedral : 13.337 149.658 4732 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 16.33 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3750 helix: 1.62 (0.13), residues: 1626 sheet: 0.40 (0.20), residues: 646 loop : -1.15 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 100 TYR 0.013 0.001 TYR N 134 PHE 0.018 0.001 PHE P 174 TRP 0.038 0.001 TRP C 145 HIS 0.026 0.001 HIS N 12 Details of bonding type rmsd covalent geometry : bond 0.00229 (33032) covalent geometry : angle 0.51110 (44970) hydrogen bonds : bond 0.03064 ( 1443) hydrogen bonds : angle 4.51428 ( 4154) metal coordination : bond 0.06963 ( 48) metal coordination : angle 9.87716 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.217 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: A 80 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: A 116 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: B 80 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: B 145 TRP cc_start: 0.4201 (m-10) cc_final: 0.3687 (t60) REVERT: C 24 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8113 (mm) REVERT: C 123 PHE cc_start: 0.3042 (OUTLIER) cc_final: 0.2426 (t80) REVERT: C 198 MET cc_start: 0.7628 (ttp) cc_final: 0.7356 (ttp) REVERT: D 82 ASN cc_start: 0.5013 (t0) cc_final: 0.4754 (m-40) REVERT: D 114 SER cc_start: 0.5609 (t) cc_final: 0.5158 (p) REVERT: E 109 MET cc_start: 0.6535 (mpp) cc_final: 0.6254 (mpp) REVERT: F 47 LYS cc_start: 0.4378 (OUTLIER) cc_final: 0.3546 (mppt) REVERT: F 63 TRP cc_start: 0.6176 (m100) cc_final: 0.5908 (m100) REVERT: F 170 MET cc_start: 0.0012 (ptt) cc_final: -0.0769 (pmm) REVERT: G 109 MET cc_start: 0.5047 (pmm) cc_final: 0.3380 (mtp) REVERT: I 80 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: I 116 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: J 80 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: J 145 TRP cc_start: 0.4118 (m-10) cc_final: 0.3730 (t60) REVERT: K 198 MET cc_start: 0.7495 (ttp) cc_final: 0.7224 (ttp) REVERT: M 7 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7412 (pp) REVERT: N 170 MET cc_start: -0.0135 (ptt) cc_final: -0.0956 (pmm) REVERT: O 109 MET cc_start: 0.5152 (pmm) cc_final: 0.3092 (mtp) outliers start: 60 outliers final: 37 residues processed: 282 average time/residue: 0.1777 time to fit residues: 83.8563 Evaluate side-chains 270 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 183 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 278 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 0.0010 chunk 213 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 69 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 234 optimal weight: 0.3980 chunk 191 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 186 ASN I 242 GLN K 186 ASN N 146 ASN O 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.223343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.193513 restraints weight = 48336.090| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.46 r_work: 0.4164 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.4122 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.298 33080 Z= 0.118 Angle : 0.563 34.871 44992 Z= 0.272 Chirality : 0.042 0.167 4830 Planarity : 0.004 0.041 5568 Dihedral : 13.275 149.660 4732 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.78 % Allowed : 16.60 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3750 helix: 1.68 (0.13), residues: 1626 sheet: 0.49 (0.20), residues: 670 loop : -1.10 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 100 TYR 0.029 0.001 TYR C 107 PHE 0.018 0.001 PHE G 174 TRP 0.061 0.001 TRP H 63 HIS 0.026 0.001 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00231 (33032) covalent geometry : angle 0.51376 (44970) hydrogen bonds : bond 0.02966 ( 1443) hydrogen bonds : angle 4.47421 ( 4154) metal coordination : bond 0.07304 ( 48) metal coordination : angle 10.45870 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 236 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 260 ARG cc_start: 0.6744 (mmm160) cc_final: 0.6239 (tpt90) REVERT: B 80 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: B 145 TRP cc_start: 0.4179 (m-10) cc_final: 0.3704 (t60) REVERT: C 123 PHE cc_start: 0.2957 (OUTLIER) cc_final: 0.2456 (t80) REVERT: C 198 MET cc_start: 0.7502 (ttp) cc_final: 0.7250 (ttp) REVERT: E 109 MET cc_start: 0.6376 (mpp) cc_final: 0.6124 (mpp) REVERT: F 63 TRP cc_start: 0.6172 (m100) cc_final: 0.5914 (m100) REVERT: F 170 MET cc_start: 0.0078 (ptt) cc_final: -0.0731 (pmm) REVERT: G 109 MET cc_start: 0.4677 (pmm) cc_final: 0.3844 (ptm) REVERT: I 80 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: I 116 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: J 80 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: J 145 TRP cc_start: 0.4148 (m-10) cc_final: 0.3659 (t60) REVERT: K 198 MET cc_start: 0.7417 (ttp) cc_final: 0.7158 (ttp) REVERT: M 7 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7391 (pp) REVERT: N 170 MET cc_start: 0.0046 (ptt) cc_final: -0.0942 (pmm) REVERT: O 109 MET cc_start: 0.5188 (pmm) cc_final: 0.3132 (mtp) outliers start: 59 outliers final: 39 residues processed: 278 average time/residue: 0.1753 time to fit residues: 81.8783 Evaluate side-chains 265 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 175 optimal weight: 7.9990 chunk 319 optimal weight: 0.9980 chunk 151 optimal weight: 50.0000 chunk 330 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 98 optimal weight: 0.0170 chunk 286 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 overall best weight: 2.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 242 GLN C 186 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS H 242 GLN I 204 ASN J 129 GLN K 186 ASN P 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.219918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.189660 restraints weight = 48161.428| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 2.40 r_work: 0.4109 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.854 33080 Z= 0.252 Angle : 0.668 50.498 44992 Z= 0.322 Chirality : 0.046 0.577 4830 Planarity : 0.004 0.056 5568 Dihedral : 13.583 151.226 4732 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.91 % Rotamer: Outliers : 1.96 % Allowed : 16.66 % Favored : 81.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3750 helix: 1.52 (0.13), residues: 1626 sheet: 0.32 (0.19), residues: 692 loop : -1.17 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 58 TYR 0.020 0.002 TYR A 134 PHE 0.024 0.002 PHE L 203 TRP 0.058 0.002 TRP F 15 HIS 0.035 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00511 (33032) covalent geometry : angle 0.59738 (44970) hydrogen bonds : bond 0.03984 ( 1443) hydrogen bonds : angle 4.63191 ( 4154) metal coordination : bond 0.16986 ( 48) metal coordination : angle 13.54070 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.997 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: A 80 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 116 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8007 (tt0) REVERT: A 243 VAL cc_start: 0.8561 (t) cc_final: 0.8348 (p) REVERT: B 80 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: B 145 TRP cc_start: 0.4198 (m-10) cc_final: 0.3708 (t60) REVERT: C 123 PHE cc_start: 0.3201 (OUTLIER) cc_final: 0.2570 (t80) REVERT: E 135 LEU cc_start: 0.0879 (OUTLIER) cc_final: -0.0113 (mt) REVERT: F 63 TRP cc_start: 0.6259 (m100) cc_final: 0.5989 (m100) REVERT: F 170 MET cc_start: 0.0419 (ptt) cc_final: -0.0664 (pmm) REVERT: G 109 MET cc_start: 0.4731 (pmm) cc_final: 0.3683 (ptm) REVERT: I 80 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: I 116 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: J 80 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: J 145 TRP cc_start: 0.4224 (m-10) cc_final: 0.3689 (t60) REVERT: L 114 SER cc_start: 0.5923 (t) cc_final: 0.5431 (p) REVERT: M 7 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7492 (pp) REVERT: M 135 LEU cc_start: 0.0826 (OUTLIER) cc_final: -0.0193 (mt) REVERT: N 170 MET cc_start: 0.0175 (ptt) cc_final: -0.0865 (pmm) REVERT: O 104 MET cc_start: 0.2767 (ppp) cc_final: 0.2247 (ptm) outliers start: 65 outliers final: 44 residues processed: 277 average time/residue: 0.1691 time to fit residues: 79.3416 Evaluate side-chains 268 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain H residue 253 VAL Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 238 GLN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 196 SER Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 286 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 204 optimal weight: 0.5980 chunk 356 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 186 ASN E 186 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN K 186 ASN M 186 ASN O 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.222495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.192627 restraints weight = 48815.100| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.44 r_work: 0.4143 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.4108 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.818 33080 Z= 0.182 Angle : 0.620 53.808 44992 Z= 0.298 Chirality : 0.044 0.612 4830 Planarity : 0.004 0.120 5568 Dihedral : 13.513 150.358 4732 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 1.66 % Allowed : 16.99 % Favored : 81.36 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3750 helix: 1.59 (0.13), residues: 1626 sheet: 0.32 (0.20), residues: 686 loop : -1.18 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 100 TYR 0.015 0.001 TYR A 134 PHE 0.026 0.001 PHE D 203 TRP 0.046 0.002 TRP C 145 HIS 0.090 0.002 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00292 (33032) covalent geometry : angle 0.54531 (44970) hydrogen bonds : bond 0.03271 ( 1443) hydrogen bonds : angle 4.58908 ( 4154) metal coordination : bond 0.16730 ( 48) metal coordination : angle 13.38482 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7500 Ramachandran restraints generated. 3750 Oldfield, 0 Emsley, 3750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 1.253 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: A 80 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: A 116 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: B 80 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: B 145 TRP cc_start: 0.4089 (m-10) cc_final: 0.3598 (t60) REVERT: C 123 PHE cc_start: 0.3200 (OUTLIER) cc_final: 0.2595 (t80) REVERT: D 104 MET cc_start: 0.6521 (tpp) cc_final: 0.6300 (tpt) REVERT: E 135 LEU cc_start: 0.0869 (OUTLIER) cc_final: -0.0065 (mt) REVERT: F 63 TRP cc_start: 0.6165 (m100) cc_final: 0.5911 (m100) REVERT: F 170 MET cc_start: 0.0440 (ptt) cc_final: -0.0722 (pmm) REVERT: G 109 MET cc_start: 0.4683 (pmm) cc_final: 0.3757 (ptm) REVERT: I 80 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8019 (tm-30) REVERT: I 116 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: J 80 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: J 145 TRP cc_start: 0.4197 (m-10) cc_final: 0.3681 (t60) REVERT: K 24 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8155 (mm) REVERT: L 114 SER cc_start: 0.5779 (t) cc_final: 0.5374 (p) REVERT: M 7 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (pp) REVERT: M 78 TRP cc_start: 0.3523 (t60) cc_final: 0.3177 (t60) REVERT: M 135 LEU cc_start: 0.0644 (OUTLIER) cc_final: -0.0265 (mt) REVERT: N 170 MET cc_start: 0.0132 (ptt) cc_final: -0.0881 (pmm) REVERT: O 104 MET cc_start: 0.2645 (ppp) cc_final: 0.2263 (ptm) REVERT: O 109 MET cc_start: 0.5330 (pmm) cc_final: 0.3440 (ptm) outliers start: 55 outliers final: 37 residues processed: 270 average time/residue: 0.1747 time to fit residues: 79.3317 Evaluate side-chains 264 residues out of total 3320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 23 HIS Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 196 SER Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 196 SER Chi-restraints excluded: chain G residue 209 ARG Chi-restraints excluded: chain I residue 17 GLN Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain J residue 80 GLU Chi-restraints excluded: chain J residue 198 MET Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 210 ILE Chi-restraints excluded: chain L residue 215 LYS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 23 HIS Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain O residue 101 VAL Chi-restraints excluded: chain O residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 364 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 138 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN C 186 ASN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN G 207 GLN K 186 ASN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.217653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185682 restraints weight = 47664.422| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.46 r_work: 0.4061 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.792 33080 Z= 0.351 Angle : 0.798 53.652 44992 Z= 0.392 Chirality : 0.051 0.813 4830 Planarity : 0.005 0.085 5568 Dihedral : 13.924 153.087 4732 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.93 % Allowed : 16.69 % Favored : 81.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3750 helix: 1.23 (0.13), residues: 1636 sheet: -0.14 (0.18), residues: 758 loop : -1.31 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 260 TYR 0.026 0.002 TYR B 134 PHE 0.026 0.002 PHE I 110 TRP 0.065 0.003 TRP N 15 HIS 0.047 0.003 HIS F 16 Details of bonding type rmsd covalent geometry : bond 0.00754 (33032) covalent geometry : angle 0.70321 (44970) hydrogen bonds : bond 0.05066 ( 1443) hydrogen bonds : angle 4.87860 ( 4154) metal coordination : bond 0.21101 ( 48) metal coordination : angle 17.10566 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7026.73 seconds wall clock time: 121 minutes 26.60 seconds (7286.60 seconds total)