Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 06:25:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_26322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_26322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_26322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_26322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u32_26322/07_2023/7u32_26322.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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: 15.00, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.13 Conformation dependent library (CDL) restraints added in 4.9 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: 9.16 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: 11.08 Time building geometry restraints manager: 14.10 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: 99.01 - 106.49: 1357 106.49 - 113.96: 18632 113.96 - 121.44: 16597 121.44 - 128.92: 7984 128.92 - 136.39: 400 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: 18707 30.17 - 60.35: 725 60.35 - 90.52: 40 90.52 - 120.70: 0 120.70 - 150.87: 2 Dihedral angle restraints: 19474 sinusoidal: 8510 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 19471 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 2.440 nonbonded pdb=" O ALA C 173 " pdb=" OG SER C 176 " model vdw 2.170 2.440 nonbonded pdb=" OG SER N 83 " pdb=" O PRO N 197 " model vdw 2.211 2.440 nonbonded pdb=" OG SER F 83 " pdb=" O PRO F 197 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR E 261 " pdb=" OD1 ASP H 248 " model vdw 2.237 2.440 ... (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 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 215 or resid 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 215 or resid 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: 3.790 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: 0.030 Extract box with map and model: 14.810 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 90.220 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.560 ------------------------------------------------------------------------------- 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 33032 Z= 0.131 Angle : 0.512 14.852 44970 Z= 0.275 Chirality : 0.041 0.188 4830 Planarity : 0.003 0.034 5568 Dihedral : 14.679 150.873 12402 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 722 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 722 average time/residue: 0.4877 time to fit residues: 538.8259 Evaluate side-chains 294 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.714 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 296 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 204 ASN A 208 GLN A 238 GLN A 242 GLN B 82 ASN B 97 GLN B 211 GLN B 212 GLN C 186 ASN C 207 GLN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN F 4 ASN F 44 GLN F 211 GLN I 139 HIS I 148 GLN I 204 ASN I 208 GLN I 238 GLN I 242 GLN J 82 ASN J 97 GLN J 212 GLN K 186 ASN K 207 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 ASN N 4 ASN N 44 GLN N 211 GLN O 23 HIS O 148 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4883 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.115 33032 Z= 0.655 Angle : 0.835 9.997 44970 Z= 0.446 Chirality : 0.056 0.453 4830 Planarity : 0.006 0.061 5568 Dihedral : 13.645 152.899 4692 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.87 % Favored : 95.97 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3750 helix: 0.81 (0.13), residues: 1598 sheet: 0.17 (0.20), residues: 694 loop : -1.39 (0.15), residues: 1458 *********************** 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 410 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 318 time to evaluate : 3.684 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 outliers start: 92 outliers final: 54 residues processed: 390 average time/residue: 0.4168 time to fit residues: 264.5066 Evaluate side-chains 288 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 3.706 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3102 time to fit residues: 34.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 371 optimal weight: 7.9990 chunk 306 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 117 optimal weight: 0.0020 chunk 275 optimal weight: 7.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 242 GLN B 17 GLN C 186 ASN D 69 HIS D 157 HIS ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 146 ASN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 208 GLN I 207 GLN I 242 GLN K 186 ASN K 211 GLN L 69 HIS L 146 ASN L 157 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN N 146 ASN ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 33032 Z= 0.268 Angle : 0.585 7.976 44970 Z= 0.311 Chirality : 0.045 0.266 4830 Planarity : 0.004 0.046 5568 Dihedral : 13.362 151.173 4692 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3750 helix: 1.23 (0.13), residues: 1610 sheet: 0.11 (0.20), residues: 676 loop : -1.31 (0.15), residues: 1464 *********************** 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 314 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 20 residues processed: 301 average time/residue: 0.4321 time to fit residues: 212.9566 Evaluate side-chains 247 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3182 time to fit residues: 16.4078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 345 optimal weight: 50.0000 chunk 365 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 327 optimal weight: 20.0000 chunk 98 optimal weight: 0.0670 overall best weight: 2.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 242 GLN C 139 HIS C 186 ASN C 208 GLN D 146 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN I 211 GLN K 186 ASN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4859 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 33032 Z= 0.302 Angle : 0.585 8.202 44970 Z= 0.310 Chirality : 0.045 0.226 4830 Planarity : 0.004 0.047 5568 Dihedral : 13.429 152.446 4692 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3750 helix: 1.35 (0.13), residues: 1612 sheet: 0.15 (0.20), residues: 716 loop : -1.30 (0.15), residues: 1422 *********************** 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 306 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 243 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 39 residues processed: 288 average time/residue: 0.4005 time to fit residues: 192.8363 Evaluate side-chains 254 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 3.441 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2842 time to fit residues: 24.8848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 272 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 311 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 186 optimal weight: 40.0000 chunk 327 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 139 HIS C 186 ASN ** D 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 GLN H 242 GLN J 139 HIS K 186 ASN ** L 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS P 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.076 33032 Z= 0.444 Angle : 0.641 9.643 44970 Z= 0.342 Chirality : 0.047 0.230 4830 Planarity : 0.005 0.058 5568 Dihedral : 13.652 152.785 4692 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3750 helix: 1.24 (0.13), residues: 1612 sheet: -0.08 (0.19), residues: 756 loop : -1.44 (0.16), residues: 1382 *********************** 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 285 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 233 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 274 average time/residue: 0.4101 time to fit residues: 187.8807 Evaluate side-chains 244 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 3.470 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2888 time to fit residues: 20.2615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 365 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.0970 chunk 192 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 157 HIS ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 157 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 33032 Z= 0.184 Angle : 0.531 7.879 44970 Z= 0.280 Chirality : 0.043 0.160 4830 Planarity : 0.004 0.048 5568 Dihedral : 13.462 151.446 4692 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3750 helix: 1.57 (0.13), residues: 1610 sheet: 0.12 (0.20), residues: 678 loop : -1.37 (0.15), residues: 1462 *********************** 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 275 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 3.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 269 average time/residue: 0.4287 time to fit residues: 187.5567 Evaluate side-chains 234 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 3.706 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2871 time to fit residues: 10.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 208 optimal weight: 0.0170 chunk 267 optimal weight: 0.3980 chunk 206 optimal weight: 0.0070 chunk 307 optimal weight: 8.9990 chunk 204 optimal weight: 0.5980 chunk 364 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 chunk 168 optimal weight: 40.0000 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4811 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 33032 Z= 0.142 Angle : 0.509 7.756 44970 Z= 0.266 Chirality : 0.042 0.177 4830 Planarity : 0.004 0.044 5568 Dihedral : 13.406 150.686 4692 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.28 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3750 helix: 1.74 (0.13), residues: 1612 sheet: 0.27 (0.20), residues: 680 loop : -1.27 (0.15), residues: 1458 *********************** 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 264 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 242 time to evaluate : 3.785 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 258 average time/residue: 0.4074 time to fit residues: 176.7172 Evaluate side-chains 222 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 4.013 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3009 time to fit residues: 8.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 217 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 0.0060 chunk 231 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 157 HIS ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN L 157 HIS ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4827 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 33032 Z= 0.177 Angle : 0.515 9.085 44970 Z= 0.271 Chirality : 0.042 0.157 4830 Planarity : 0.004 0.045 5568 Dihedral : 13.468 150.793 4692 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.85 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3750 helix: 1.77 (0.14), residues: 1602 sheet: 0.20 (0.19), residues: 730 loop : -1.23 (0.15), residues: 1418 *********************** 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 237 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 232 average time/residue: 0.4242 time to fit residues: 164.2748 Evaluate side-chains 218 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 4.457 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2841 time to fit residues: 8.3415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 349 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 339 optimal weight: 30.0000 chunk 348 optimal weight: 0.0670 chunk 204 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 overall best weight: 2.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 33032 Z= 0.357 Angle : 0.595 9.633 44970 Z= 0.315 Chirality : 0.045 0.162 4830 Planarity : 0.004 0.049 5568 Dihedral : 13.711 152.394 4692 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.13 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3750 helix: 1.57 (0.13), residues: 1616 sheet: -0.05 (0.19), residues: 742 loop : -1.36 (0.16), residues: 1392 *********************** 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 244 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 237 average time/residue: 0.4515 time to fit residues: 174.8088 Evaluate side-chains 220 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2917 time to fit residues: 9.3495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 359 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 249 optimal weight: 3.9990 chunk 376 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 299 optimal weight: 0.0000 chunk 31 optimal weight: 3.9990 chunk 231 optimal weight: 0.0870 overall best weight: 1.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 157 HIS ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 69 HIS ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS O 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4845 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 33032 Z= 0.223 Angle : 0.549 10.587 44970 Z= 0.290 Chirality : 0.043 0.155 4830 Planarity : 0.004 0.046 5568 Dihedral : 13.618 151.886 4692 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3750 helix: 1.62 (0.13), residues: 1624 sheet: -0.01 (0.19), residues: 724 loop : -1.28 (0.16), residues: 1402 ********************** 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 226 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 223 average time/residue: 0.4478 time to fit residues: 163.4637 Evaluate side-chains 213 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3047 time to fit residues: 5.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 0.2980 chunk 91 optimal weight: 0.2980 chunk 276 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 300 optimal weight: 0.0980 chunk 125 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS E 69 HIS F 23 HIS K 186 ASN ** L 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 HIS M 186 ASN O 64 GLN ** O 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.217539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.178821 restraints weight = 47172.144| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.71 r_work: 0.3907 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33032 Z= 0.167 Angle : 0.534 11.866 44970 Z= 0.280 Chirality : 0.042 0.147 4830 Planarity : 0.004 0.045 5568 Dihedral : 13.529 151.181 4692 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.20 % Favored : 96.75 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3750 helix: 1.71 (0.13), residues: 1634 sheet: 0.08 (0.19), residues: 724 loop : -1.24 (0.16), residues: 1392 =============================================================================== Job complete usr+sys time: 6185.17 seconds wall clock time: 113 minutes 25.70 seconds (6805.70 seconds total)