Starting phenix.real_space_refine on Mon Jul 6 12:51:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z1z_14453/07_2026/7z1z_14453.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 138 5.49 5 S 132 5.16 5 C 22213 2.51 5 N 6243 2.21 5 O 6867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35605 Number of models: 1 Model: "" Number of chains: 36 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: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "D" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 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: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} 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: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 674 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 667 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "X" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "W" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 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: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} 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: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Z" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "a" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 52.555 98.275 57.044 1.00 82.30 S ATOM 350 SG CYS A 43 55.029 100.117 57.886 1.00 80.20 S ATOM 2550 SG CYS B 40 141.347 77.147 78.894 1.00234.54 S ATOM 2571 SG CYS B 43 140.373 75.690 76.304 1.00237.78 S ATOM 4203 SG CYS C 40 112.859 55.219 47.405 1.00165.74 S ATOM 4224 SG CYS C 43 115.169 57.021 48.375 1.00154.11 S ATOM 8384 SG CYS E 40 35.028 89.415 83.743 1.00201.72 S ATOM 8405 SG CYS E 43 36.217 86.876 85.415 1.00192.57 S ATOM 10469 SG CYS F 40 51.442 57.845 50.351 1.00254.89 S ATOM 10490 SG CYS F 43 49.499 55.856 51.548 1.00254.39 S ATOM 12615 SG CYS G 40 27.432 33.168 82.886 1.00236.12 S ATOM 12636 SG CYS G 43 28.446 35.251 80.527 1.00234.83 S ATOM 18796 SG CYS I 40 112.929 111.593 57.211 1.00 82.30 S ATOM 18817 SG CYS I 43 110.445 109.764 58.051 1.00 80.20 S ATOM 21017 SG CYS J 40 23.984 133.086 78.061 1.00234.54 S ATOM 21038 SG CYS J 43 24.983 134.515 75.464 1.00237.78 S ATOM 22670 SG CYS K 40 52.782 154.640 46.597 1.00165.74 S ATOM 22691 SG CYS K 43 50.461 152.852 47.564 1.00154.11 S ATOM 26851 SG CYS M 40 130.237 120.704 83.969 1.00201.72 S ATOM 26872 SG CYS M 43 129.036 123.262 85.604 1.00192.57 S ATOM 28936 SG CYS N 40 114.167 151.949 50.107 1.00254.89 S ATOM 28957 SG CYS N 43 116.103 153.948 51.301 1.00254.39 S ATOM 31082 SG CYS O 40 137.932 176.928 82.593 1.00236.12 S ATOM 31103 SG CYS O 43 136.935 174.822 80.247 1.00234.83 S Time building chain proxies: 7.74, per 1000 atoms: 0.22 Number of scatterers: 35605 At special positions: 0 Unit cell: (165.6, 211.14, 121.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 132 16.00 P 138 15.00 O 6867 8.00 N 6243 7.00 C 22213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 40 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " 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 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " 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 43 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 40 " 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 43 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 40 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 40 " 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 43 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 40 " 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 43 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 40 " 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 43 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 40 " Number of angles added : 23 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7538 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 54 sheets defined 51.6% alpha, 15.3% beta 62 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 3.84 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 removed outlier: 3.502A pdb=" N GLN A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.505A pdb=" N ASN A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.936A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.756A 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 210 through 216 removed outlier: 3.820A pdb=" N SER A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.556A pdb=" N ARG B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 101 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 removed outlier: 3.784A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.546A pdb=" N THR B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 216 removed outlier: 3.685A pdb=" N ARG B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 211 " --> pdb=" O GLN B 207 " (cutoff:3.500A) 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 40 Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 168 removed outlier: 3.556A pdb=" N ARG C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 removed outlier: 3.602A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.715A pdb=" N ILE C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 201 " --> pdb=" O PRO C 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.516A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.666A pdb=" N LYS D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.935A pdb=" N ASP D 35 " --> pdb=" O THR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 removed outlier: 3.501A pdb=" N PHE D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.556A pdb=" N LEU D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 188 Processing helix chain 'D' and resid 196 through 220 removed outlier: 4.080A pdb=" N LYS D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS D 217 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 4.271A 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 45 Processing helix chain 'E' and resid 95 through 110 removed outlier: 3.505A pdb=" N PHE E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.607A pdb=" N LEU E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 168 removed outlier: 3.811A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 187 removed outlier: 3.752A pdb=" N THR E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR E 184 " --> pdb=" O GLY E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 216 removed outlier: 3.946A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) 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: 3.529A pdb=" N ASN F 46 " --> pdb=" O VAL F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 110 removed outlier: 3.558A pdb=" N VAL F 101 " --> pdb=" O GLN F 97 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE F 110 " --> pdb=" O TRP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 135 removed outlier: 3.712A pdb=" N LEU F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.987A pdb=" N ARG F 155 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 188 removed outlier: 3.720A pdb=" N GLY F 180 " --> pdb=" O SER F 176 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE F 183 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASN F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 218 removed outlier: 3.731A pdb=" N GLN F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE F 210 " --> pdb=" O GLU F 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS F 217 " --> pdb=" O GLN F 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 removed outlier: 3.508A pdb=" N ASN G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 removed outlier: 3.795A pdb=" N MET G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 136 removed outlier: 4.366A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 168 removed outlier: 4.165A pdb=" N VAL G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU G 154 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS G 157 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS G 166 " --> pdb=" O ASN G 162 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 167 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 187 removed outlier: 3.561A pdb=" N ILE G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR G 184 " --> pdb=" O GLY G 180 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 215 removed outlier: 3.880A pdb=" N GLN G 207 " --> pdb=" O PHE G 203 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN G 208 " --> pdb=" O ASN G 204 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN G 212 " --> pdb=" O GLN G 208 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN G 213 " --> pdb=" O ARG G 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 110 removed outlier: 4.363A 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: 3.810A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 189 removed outlier: 3.755A pdb=" N THR H 184 " --> pdb=" O GLY H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 207 Processing helix chain 'H' and resid 208 through 215 removed outlier: 6.246A pdb=" N GLN H 211 " --> pdb=" O GLN H 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS H 215 " --> pdb=" O GLN H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'R' and resid 349 through 363 Processing helix chain 'R' and resid 369 through 383 removed outlier: 3.707A pdb=" N CYS R 373 " --> pdb=" O ASP R 369 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP R 378 " --> pdb=" O ILE R 374 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 383 " --> pdb=" O GLU R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 386 through 392 removed outlier: 3.542A pdb=" N ALA R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 404 removed outlier: 4.004A pdb=" N LYS R 402 " --> pdb=" O THR R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 409 through 429 removed outlier: 3.857A pdb=" N MET R 413 " --> pdb=" O SER R 409 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 363 Processing helix chain 'Q' and resid 369 through 383 removed outlier: 3.542A pdb=" N LEU Q 383 " --> pdb=" O GLU Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 392 Processing helix chain 'Q' and resid 394 through 404 removed outlier: 3.635A pdb=" N LYS Q 402 " --> pdb=" O THR Q 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 428 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 removed outlier: 3.503A pdb=" N GLN I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 46 removed outlier: 3.505A pdb=" N ASN I 46 " --> pdb=" O VAL I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 126 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 removed outlier: 3.937A pdb=" N GLN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS I 166 " --> pdb=" O ASN I 162 " (cutoff:3.500A) removed outlier: 3.756A 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 210 through 216 removed outlier: 3.819A pdb=" N SER I 216 " --> pdb=" O GLN I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 95 through 110 removed outlier: 3.557A pdb=" N ARG J 100 " --> pdb=" O GLY J 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL J 101 " --> pdb=" O GLN J 97 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET J 109 " --> pdb=" O LYS J 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE J 110 " --> pdb=" O TRP J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 removed outlier: 3.783A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS J 166 " --> pdb=" O ASN J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 187 removed outlier: 3.545A pdb=" N THR J 184 " --> pdb=" O GLY J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 216 removed outlier: 3.685A pdb=" N ARG J 209 " --> pdb=" O LYS J 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE J 210 " --> pdb=" O GLU J 206 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN J 211 " --> pdb=" O GLN J 207 " (cutoff:3.500A) 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 40 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 168 removed outlier: 3.556A pdb=" N ARG K 155 " --> pdb=" O ALA K 151 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS K 166 " --> pdb=" O ASN K 162 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU K 167 " --> pdb=" O THR K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 removed outlier: 3.603A pdb=" N LEU K 182 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 187 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 211 removed outlier: 3.715A pdb=" N ILE K 200 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 201 " --> pdb=" O PRO K 197 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU K 206 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 207 " --> pdb=" O PHE K 203 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN K 211 " --> pdb=" O GLN K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 219 removed outlier: 4.516A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.667A pdb=" N LYS L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 26 Processing helix chain 'L' and resid 29 through 35 removed outlier: 3.936A pdb=" N ASP L 35 " --> pdb=" O THR L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 removed outlier: 3.500A pdb=" N PHE L 99 " --> pdb=" O THR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 135 removed outlier: 3.555A pdb=" N LEU L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 188 Processing helix chain 'L' and resid 196 through 220 removed outlier: 4.081A pdb=" N LYS L 215 " --> pdb=" O GLN L 211 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER L 216 " --> pdb=" O GLN L 212 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS L 217 " --> pdb=" O GLN L 213 " (cutoff:3.500A) removed outlier: 4.271A 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 45 Processing helix chain 'M' and resid 95 through 110 removed outlier: 3.505A pdb=" N PHE M 99 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG M 100 " --> pdb=" O GLY M 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET M 104 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS M 105 " --> pdb=" O VAL M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 136 removed outlier: 3.606A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS M 133 " --> pdb=" O GLN M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 168 removed outlier: 3.810A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 187 removed outlier: 3.751A pdb=" N THR M 181 " --> pdb=" O ALA M 177 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 183 " --> pdb=" O ALA M 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR M 184 " --> pdb=" O GLY M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 216 removed outlier: 3.946A pdb=" N GLN M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN M 212 " --> pdb=" O GLN M 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) 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: 3.528A pdb=" N ASN N 46 " --> pdb=" O VAL N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 110 removed outlier: 3.557A pdb=" N VAL N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE N 110 " --> pdb=" O TRP N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 125 through 135 removed outlier: 3.713A pdb=" N LEU N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 165 removed outlier: 3.986A pdb=" N ARG N 155 " --> pdb=" O ALA N 151 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS N 157 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU N 165 " --> pdb=" O LYS N 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 188 removed outlier: 3.719A pdb=" N GLY N 180 " --> pdb=" O SER N 176 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR N 181 " --> pdb=" O ALA N 177 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR N 184 " --> pdb=" O GLY N 180 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN N 186 " --> pdb=" O LEU N 182 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS N 188 " --> pdb=" O THR N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 196 through 218 removed outlier: 3.731A pdb=" N GLN N 208 " --> pdb=" O ASN N 204 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG N 209 " --> pdb=" O LYS N 205 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE N 210 " --> pdb=" O GLU N 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS N 215 " --> pdb=" O GLN N 211 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER N 216 " --> pdb=" O GLN N 212 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS N 217 " --> pdb=" O GLN N 213 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 removed outlier: 3.509A pdb=" N ASN O 46 " --> pdb=" O VAL O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 110 removed outlier: 3.794A pdb=" N MET O 104 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 136 removed outlier: 4.366A pdb=" N TYR O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 168 removed outlier: 4.165A pdb=" N VAL O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU O 154 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG O 155 " --> pdb=" O ALA O 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS O 157 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN O 158 " --> pdb=" O GLU O 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS O 166 " --> pdb=" O ASN O 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU O 167 " --> pdb=" O THR O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 187 removed outlier: 3.561A pdb=" N ILE O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR O 184 " --> pdb=" O GLY O 180 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU O 185 " --> pdb=" O THR O 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 215 removed outlier: 3.881A pdb=" N GLN O 207 " --> pdb=" O PHE O 203 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN O 212 " --> pdb=" O GLN O 208 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN O 213 " --> pdb=" O ARG O 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 110 removed outlier: 4.362A 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: 3.809A pdb=" N GLU P 165 " --> pdb=" O LYS P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 189 removed outlier: 3.754A pdb=" N THR P 184 " --> pdb=" O GLY P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 207 Processing helix chain 'P' and resid 208 through 215 removed outlier: 6.245A pdb=" N GLN P 211 " --> pdb=" O GLN P 208 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS P 215 " --> pdb=" O GLN P 212 " (cutoff:3.500A) 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 63 through 69 Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 117 removed outlier: 6.390A pdb=" N LEU A 115 " --> pdb=" O THR A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA4, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.895A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.566A pdb=" N TRP B 63 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 115 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 91 removed outlier: 3.690A pdb=" N GLU C 89 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE C 75 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 68 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 63 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 115 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 242 removed outlier: 6.005A pdb=" N CYS C 224 " --> pdb=" O PRO C 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.966A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 252 " --> pdb=" O TRP C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.887A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 86 through 87 removed outlier: 5.875A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 117 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 242 removed outlier: 5.507A pdb=" N GLY D 239 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N TYR D 226 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 241 " --> pdb=" O CYS D 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.556A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.743A pdb=" N GLU E 89 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 76 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 74 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 77 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 117 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 233 through 241 removed outlier: 6.278A pdb=" N GLY E 235 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 230 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP E 237 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR E 228 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY E 239 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR E 226 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 245 through 246 removed outlier: 3.615A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE E 264 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 63 through 69 removed outlier: 3.694A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 89 " --> pdb=" O LEU F 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.867A pdb=" N LEU F 115 " --> pdb=" O THR F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 238 through 242 removed outlier: 6.575A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC3, first strand: chain 'F' and resid 250 through 254 Processing sheet with id=AC4, first strand: chain 'G' and resid 86 through 87 removed outlier: 4.267A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 86 through 87 removed outlier: 3.627A pdb=" N ILE G 75 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 79 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP G 63 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR G 140 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 117 " --> pdb=" O THR G 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 86 through 91 removed outlier: 4.104A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU H 115 " --> pdb=" O THR H 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 223 through 224 Processing sheet with id=AC8, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AC9, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.811A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 63 through 69 Processing sheet with id=AD2, first strand: chain 'I' and resid 114 through 117 removed outlier: 6.390A pdb=" N LEU I 115 " --> pdb=" O THR I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 240 through 242 Processing sheet with id=AD4, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD5, first strand: chain 'I' and resid 245 through 246 removed outlier: 3.896A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 86 through 90 removed outlier: 3.567A pdb=" N TRP J 63 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU J 115 " --> pdb=" O THR J 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 86 through 91 removed outlier: 3.689A pdb=" N GLU K 89 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE K 75 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR K 68 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP K 63 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 115 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 238 through 242 removed outlier: 6.005A pdb=" N CYS K 224 " --> pdb=" O PRO K 240 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.966A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL K 252 " --> pdb=" O TRP K 245 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.887A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 86 through 87 removed outlier: 5.874A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER L 117 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 238 through 242 removed outlier: 5.507A pdb=" N GLY L 239 " --> pdb=" O TYR L 226 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR L 226 " --> pdb=" O GLY L 239 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 241 " --> pdb=" O CYS L 224 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 245 through 246 removed outlier: 3.556A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.744A pdb=" N GLU M 89 " --> pdb=" O LEU M 76 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU M 76 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE M 74 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 77 " --> pdb=" O ASP M 66 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 117 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 233 through 241 removed outlier: 6.277A pdb=" N GLY M 235 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS M 230 " --> pdb=" O GLY M 235 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP M 237 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR M 228 " --> pdb=" O TRP M 237 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY M 239 " --> pdb=" O TYR M 226 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR M 226 " --> pdb=" O GLY M 239 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 245 through 246 removed outlier: 3.616A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE M 264 " --> pdb=" O ILE M 251 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 63 through 69 removed outlier: 3.694A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU N 89 " --> pdb=" O LEU N 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 114 through 117 removed outlier: 6.866A pdb=" N LEU N 115 " --> pdb=" O THR N 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'N' and resid 238 through 242 removed outlier: 6.576A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AF3, first strand: chain 'N' and resid 250 through 254 Processing sheet with id=AF4, first strand: chain 'O' and resid 86 through 87 removed outlier: 4.266A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 86 through 87 removed outlier: 3.627A pdb=" N ILE O 75 " --> pdb=" O THR O 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL O 79 " --> pdb=" O GLN O 64 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TRP O 63 " --> pdb=" O GLN O 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR O 140 " --> pdb=" O LEU O 115 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER O 117 " --> pdb=" O THR O 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 86 through 91 removed outlier: 4.104A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU P 115 " --> pdb=" O THR P 140 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 223 through 224 Processing sheet with id=AF8, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AF9, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.810A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) 1552 hydrogen bonds defined for protein. 4542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 150 hydrogen bonds 300 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 3.67 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: 10707 1.34 - 1.46: 6374 1.46 - 1.57: 19126 1.57 - 1.69: 272 1.69 - 1.81: 226 Bond restraints: 36705 Sorted by residual: bond pdb=" C3' DC Y 17 " pdb=" C2' DC Y 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC Z 28 " pdb=" C2' DC Z 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC X 17 " pdb=" C2' DC X 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC W 28 " pdb=" C2' DC W 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC X 14 " pdb=" C2' DC X 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 36700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 48772 1.39 - 2.77: 1211 2.77 - 4.16: 188 4.16 - 5.54: 43 5.54 - 6.93: 34 Bond angle restraints: 50248 Sorted by residual: angle pdb=" N3 DT W 34 " pdb=" C4 DT W 34 " pdb=" O4 DT W 34 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT a 9 " pdb=" C4 DT a 9 " pdb=" O4 DT a 9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT U 10 " pdb=" C4 DT U 10 " pdb=" O4 DT U 10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT Y 15 " pdb=" C4 DT Y 15 " pdb=" O4 DT Y 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 50243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 20355 27.60 - 55.20: 1066 55.20 - 82.79: 117 82.79 - 110.39: 12 110.39 - 137.99: 2 Dihedral angle restraints: 21552 sinusoidal: 9895 harmonic: 11657 Sorted by residual: dihedral pdb=" C4' DG W 20 " pdb=" C3' DG W 20 " pdb=" O3' DG W 20 " pdb=" P DT W 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DG Z 20 " pdb=" C3' DG Z 20 " pdb=" O3' DG Z 20 " pdb=" P DT Z 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.02 137.98 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU H 219 " pdb=" C GLU H 219 " pdb=" N LYS H 220 " pdb=" CA LYS H 220 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3605 0.034 - 0.069: 1198 0.069 - 0.103: 469 0.103 - 0.137: 146 0.137 - 0.172: 14 Chirality restraints: 5432 Sorted by residual: chirality pdb=" CA VAL H 79 " pdb=" N VAL H 79 " pdb=" C VAL H 79 " pdb=" CB VAL H 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA VAL P 79 " pdb=" N VAL P 79 " pdb=" C VAL P 79 " pdb=" CB VAL P 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA GLN D 218 " pdb=" N GLN D 218 " pdb=" C GLN D 218 " pdb=" CB GLN D 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 5429 not shown) Planarity restraints: 5969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 273 " -0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO I 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 273 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 273 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.046 5.00e-02 4.00e+02 ... (remaining 5966 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5048 2.76 - 3.29: 34919 3.29 - 3.83: 59506 3.83 - 4.36: 67800 4.36 - 4.90: 111512 Nonbonded interactions: 278785 Sorted by model distance: nonbonded pdb=" OG1 THR M 95 " pdb=" OE1 GLU M 98 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR E 95 " pdb=" OE1 GLU E 98 " model vdw 2.225 3.040 nonbonded pdb=" O ASP L 61 " pdb=" OG SER L 114 " model vdw 2.225 3.040 nonbonded pdb=" O ASP D 61 " pdb=" OG SER D 114 " model vdw 2.226 3.040 nonbonded pdb=" O ASP C 18 " pdb=" OG SER C 21 " model vdw 2.227 3.040 ... (remaining 278780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'C' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'D' and resid 4 through 272) selection = (chain 'E' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'F' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'I' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'K' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'L' and resid 4 through 272) selection = (chain 'M' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'N' and (resid 4 through 36 or resid 61 through 272)) } ncs_group { reference = (chain 'B' and (resid 2 through 215 or resid 301)) selection = (chain 'G' and resid 2 through 301) selection = (chain 'J' and (resid 2 through 215 or resid 301)) selection = (chain 'O' and resid 2 through 301) } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 348 through 428) } ncs_group { reference = chain 'U' selection = chain 'a' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 36.480 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 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 : 0.003 0.263 36753 Z= 0.237 Angle : 1.184 75.246 50271 Z= 0.405 Chirality : 0.042 0.172 5432 Planarity : 0.004 0.097 5969 Dihedral : 15.201 137.992 14014 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 3971 helix: 1.14 (0.12), residues: 1808 sheet: 0.22 (0.21), residues: 694 loop : -1.02 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 155 TYR 0.014 0.001 TYR M 225 PHE 0.020 0.001 PHE N 203 TRP 0.017 0.001 TRP C 245 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.23 (36705) covalent geometry : angle 0.54245 / 0.35 (50248) hydrogen bonds : bond 0.21904 / 14.64 ( 1694) hydrogen bonds : angle 7.66322 / 5.51 ( 4842) metal coordination : bond 0.05432 / 3.63 ( 48) metal coordination : angle 49.21018 / 35.23 ( 23) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 929 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6596 (mm-30) REVERT: A 35 ASP cc_start: 0.7200 (t70) cc_final: 0.6947 (t0) REVERT: A 57 LYS cc_start: 0.7255 (tttm) cc_final: 0.7036 (ttmm) REVERT: A 76 LEU cc_start: 0.7704 (tp) cc_final: 0.7502 (tp) REVERT: A 98 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 118 ASP cc_start: 0.7437 (p0) cc_final: 0.7225 (p0) REVERT: A 162 ASN cc_start: 0.8250 (t0) cc_final: 0.7718 (t0) REVERT: A 165 GLU cc_start: 0.7374 (tp30) cc_final: 0.7154 (tp30) REVERT: A 199 ASP cc_start: 0.6741 (t0) cc_final: 0.6433 (t0) REVERT: A 255 ASP cc_start: 0.5707 (t0) cc_final: 0.5411 (t0) REVERT: A 262 LEU cc_start: 0.6868 (mm) cc_final: 0.6650 (mt) REVERT: B 89 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6116 (mt-10) REVERT: B 97 GLN cc_start: 0.7627 (tp40) cc_final: 0.7247 (tp40) REVERT: B 124 VAL cc_start: 0.7406 (t) cc_final: 0.7200 (p) REVERT: B 129 GLN cc_start: 0.7735 (tt0) cc_final: 0.7365 (mt0) REVERT: B 140 THR cc_start: 0.8113 (m) cc_final: 0.7818 (t) REVERT: B 190 LYS cc_start: 0.8676 (mttp) cc_final: 0.8471 (mttm) REVERT: C 9 GLU cc_start: 0.7588 (tp30) cc_final: 0.7107 (tp30) REVERT: C 24 LEU cc_start: 0.7872 (mm) cc_final: 0.7517 (mp) REVERT: C 105 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7361 (ttpp) REVERT: C 186 ASN cc_start: 0.7990 (m-40) cc_final: 0.7616 (t0) REVERT: C 203 PHE cc_start: 0.7336 (t80) cc_final: 0.7006 (t80) REVERT: C 204 ASN cc_start: 0.8471 (m-40) cc_final: 0.8162 (m110) REVERT: C 208 GLN cc_start: 0.7119 (tt0) cc_final: 0.6382 (tp40) REVERT: C 238 GLN cc_start: 0.6901 (mt0) cc_final: 0.6698 (mt0) REVERT: C 245 TRP cc_start: 0.7866 (m-90) cc_final: 0.7525 (m-90) REVERT: C 254 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7568 (ttmm) REVERT: D 70 TYR cc_start: 0.6979 (t80) cc_final: 0.6313 (t80) REVERT: D 103 THR cc_start: 0.6824 (t) cc_final: 0.6274 (p) REVERT: D 104 MET cc_start: 0.6727 (mmp) cc_final: 0.5872 (mmp) REVERT: D 167 LEU cc_start: 0.8632 (tt) cc_final: 0.8344 (tt) REVERT: D 236 GLU cc_start: 0.7259 (mp0) cc_final: 0.6759 (mp0) REVERT: D 238 GLN cc_start: 0.8824 (mt0) cc_final: 0.8402 (mt0) REVERT: D 268 ASP cc_start: 0.7322 (p0) cc_final: 0.6545 (p0) REVERT: E 38 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7790 (mm-40) REVERT: E 61 ASP cc_start: 0.7859 (t70) cc_final: 0.7028 (t0) REVERT: E 80 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7535 (tm-30) REVERT: E 99 PHE cc_start: 0.7884 (m-80) cc_final: 0.6989 (m-80) REVERT: E 103 THR cc_start: 0.8484 (t) cc_final: 0.8186 (p) REVERT: E 131 LEU cc_start: 0.8968 (mt) cc_final: 0.8465 (mt) REVERT: E 153 VAL cc_start: 0.8851 (t) cc_final: 0.8012 (p) REVERT: E 155 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7174 (mtt180) REVERT: E 157 HIS cc_start: 0.8442 (m90) cc_final: 0.8036 (m-70) REVERT: E 158 GLN cc_start: 0.8066 (pt0) cc_final: 0.7852 (pt0) REVERT: E 163 THR cc_start: 0.8088 (p) cc_final: 0.7736 (p) REVERT: E 181 THR cc_start: 0.8499 (p) cc_final: 0.8169 (p) REVERT: E 202 ILE cc_start: 0.7675 (tp) cc_final: 0.7439 (tp) REVERT: E 211 GLN cc_start: 0.8042 (pm20) cc_final: 0.7408 (pp30) REVERT: E 224 CYS cc_start: 0.7782 (t) cc_final: 0.7402 (p) REVERT: E 271 PHE cc_start: 0.7705 (m-80) cc_final: 0.6859 (m-80) REVERT: F 62 HIS cc_start: 0.7415 (m170) cc_final: 0.6815 (m170) REVERT: F 77 VAL cc_start: 0.8537 (t) cc_final: 0.8193 (m) REVERT: F 103 THR cc_start: 0.7745 (t) cc_final: 0.7501 (p) REVERT: F 113 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7020 (mmtm) REVERT: F 157 HIS cc_start: 0.8966 (m90) cc_final: 0.8751 (m90) REVERT: F 160 LEU cc_start: 0.8968 (tp) cc_final: 0.8557 (tp) REVERT: F 176 SER cc_start: 0.7907 (m) cc_final: 0.7664 (p) REVERT: F 210 ILE cc_start: 0.8151 (mm) cc_final: 0.7861 (mm) REVERT: F 267 LYS cc_start: 0.8281 (pttp) cc_final: 0.8063 (pttm) REVERT: G 63 TRP cc_start: 0.6040 (t-100) cc_final: 0.5805 (m100) REVERT: G 110 PHE cc_start: 0.7599 (m-80) cc_final: 0.7223 (m-80) REVERT: G 150 GLN cc_start: 0.7687 (mm110) cc_final: 0.7334 (mm110) REVERT: G 157 HIS cc_start: 0.8536 (m90) cc_final: 0.8329 (m90) REVERT: G 186 ASN cc_start: 0.6861 (m-40) cc_final: 0.6525 (m110) REVERT: H 85 LEU cc_start: 0.7810 (tp) cc_final: 0.7489 (tp) REVERT: H 87 TYR cc_start: 0.7624 (t80) cc_final: 0.7396 (t80) REVERT: H 104 MET cc_start: 0.8590 (mpp) cc_final: 0.8301 (mpp) REVERT: H 132 MET cc_start: 0.7736 (tpt) cc_final: 0.7154 (tpt) REVERT: H 161 LYS cc_start: 0.8471 (mttt) cc_final: 0.7970 (ptpp) REVERT: H 164 LEU cc_start: 0.8159 (mt) cc_final: 0.7889 (tp) REVERT: H 184 THR cc_start: 0.8248 (m) cc_final: 0.7967 (p) REVERT: H 186 ASN cc_start: 0.8157 (m-40) cc_final: 0.7898 (p0) REVERT: H 198 MET cc_start: 0.8118 (mpp) cc_final: 0.7862 (mpp) REVERT: H 201 PHE cc_start: 0.8356 (t80) cc_final: 0.7947 (t80) REVERT: H 205 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8202 (mmmm) REVERT: H 210 ILE cc_start: 0.7840 (mm) cc_final: 0.7625 (tp) REVERT: R 367 ASN cc_start: 0.6514 (t0) cc_final: 0.6120 (t0) REVERT: R 413 MET cc_start: 0.6828 (mmm) cc_final: 0.6517 (mmm) REVERT: R 418 MET cc_start: 0.7396 (ppp) cc_final: 0.6946 (ppp) REVERT: Q 360 LYS cc_start: 0.5100 (ptpp) cc_final: 0.4809 (ptpp) REVERT: Q 387 MET cc_start: 0.7417 (tpp) cc_final: 0.6993 (mmm) REVERT: Q 418 MET cc_start: 0.7470 (ppp) cc_final: 0.7012 (ppp) REVERT: I 72 ASP cc_start: 0.7317 (t70) cc_final: 0.7110 (t70) REVERT: I 92 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7771 (mtpp) REVERT: I 95 THR cc_start: 0.8312 (p) cc_final: 0.8102 (t) REVERT: I 98 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6629 (mm-30) REVERT: I 162 ASN cc_start: 0.7896 (t0) cc_final: 0.7574 (t0) REVERT: I 238 GLN cc_start: 0.6839 (tm-30) cc_final: 0.6560 (tm-30) REVERT: I 254 LYS cc_start: 0.7525 (tptp) cc_final: 0.7283 (tptp) REVERT: J 92 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7717 (mtpp) REVERT: J 129 GLN cc_start: 0.7665 (tt0) cc_final: 0.7170 (mt0) REVERT: J 206 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7202 (tp30) REVERT: K 26 PHE cc_start: 0.6774 (m-80) cc_final: 0.6510 (m-80) REVERT: K 170 MET cc_start: 0.4922 (tmm) cc_final: 0.2986 (pmm) REVERT: K 222 ARG cc_start: 0.6460 (mtm110) cc_final: 0.5822 (ptp90) REVERT: L 104 MET cc_start: 0.5615 (mmp) cc_final: 0.5201 (mmp) REVERT: L 248 ASP cc_start: 0.6931 (p0) cc_final: 0.6631 (p0) REVERT: L 260 ARG cc_start: 0.6791 (mmm-85) cc_final: 0.6314 (mmm-85) REVERT: L 268 ASP cc_start: 0.7177 (p0) cc_final: 0.6925 (p0) REVERT: M 17 GLN cc_start: 0.6100 (mp-120) cc_final: 0.5863 (mp10) REVERT: M 35 ASP cc_start: 0.6469 (m-30) cc_final: 0.6125 (m-30) REVERT: M 61 ASP cc_start: 0.7561 (t70) cc_final: 0.6286 (t0) REVERT: M 62 HIS cc_start: 0.6465 (t70) cc_final: 0.5174 (t70) REVERT: M 99 PHE cc_start: 0.8074 (m-80) cc_final: 0.7118 (m-80) REVERT: M 101 VAL cc_start: 0.8568 (t) cc_final: 0.8171 (t) REVERT: M 155 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7522 (mtt180) REVERT: M 161 LYS cc_start: 0.8641 (mttt) cc_final: 0.8006 (mttt) REVERT: M 164 LEU cc_start: 0.8355 (mt) cc_final: 0.7522 (pp) REVERT: M 165 GLU cc_start: 0.7734 (mp0) cc_final: 0.7533 (mp0) REVERT: M 205 LYS cc_start: 0.7638 (tptt) cc_final: 0.7393 (tptt) REVERT: M 224 CYS cc_start: 0.7312 (t) cc_final: 0.6950 (t) REVERT: N 61 ASP cc_start: 0.5695 (t70) cc_final: 0.5437 (t70) REVERT: N 113 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7418 (mmtm) REVERT: N 157 HIS cc_start: 0.8721 (m90) cc_final: 0.8470 (m90) REVERT: N 176 SER cc_start: 0.7092 (m) cc_final: 0.6824 (p) REVERT: N 200 ILE cc_start: 0.7107 (mm) cc_final: 0.6884 (pt) REVERT: N 243 VAL cc_start: 0.8273 (t) cc_final: 0.7742 (m) REVERT: N 260 ARG cc_start: 0.6850 (mtm-85) cc_final: 0.6412 (mtm-85) REVERT: O 11 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8168 (mm-30) REVERT: O 104 MET cc_start: 0.7202 (mmp) cc_final: 0.6306 (mmp) REVERT: O 132 MET cc_start: 0.8071 (mpp) cc_final: 0.7825 (mpp) REVERT: O 155 ARG cc_start: 0.8687 (pmt170) cc_final: 0.8078 (tpt170) REVERT: O 201 PHE cc_start: 0.8538 (t80) cc_final: 0.7885 (t80) REVERT: O 205 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7931 (mttp) REVERT: O 208 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7462 (tm-30) REVERT: P 63 TRP cc_start: 0.6884 (m100) cc_final: 0.5748 (m100) REVERT: P 85 LEU cc_start: 0.6607 (tp) cc_final: 0.6083 (tp) REVERT: P 104 MET cc_start: 0.8189 (mpp) cc_final: 0.7697 (mpp) REVERT: P 132 MET cc_start: 0.7973 (tpt) cc_final: 0.7337 (tpt) REVERT: P 187 ILE cc_start: 0.8874 (mt) cc_final: 0.8571 (mt) REVERT: P 198 MET cc_start: 0.8087 (mpp) cc_final: 0.7877 (pmm) REVERT: P 201 PHE cc_start: 0.8450 (t80) cc_final: 0.7478 (t80) REVERT: P 202 ILE cc_start: 0.8811 (pt) cc_final: 0.8599 (pt) REVERT: P 205 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7397 (mmmm) REVERT: P 261 TYR cc_start: 0.7091 (m-80) cc_final: 0.6767 (m-80) outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.2144 time to fit residues: 316.9881 Evaluate side-chains 833 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 833 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.0870 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN B 13 ASN B 82 ASN C 39 GLN C 233 HIS ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 62 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 148 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 212 GLN H 162 ASN H 266 ASN I 4 ASN I 17 GLN I 38 GLN ** I 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN K 233 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 139 HIS M 157 HIS M 204 ASN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN O 82 ASN O 212 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.246957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.191551 restraints weight = 64682.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.197206 restraints weight = 30303.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.198978 restraints weight = 18698.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.200439 restraints weight = 14816.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.201392 restraints weight = 12300.732| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 36753 Z= 0.173 Angle : 0.718 21.838 50271 Z= 0.368 Chirality : 0.047 0.267 5432 Planarity : 0.005 0.072 5969 Dihedral : 16.209 141.332 5791 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.47 % Allowed : 9.27 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 3971 helix: 1.21 (0.12), residues: 1866 sheet: 0.24 (0.20), residues: 720 loop : -1.17 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 30 TYR 0.020 0.002 TYR N 134 PHE 0.021 0.001 PHE E 203 TRP 0.037 0.001 TRP P 245 HIS 0.027 0.002 HIS K 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (36705) covalent geometry : angle 0.66973 / 0.36 (50248) hydrogen bonds : bond 0.06487 / 4.31 ( 1694) hydrogen bonds : angle 5.37771 / 3.85 ( 4842) metal coordination : bond 0.05800 / 4.48 ( 48) metal coordination : angle 12.06854 / 8.60 ( 23) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 871 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.6000 (tp30) REVERT: A 76 LEU cc_start: 0.8183 (tp) cc_final: 0.7974 (tp) REVERT: A 98 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 162 ASN cc_start: 0.8167 (t0) cc_final: 0.7723 (t0) REVERT: A 199 ASP cc_start: 0.6877 (t0) cc_final: 0.6583 (t0) REVERT: A 206 GLU cc_start: 0.6706 (tp30) cc_final: 0.6316 (tm-30) REVERT: A 223 PHE cc_start: 0.8155 (m-80) cc_final: 0.7517 (m-80) REVERT: A 238 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 129 GLN cc_start: 0.7379 (tt0) cc_final: 0.7171 (mt0) REVERT: B 140 THR cc_start: 0.8047 (m) cc_final: 0.7782 (t) REVERT: B 206 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6962 (tp30) REVERT: B 208 GLN cc_start: 0.7505 (tt0) cc_final: 0.7198 (tt0) REVERT: C 9 GLU cc_start: 0.7769 (tp30) cc_final: 0.7501 (tp30) REVERT: C 24 LEU cc_start: 0.8200 (mm) cc_final: 0.7744 (mp) REVERT: C 186 ASN cc_start: 0.8206 (m-40) cc_final: 0.7901 (t0) REVERT: C 198 MET cc_start: 0.6964 (pmm) cc_final: 0.6311 (pmm) REVERT: C 203 PHE cc_start: 0.7051 (t80) cc_final: 0.6691 (t80) REVERT: C 204 ASN cc_start: 0.8135 (m-40) cc_final: 0.7919 (m110) REVERT: C 205 LYS cc_start: 0.8420 (mmmt) cc_final: 0.7906 (mmmt) REVERT: C 245 TRP cc_start: 0.7651 (m-90) cc_final: 0.7299 (m-90) REVERT: C 267 LYS cc_start: 0.8242 (pttp) cc_final: 0.7875 (pttp) REVERT: D 70 TYR cc_start: 0.6730 (t80) cc_final: 0.6496 (t80) REVERT: D 103 THR cc_start: 0.6656 (t) cc_final: 0.6006 (p) REVERT: D 104 MET cc_start: 0.6739 (mmp) cc_final: 0.5769 (mmp) REVERT: D 205 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7395 (tppt) REVERT: D 212 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6660 (tm-30) REVERT: D 236 GLU cc_start: 0.6927 (mp0) cc_final: 0.6619 (mp0) REVERT: D 238 GLN cc_start: 0.8442 (mt0) cc_final: 0.8168 (mt0) REVERT: D 268 ASP cc_start: 0.7024 (p0) cc_final: 0.6422 (p0) REVERT: E 99 PHE cc_start: 0.7245 (m-80) cc_final: 0.6763 (m-80) REVERT: E 153 VAL cc_start: 0.8771 (t) cc_final: 0.7604 (p) REVERT: E 158 GLN cc_start: 0.7878 (pt0) cc_final: 0.7446 (pt0) REVERT: E 163 THR cc_start: 0.7566 (p) cc_final: 0.7113 (p) REVERT: E 181 THR cc_start: 0.8308 (p) cc_final: 0.7815 (t) REVERT: E 202 ILE cc_start: 0.7990 (tp) cc_final: 0.7758 (tp) REVERT: E 225 TYR cc_start: 0.5067 (t80) cc_final: 0.4361 (t80) REVERT: E 270 LYS cc_start: 0.7044 (mtpt) cc_final: 0.6568 (mtpt) REVERT: E 271 PHE cc_start: 0.7187 (m-80) cc_final: 0.6632 (m-80) REVERT: F 62 HIS cc_start: 0.6808 (m170) cc_final: 0.6360 (m170) REVERT: F 213 GLN cc_start: 0.7798 (pp30) cc_final: 0.7531 (pp30) REVERT: F 230 LYS cc_start: 0.8224 (tppp) cc_final: 0.7829 (tppp) REVERT: F 254 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7640 (tmtt) REVERT: G 110 PHE cc_start: 0.7350 (m-80) cc_final: 0.7047 (m-80) REVERT: G 155 ARG cc_start: 0.8047 (pmt170) cc_final: 0.7678 (tpt170) REVERT: G 198 MET cc_start: 0.8120 (tpt) cc_final: 0.7812 (tpt) REVERT: G 211 GLN cc_start: 0.6130 (mm-40) cc_final: 0.5925 (tp40) REVERT: H 132 MET cc_start: 0.7513 (tpt) cc_final: 0.6948 (tpt) REVERT: H 166 LYS cc_start: 0.7467 (tptp) cc_final: 0.7264 (tptp) REVERT: H 198 MET cc_start: 0.7632 (mpp) cc_final: 0.7328 (mpp) REVERT: H 201 PHE cc_start: 0.8001 (t80) cc_final: 0.7609 (t80) REVERT: H 205 LYS cc_start: 0.8256 (mmmm) cc_final: 0.7776 (mmmm) REVERT: H 262 LEU cc_start: 0.6725 (mm) cc_final: 0.6491 (mm) REVERT: R 413 MET cc_start: 0.6484 (mmm) cc_final: 0.6107 (mmm) REVERT: R 418 MET cc_start: 0.7352 (ppp) cc_final: 0.6792 (ppp) REVERT: Q 360 LYS cc_start: 0.5524 (ptpp) cc_final: 0.5287 (ptpp) REVERT: Q 387 MET cc_start: 0.7294 (tpp) cc_final: 0.7035 (mmm) REVERT: Q 418 MET cc_start: 0.7431 (ppp) cc_final: 0.6849 (ppp) REVERT: I 72 ASP cc_start: 0.7082 (t70) cc_final: 0.6800 (t70) REVERT: I 98 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6628 (mm-30) REVERT: J 129 GLN cc_start: 0.7563 (tt0) cc_final: 0.7082 (mt0) REVERT: J 206 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7474 (tp30) REVERT: J 211 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6749 (tm-30) REVERT: K 109 MET cc_start: 0.7628 (tpp) cc_final: 0.7299 (pmm) REVERT: L 104 MET cc_start: 0.5323 (mmp) cc_final: 0.4905 (mmp) REVERT: L 110 PHE cc_start: 0.7089 (m-80) cc_final: 0.6662 (t80) REVERT: L 221 ILE cc_start: 0.6950 (mt) cc_final: 0.6642 (tt) REVERT: L 260 ARG cc_start: 0.6709 (mmm-85) cc_final: 0.6365 (mmm-85) REVERT: L 268 ASP cc_start: 0.7115 (p0) cc_final: 0.6761 (p0) REVERT: M 35 ASP cc_start: 0.6498 (m-30) cc_final: 0.6065 (m-30) REVERT: M 38 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7204 (tm-30) REVERT: M 61 ASP cc_start: 0.7150 (t70) cc_final: 0.6527 (t0) REVERT: M 62 HIS cc_start: 0.6215 (t70) cc_final: 0.6007 (t70) REVERT: M 99 PHE cc_start: 0.7552 (m-80) cc_final: 0.6942 (m-80) REVERT: M 157 HIS cc_start: 0.8161 (m170) cc_final: 0.7936 (m-70) REVERT: M 161 LYS cc_start: 0.8691 (mttt) cc_final: 0.8352 (mttt) REVERT: M 207 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7520 (mm-40) REVERT: M 208 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6992 (tm-30) REVERT: M 259 ASP cc_start: 0.7454 (t0) cc_final: 0.7254 (t0) REVERT: M 271 PHE cc_start: 0.6774 (m-80) cc_final: 0.6125 (m-80) REVERT: N 213 GLN cc_start: 0.7634 (pp30) cc_final: 0.7132 (pp30) REVERT: N 241 THR cc_start: 0.8095 (t) cc_final: 0.7742 (m) REVERT: N 252 VAL cc_start: 0.8205 (p) cc_final: 0.7952 (m) REVERT: N 260 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: O 104 MET cc_start: 0.7058 (mmp) cc_final: 0.6157 (mmp) REVERT: O 110 PHE cc_start: 0.7335 (m-80) cc_final: 0.7004 (m-80) REVERT: O 132 MET cc_start: 0.8214 (mpp) cc_final: 0.7806 (mpp) REVERT: O 200 ILE cc_start: 0.8096 (mm) cc_final: 0.7793 (mm) REVERT: O 208 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7164 (tm-30) REVERT: P 63 TRP cc_start: 0.6548 (m100) cc_final: 0.5936 (m100) REVERT: P 110 PHE cc_start: 0.6946 (m-80) cc_final: 0.6640 (m-80) REVERT: P 132 MET cc_start: 0.7813 (tpt) cc_final: 0.7033 (tpt) REVERT: P 187 ILE cc_start: 0.8417 (mt) cc_final: 0.8164 (pt) REVERT: P 201 PHE cc_start: 0.8303 (t80) cc_final: 0.7444 (t80) REVERT: P 202 ILE cc_start: 0.8644 (pt) cc_final: 0.8343 (pt) REVERT: P 205 LYS cc_start: 0.8098 (mmmm) cc_final: 0.7185 (mmmm) REVERT: P 206 GLU cc_start: 0.6780 (pp20) cc_final: 0.6035 (pp20) outliers start: 52 outliers final: 29 residues processed: 881 average time/residue: 0.2164 time to fit residues: 304.5548 Evaluate side-chains 855 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 824 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 309 optimal weight: 0.8980 chunk 372 optimal weight: 0.1980 chunk 297 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 328 optimal weight: 0.2980 chunk 258 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 378 optimal weight: 0.0470 chunk 196 optimal weight: 9.9990 chunk 357 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 242 GLN E 69 HIS E 139 HIS ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS I 207 GLN J 13 ASN J 172 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.246879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190288 restraints weight = 65686.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.195921 restraints weight = 30659.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197861 restraints weight = 19228.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.199303 restraints weight = 15103.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199915 restraints weight = 12955.329| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 36753 Z= 0.155 Angle : 0.694 21.199 50271 Z= 0.356 Chirality : 0.046 0.326 5432 Planarity : 0.004 0.060 5969 Dihedral : 16.486 142.056 5791 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.92 % Allowed : 12.58 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.13), residues: 3971 helix: 1.12 (0.12), residues: 1870 sheet: -0.03 (0.19), residues: 754 loop : -1.16 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 155 TYR 0.016 0.002 TYR M 70 PHE 0.029 0.001 PHE N 99 TRP 0.040 0.001 TRP P 245 HIS 0.031 0.002 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (36705) covalent geometry : angle 0.65874 / 0.35 (50248) hydrogen bonds : bond 0.05274 / 3.53 ( 1694) hydrogen bonds : angle 5.09691 / 3.65 ( 4842) metal coordination : bond 0.03958 / 2.88 ( 48) metal coordination : angle 10.18489 / 6.92 ( 23) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 852 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.6985 (t70) cc_final: 0.6721 (t0) REVERT: A 98 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 109 MET cc_start: 0.7489 (tpp) cc_final: 0.7232 (tpt) REVERT: A 162 ASN cc_start: 0.8173 (t0) cc_final: 0.7676 (t0) REVERT: A 165 GLU cc_start: 0.7496 (tp30) cc_final: 0.7092 (tp30) REVERT: A 199 ASP cc_start: 0.6847 (t0) cc_final: 0.6416 (t0) REVERT: A 206 GLU cc_start: 0.6694 (tp30) cc_final: 0.6428 (tm-30) REVERT: A 223 PHE cc_start: 0.8231 (m-80) cc_final: 0.7524 (m-80) REVERT: A 238 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 255 ASP cc_start: 0.6868 (t0) cc_final: 0.6650 (t0) REVERT: B 116 GLN cc_start: 0.6721 (tt0) cc_final: 0.6506 (tt0) REVERT: B 118 ASP cc_start: 0.7288 (p0) cc_final: 0.7084 (p0) REVERT: B 124 VAL cc_start: 0.8102 (p) cc_final: 0.7594 (m) REVERT: B 140 THR cc_start: 0.8038 (m) cc_final: 0.7809 (t) REVERT: B 206 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6943 (tp30) REVERT: B 208 GLN cc_start: 0.7532 (tt0) cc_final: 0.7220 (tt0) REVERT: C 9 GLU cc_start: 0.7735 (tp30) cc_final: 0.7529 (tp30) REVERT: C 24 LEU cc_start: 0.8148 (mm) cc_final: 0.7700 (mp) REVERT: C 186 ASN cc_start: 0.8170 (m-40) cc_final: 0.7891 (t0) REVERT: C 198 MET cc_start: 0.6948 (pmm) cc_final: 0.6180 (pmm) REVERT: C 203 PHE cc_start: 0.6979 (t80) cc_final: 0.6656 (t80) REVERT: C 245 TRP cc_start: 0.7676 (m-90) cc_final: 0.7274 (m-90) REVERT: C 267 LYS cc_start: 0.8295 (pttp) cc_final: 0.7877 (pttp) REVERT: D 70 TYR cc_start: 0.6771 (t80) cc_final: 0.6533 (t80) REVERT: D 103 THR cc_start: 0.6586 (t) cc_final: 0.5875 (p) REVERT: D 104 MET cc_start: 0.6756 (mmp) cc_final: 0.5764 (mmp) REVERT: D 208 GLN cc_start: 0.7620 (mt0) cc_final: 0.7237 (mt0) REVERT: D 212 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6673 (tm-30) REVERT: D 236 GLU cc_start: 0.6920 (mp0) cc_final: 0.6611 (mp0) REVERT: D 238 GLN cc_start: 0.8409 (mt0) cc_final: 0.8114 (mt0) REVERT: D 268 ASP cc_start: 0.7018 (p0) cc_final: 0.6406 (p0) REVERT: E 34 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6414 (mm-30) REVERT: E 85 LEU cc_start: 0.8030 (tt) cc_final: 0.7827 (tp) REVERT: E 155 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6714 (mtt180) REVERT: E 157 HIS cc_start: 0.7921 (m-70) cc_final: 0.7310 (m90) REVERT: E 181 THR cc_start: 0.8277 (p) cc_final: 0.7804 (t) REVERT: E 202 ILE cc_start: 0.8001 (tp) cc_final: 0.7787 (tp) REVERT: E 208 GLN cc_start: 0.7182 (tp-100) cc_final: 0.6850 (tm-30) REVERT: E 271 PHE cc_start: 0.7149 (m-80) cc_final: 0.6615 (m-80) REVERT: F 64 GLN cc_start: 0.6331 (tp-100) cc_final: 0.6015 (tp-100) REVERT: F 213 GLN cc_start: 0.7890 (pp30) cc_final: 0.7592 (pp30) REVERT: F 230 LYS cc_start: 0.8273 (tppp) cc_final: 0.7864 (tppp) REVERT: G 110 PHE cc_start: 0.7433 (m-80) cc_final: 0.7002 (m-10) REVERT: H 87 TYR cc_start: 0.7028 (t80) cc_final: 0.6489 (t80) REVERT: H 132 MET cc_start: 0.7567 (tpt) cc_final: 0.6983 (tpt) REVERT: H 201 PHE cc_start: 0.8055 (t80) cc_final: 0.7627 (t80) REVERT: H 205 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7749 (mmmm) REVERT: R 418 MET cc_start: 0.7405 (ppp) cc_final: 0.6815 (ppp) REVERT: Q 360 LYS cc_start: 0.5544 (ptpp) cc_final: 0.5270 (ptpp) REVERT: Q 413 MET cc_start: 0.6206 (mmt) cc_final: 0.5882 (mmt) REVERT: Q 418 MET cc_start: 0.7494 (ppp) cc_final: 0.6870 (ppp) REVERT: I 10 GLU cc_start: 0.6844 (tp30) cc_final: 0.6636 (tp30) REVERT: I 72 ASP cc_start: 0.7107 (t70) cc_final: 0.6781 (t0) REVERT: I 165 GLU cc_start: 0.7104 (tp30) cc_final: 0.6797 (tp30) REVERT: I 238 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7303 (tp40) REVERT: I 254 LYS cc_start: 0.7768 (tppt) cc_final: 0.7353 (tppt) REVERT: J 86 ILE cc_start: 0.7889 (mp) cc_final: 0.7674 (mm) REVERT: J 94 GLU cc_start: 0.6262 (pp20) cc_final: 0.6026 (pp20) REVERT: J 98 GLU cc_start: 0.7331 (tp30) cc_final: 0.7099 (tp30) REVERT: J 129 GLN cc_start: 0.7594 (tt0) cc_final: 0.7134 (mt0) REVERT: J 132 MET cc_start: 0.7727 (tpp) cc_final: 0.7296 (mmt) REVERT: J 206 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7444 (tp30) REVERT: J 211 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6813 (tm-30) REVERT: K 109 MET cc_start: 0.7694 (tpp) cc_final: 0.7260 (pmm) REVERT: K 186 ASN cc_start: 0.7856 (t0) cc_final: 0.7651 (t0) REVERT: K 222 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.3914 (ttt90) REVERT: L 104 MET cc_start: 0.5402 (mmp) cc_final: 0.5080 (mmp) REVERT: L 110 PHE cc_start: 0.7068 (m-80) cc_final: 0.6677 (t80) REVERT: L 221 ILE cc_start: 0.7012 (mt) cc_final: 0.6707 (tt) REVERT: L 268 ASP cc_start: 0.7160 (p0) cc_final: 0.6588 (p0) REVERT: M 7 LEU cc_start: 0.7892 (tt) cc_final: 0.7638 (tt) REVERT: M 35 ASP cc_start: 0.6660 (m-30) cc_final: 0.6264 (m-30) REVERT: M 38 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7290 (tm-30) REVERT: M 61 ASP cc_start: 0.7493 (t70) cc_final: 0.6720 (t0) REVERT: M 62 HIS cc_start: 0.6290 (t70) cc_final: 0.5995 (t70) REVERT: M 99 PHE cc_start: 0.7506 (m-80) cc_final: 0.6901 (m-80) REVERT: M 155 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7248 (mtt180) REVERT: M 211 GLN cc_start: 0.7789 (pp30) cc_final: 0.7281 (pp30) REVERT: M 215 LYS cc_start: 0.8368 (pttt) cc_final: 0.8092 (pttt) REVERT: M 259 ASP cc_start: 0.7398 (t0) cc_final: 0.7191 (t0) REVERT: M 271 PHE cc_start: 0.6814 (m-80) cc_final: 0.6167 (m-80) REVERT: N 64 GLN cc_start: 0.6411 (tp40) cc_final: 0.5941 (tp-100) REVERT: N 213 GLN cc_start: 0.7893 (pp30) cc_final: 0.7369 (pp30) REVERT: N 241 THR cc_start: 0.8159 (t) cc_final: 0.7803 (m) REVERT: N 252 VAL cc_start: 0.8212 (p) cc_final: 0.7966 (m) REVERT: N 260 ARG cc_start: 0.6699 (mtm-85) cc_final: 0.6267 (mtm-85) REVERT: O 11 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7647 (mm-30) REVERT: O 36 ILE cc_start: 0.6510 (mm) cc_final: 0.6239 (mm) REVERT: O 104 MET cc_start: 0.7036 (mmp) cc_final: 0.6131 (mmp) REVERT: O 110 PHE cc_start: 0.7193 (m-80) cc_final: 0.6952 (m-80) REVERT: O 132 MET cc_start: 0.8230 (mpp) cc_final: 0.7697 (mpp) REVERT: O 208 GLN cc_start: 0.7587 (tm-30) cc_final: 0.7278 (tm-30) REVERT: P 63 TRP cc_start: 0.6702 (m100) cc_final: 0.5517 (m100) REVERT: P 110 PHE cc_start: 0.6967 (m-80) cc_final: 0.6760 (m-80) REVERT: P 132 MET cc_start: 0.7857 (tpt) cc_final: 0.7078 (tpt) REVERT: P 186 ASN cc_start: 0.8545 (m-40) cc_final: 0.8269 (t0) REVERT: P 198 MET cc_start: 0.7341 (mpp) cc_final: 0.7041 (mpp) REVERT: P 201 PHE cc_start: 0.8260 (t80) cc_final: 0.7695 (t80) REVERT: P 202 ILE cc_start: 0.8619 (pt) cc_final: 0.8382 (pt) REVERT: P 206 GLU cc_start: 0.6707 (pp20) cc_final: 0.5179 (pp20) outliers start: 68 outliers final: 46 residues processed: 863 average time/residue: 0.2107 time to fit residues: 290.2763 Evaluate side-chains 865 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 818 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain Q residue 426 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 266 ASN Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 204 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 264 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 186 optimal weight: 0.4980 chunk 406 optimal weight: 9.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS ** K 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN M 139 HIS M 157 HIS ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 211 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.271414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.253572 restraints weight = 85192.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.250955 restraints weight = 105243.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.249210 restraints weight = 85212.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.249062 restraints weight = 80792.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.248512 restraints weight = 75211.842| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 36753 Z= 0.203 Angle : 0.718 23.087 50271 Z= 0.373 Chirality : 0.047 0.320 5432 Planarity : 0.005 0.061 5969 Dihedral : 16.712 143.191 5791 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 15.10 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 3971 helix: 1.00 (0.12), residues: 1871 sheet: -0.15 (0.19), residues: 772 loop : -1.20 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 222 TYR 0.025 0.002 TYR I 134 PHE 0.032 0.002 PHE N 99 TRP 0.047 0.002 TRP M 1 HIS 0.020 0.002 HIS K 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (36705) covalent geometry : angle 0.68819 / 0.37 (50248) hydrogen bonds : bond 0.05147 / 3.44 ( 1694) hydrogen bonds : angle 5.00100 / 3.58 ( 4842) metal coordination : bond 0.04120 / 2.83 ( 48) metal coordination : angle 9.60444 / 6.27 ( 23) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 838 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: A 72 ASP cc_start: 0.7008 (t70) cc_final: 0.6642 (t0) REVERT: A 98 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6780 (mm-30) REVERT: A 121 PRO cc_start: 0.8360 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: A 165 GLU cc_start: 0.7477 (tp30) cc_final: 0.6994 (tp30) REVERT: A 199 ASP cc_start: 0.6576 (t0) cc_final: 0.6175 (t0) REVERT: A 223 PHE cc_start: 0.8364 (m-80) cc_final: 0.7641 (m-80) REVERT: A 238 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 254 LYS cc_start: 0.7623 (tppt) cc_final: 0.7337 (ttmt) REVERT: A 255 ASP cc_start: 0.7101 (t0) cc_final: 0.6887 (t0) REVERT: B 118 ASP cc_start: 0.7250 (p0) cc_final: 0.7013 (p0) REVERT: B 124 VAL cc_start: 0.8157 (p) cc_final: 0.7756 (m) REVERT: B 140 THR cc_start: 0.8038 (m) cc_final: 0.7777 (t) REVERT: B 185 LEU cc_start: 0.7686 (mt) cc_final: 0.7111 (mp) REVERT: B 206 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7238 (tp30) REVERT: B 208 GLN cc_start: 0.7740 (tt0) cc_final: 0.7446 (tt0) REVERT: C 24 LEU cc_start: 0.8061 (mm) cc_final: 0.7545 (mp) REVERT: C 203 PHE cc_start: 0.6798 (t80) cc_final: 0.6358 (t80) REVERT: C 267 LYS cc_start: 0.7949 (pttp) cc_final: 0.7625 (pttp) REVERT: D 103 THR cc_start: 0.5651 (t) cc_final: 0.5277 (p) REVERT: D 104 MET cc_start: 0.6268 (mmp) cc_final: 0.5551 (mmp) REVERT: D 132 MET cc_start: 0.8093 (ppp) cc_final: 0.7776 (ppp) REVERT: D 236 GLU cc_start: 0.7025 (mp0) cc_final: 0.6635 (mp0) REVERT: D 238 GLN cc_start: 0.8466 (mt0) cc_final: 0.8146 (mt0) REVERT: E 157 HIS cc_start: 0.7743 (m-70) cc_final: 0.6829 (m-70) REVERT: E 161 LYS cc_start: 0.8315 (mttt) cc_final: 0.7842 (mttt) REVERT: E 181 THR cc_start: 0.8194 (p) cc_final: 0.7825 (t) REVERT: E 208 GLN cc_start: 0.7423 (tp40) cc_final: 0.7083 (tm-30) REVERT: E 212 GLN cc_start: 0.7251 (mp10) cc_final: 0.6568 (mp10) REVERT: E 270 LYS cc_start: 0.6846 (mtpt) cc_final: 0.6642 (mtpt) REVERT: F 102 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6196 (tp-100) REVERT: F 113 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7078 (mmtm) REVERT: F 213 GLN cc_start: 0.7997 (pp30) cc_final: 0.7778 (pp30) REVERT: F 230 LYS cc_start: 0.8332 (tppp) cc_final: 0.7923 (tppp) REVERT: H 63 TRP cc_start: 0.5479 (m100) cc_final: 0.5133 (m100) REVERT: H 201 PHE cc_start: 0.7282 (t80) cc_final: 0.7058 (t80) REVERT: H 230 LYS cc_start: 0.4804 (pttm) cc_final: 0.4459 (pttm) REVERT: H 251 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5841 (mp) REVERT: R 418 MET cc_start: 0.6840 (ppp) cc_final: 0.6408 (ppp) REVERT: Q 360 LYS cc_start: 0.6052 (ptpp) cc_final: 0.5772 (ptpp) REVERT: Q 418 MET cc_start: 0.6871 (ppp) cc_final: 0.6391 (ppp) REVERT: I 10 GLU cc_start: 0.6826 (tp30) cc_final: 0.6549 (tp30) REVERT: I 72 ASP cc_start: 0.7170 (t70) cc_final: 0.6830 (t0) REVERT: I 98 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6605 (mm-30) REVERT: I 109 MET cc_start: 0.6645 (ttt) cc_final: 0.6010 (ttm) REVERT: I 165 GLU cc_start: 0.7276 (tp30) cc_final: 0.6873 (tp30) REVERT: I 183 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6979 (mt) REVERT: I 238 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7040 (tm-30) REVERT: I 254 LYS cc_start: 0.7814 (tppt) cc_final: 0.7523 (tppt) REVERT: J 94 GLU cc_start: 0.6302 (pp20) cc_final: 0.5971 (pp20) REVERT: J 105 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7674 (ttmt) REVERT: J 129 GLN cc_start: 0.7804 (tt0) cc_final: 0.7260 (mt0) REVERT: J 132 MET cc_start: 0.7813 (tpp) cc_final: 0.7440 (mmt) REVERT: J 206 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7442 (tp30) REVERT: J 211 GLN cc_start: 0.7337 (tm-30) cc_final: 0.7107 (tm-30) REVERT: K 222 ARG cc_start: 0.5808 (OUTLIER) cc_final: 0.3764 (ttt90) REVERT: L 104 MET cc_start: 0.4905 (mmp) cc_final: 0.4621 (mmp) REVERT: L 220 LYS cc_start: 0.5899 (mmtm) cc_final: 0.5522 (mmtm) REVERT: L 248 ASP cc_start: 0.6877 (p0) cc_final: 0.6647 (p0) REVERT: L 259 ASP cc_start: 0.7529 (p0) cc_final: 0.7175 (p0) REVERT: L 268 ASP cc_start: 0.7409 (p0) cc_final: 0.6794 (p0) REVERT: M 7 LEU cc_start: 0.8007 (tt) cc_final: 0.7775 (tt) REVERT: M 35 ASP cc_start: 0.6896 (m-30) cc_final: 0.6559 (m-30) REVERT: M 38 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7206 (tm-30) REVERT: M 61 ASP cc_start: 0.7328 (t70) cc_final: 0.6817 (t0) REVERT: M 99 PHE cc_start: 0.7015 (m-80) cc_final: 0.6650 (m-80) REVERT: M 155 ARG cc_start: 0.7320 (mtt180) cc_final: 0.7104 (mtt180) REVERT: M 195 THR cc_start: 0.8179 (m) cc_final: 0.7581 (t) REVERT: M 271 PHE cc_start: 0.6138 (m-80) cc_final: 0.5900 (m-80) REVERT: N 105 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8181 (mtmm) REVERT: N 113 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7489 (mmtm) REVERT: N 213 GLN cc_start: 0.7930 (pp30) cc_final: 0.7526 (pp30) REVERT: N 241 THR cc_start: 0.8425 (t) cc_final: 0.8017 (p) REVERT: N 252 VAL cc_start: 0.8353 (p) cc_final: 0.8071 (m) REVERT: N 260 ARG cc_start: 0.6742 (mtm-85) cc_final: 0.6346 (mtm-85) REVERT: O 132 MET cc_start: 0.7422 (mpp) cc_final: 0.7197 (mpp) REVERT: P 130 LEU cc_start: 0.8056 (mt) cc_final: 0.7726 (mt) REVERT: P 132 MET cc_start: 0.6479 (tpt) cc_final: 0.6201 (tpt) REVERT: P 201 PHE cc_start: 0.7524 (t80) cc_final: 0.7114 (t80) outliers start: 79 outliers final: 59 residues processed: 856 average time/residue: 0.2099 time to fit residues: 286.8809 Evaluate side-chains 889 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 825 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 406 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 273 optimal weight: 50.0000 chunk 174 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 336 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 242 GLN E 23 HIS E 69 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.240198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.185321 restraints weight = 66303.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187210 restraints weight = 36636.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.187639 restraints weight = 23978.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188517 restraints weight = 21946.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188792 restraints weight = 19957.204| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 36753 Z= 0.223 Angle : 0.727 20.813 50271 Z= 0.378 Chirality : 0.048 0.286 5432 Planarity : 0.005 0.054 5969 Dihedral : 16.817 144.299 5791 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.83 % Allowed : 16.79 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 3971 helix: 0.85 (0.12), residues: 1880 sheet: -0.24 (0.19), residues: 756 loop : -1.32 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 155 TYR 0.029 0.002 TYR I 134 PHE 0.032 0.002 PHE N 99 TRP 0.059 0.002 TRP M 1 HIS 0.031 0.002 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (36705) covalent geometry : angle 0.69910 / 0.38 (50248) hydrogen bonds : bond 0.05013 / 3.34 ( 1694) hydrogen bonds : angle 5.01789 / 3.60 ( 4842) metal coordination : bond 0.03580 / 2.37 ( 48) metal coordination : angle 9.33005 / 6.05 ( 23) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 834 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7250 (mt0) REVERT: A 72 ASP cc_start: 0.7136 (t70) cc_final: 0.6721 (t0) REVERT: A 98 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 165 GLU cc_start: 0.7430 (tp30) cc_final: 0.6988 (tp30) REVERT: A 199 ASP cc_start: 0.6745 (t0) cc_final: 0.6276 (t0) REVERT: A 223 PHE cc_start: 0.8422 (m-80) cc_final: 0.7561 (m-80) REVERT: A 238 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 124 VAL cc_start: 0.8221 (p) cc_final: 0.7840 (m) REVERT: B 140 THR cc_start: 0.8070 (m) cc_final: 0.7798 (t) REVERT: B 206 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7103 (tp30) REVERT: B 208 GLN cc_start: 0.7748 (tt0) cc_final: 0.7432 (tt0) REVERT: C 9 GLU cc_start: 0.7652 (tp30) cc_final: 0.7375 (tp30) REVERT: C 24 LEU cc_start: 0.8094 (mm) cc_final: 0.7583 (mp) REVERT: C 104 MET cc_start: 0.5456 (ppp) cc_final: 0.4670 (ppp) REVERT: C 203 PHE cc_start: 0.7077 (t80) cc_final: 0.6499 (t80) REVERT: C 205 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8058 (mmmt) REVERT: C 267 LYS cc_start: 0.8275 (pttp) cc_final: 0.7929 (pttp) REVERT: D 103 THR cc_start: 0.6726 (t) cc_final: 0.6026 (p) REVERT: D 104 MET cc_start: 0.6914 (mmp) cc_final: 0.6041 (mmp) REVERT: D 109 MET cc_start: 0.6565 (tpt) cc_final: 0.6311 (tmm) REVERT: D 220 LYS cc_start: 0.5648 (mmtm) cc_final: 0.5227 (mmtm) REVERT: D 236 GLU cc_start: 0.6969 (mp0) cc_final: 0.6607 (mp0) REVERT: D 238 GLN cc_start: 0.8318 (mt0) cc_final: 0.8017 (mt0) REVERT: E 35 ASP cc_start: 0.6721 (m-30) cc_final: 0.6174 (m-30) REVERT: E 89 GLU cc_start: 0.4873 (tm-30) cc_final: 0.4614 (tm-30) REVERT: E 157 HIS cc_start: 0.8329 (m-70) cc_final: 0.7249 (m-70) REVERT: E 158 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7516 (mm-40) REVERT: E 161 LYS cc_start: 0.8556 (mttt) cc_final: 0.7950 (mttt) REVERT: E 181 THR cc_start: 0.8227 (p) cc_final: 0.7918 (t) REVERT: E 195 THR cc_start: 0.8163 (m) cc_final: 0.7444 (t) REVERT: E 208 GLN cc_start: 0.7763 (tp40) cc_final: 0.7384 (tm-30) REVERT: E 212 GLN cc_start: 0.7672 (mp10) cc_final: 0.6982 (mp10) REVERT: E 213 GLN cc_start: 0.6926 (pp30) cc_final: 0.6292 (pp30) REVERT: E 270 LYS cc_start: 0.7106 (mtpt) cc_final: 0.6587 (mtpt) REVERT: E 271 PHE cc_start: 0.6857 (m-80) cc_final: 0.6633 (m-80) REVERT: F 70 TYR cc_start: 0.7474 (t80) cc_final: 0.7208 (t80) REVERT: F 97 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7573 (pm20) REVERT: F 102 GLN cc_start: 0.6947 (mm-40) cc_final: 0.6348 (tp-100) REVERT: H 63 TRP cc_start: 0.6713 (m100) cc_final: 0.5683 (m100) REVERT: H 87 TYR cc_start: 0.6720 (t80) cc_final: 0.6179 (t80) REVERT: H 110 PHE cc_start: 0.7838 (m-10) cc_final: 0.7342 (m-10) REVERT: H 201 PHE cc_start: 0.8117 (t80) cc_final: 0.7611 (t80) REVERT: H 205 LYS cc_start: 0.7978 (mmmm) cc_final: 0.7437 (mmmm) REVERT: H 251 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6322 (mp) REVERT: R 418 MET cc_start: 0.7421 (ppp) cc_final: 0.6873 (ppp) REVERT: Q 360 LYS cc_start: 0.6025 (ptpp) cc_final: 0.5641 (ptpp) REVERT: Q 413 MET cc_start: 0.6578 (mmt) cc_final: 0.6214 (mtt) REVERT: Q 418 MET cc_start: 0.7573 (ppp) cc_final: 0.6964 (ppp) REVERT: I 10 GLU cc_start: 0.6852 (tp30) cc_final: 0.6611 (tp30) REVERT: I 72 ASP cc_start: 0.7139 (t70) cc_final: 0.6846 (t0) REVERT: I 89 GLU cc_start: 0.6791 (tp30) cc_final: 0.6561 (tp30) REVERT: I 165 GLU cc_start: 0.7253 (tp30) cc_final: 0.6870 (tp30) REVERT: I 183 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7344 (mt) REVERT: I 238 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7140 (tm-30) REVERT: I 254 LYS cc_start: 0.7913 (tppt) cc_final: 0.7678 (tppt) REVERT: J 86 ILE cc_start: 0.7921 (mp) cc_final: 0.7704 (mt) REVERT: J 94 GLU cc_start: 0.6517 (pp20) cc_final: 0.6125 (pp20) REVERT: J 97 GLN cc_start: 0.7610 (tp40) cc_final: 0.7162 (tp40) REVERT: J 129 GLN cc_start: 0.7787 (tt0) cc_final: 0.7324 (mt0) REVERT: J 206 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7423 (tp30) REVERT: K 109 MET cc_start: 0.7608 (tpp) cc_final: 0.6883 (pmm) REVERT: K 222 ARG cc_start: 0.5248 (OUTLIER) cc_final: 0.4010 (ttt90) REVERT: L 80 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6017 (tm-30) REVERT: L 104 MET cc_start: 0.5361 (mmp) cc_final: 0.5018 (mmp) REVERT: L 133 LYS cc_start: 0.7604 (mmmt) cc_final: 0.7292 (mmmt) REVERT: L 220 LYS cc_start: 0.5821 (mmtm) cc_final: 0.5415 (mmtm) REVERT: L 248 ASP cc_start: 0.6957 (p0) cc_final: 0.6731 (p0) REVERT: L 256 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6640 (mtp85) REVERT: L 259 ASP cc_start: 0.7644 (p0) cc_final: 0.7278 (p0) REVERT: L 268 ASP cc_start: 0.7315 (p0) cc_final: 0.6692 (p0) REVERT: M 7 LEU cc_start: 0.8142 (tt) cc_final: 0.7941 (tt) REVERT: M 35 ASP cc_start: 0.7053 (m-30) cc_final: 0.6567 (m-30) REVERT: M 38 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7539 (tm-30) REVERT: M 44 GLN cc_start: 0.6188 (tp40) cc_final: 0.5891 (tp-100) REVERT: M 61 ASP cc_start: 0.7585 (t70) cc_final: 0.7036 (t0) REVERT: M 99 PHE cc_start: 0.7799 (m-80) cc_final: 0.7035 (m-80) REVERT: M 155 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7335 (mtt180) REVERT: M 161 LYS cc_start: 0.9005 (mttt) cc_final: 0.8516 (mttt) REVERT: M 195 THR cc_start: 0.8156 (m) cc_final: 0.7646 (t) REVERT: M 259 ASP cc_start: 0.7629 (t0) cc_final: 0.7369 (t0) REVERT: M 271 PHE cc_start: 0.7005 (m-80) cc_final: 0.6375 (m-80) REVERT: N 64 GLN cc_start: 0.6383 (tp-100) cc_final: 0.6121 (tp-100) REVERT: N 104 MET cc_start: 0.7658 (tpt) cc_final: 0.7373 (tpt) REVERT: N 105 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8161 (mtmm) REVERT: N 113 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7589 (mmtm) REVERT: N 213 GLN cc_start: 0.7794 (pp30) cc_final: 0.7375 (pp30) REVERT: N 241 THR cc_start: 0.8442 (t) cc_final: 0.8063 (p) REVERT: N 260 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6396 (mtm-85) REVERT: O 11 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7732 (mm-30) REVERT: O 132 MET cc_start: 0.8282 (mpp) cc_final: 0.7674 (mpp) REVERT: P 87 TYR cc_start: 0.6149 (t80) cc_final: 0.5730 (t80) REVERT: P 130 LEU cc_start: 0.8398 (mt) cc_final: 0.8132 (mt) REVERT: P 132 MET cc_start: 0.8109 (tpt) cc_final: 0.7275 (tpt) REVERT: P 201 PHE cc_start: 0.8300 (t80) cc_final: 0.7795 (t80) REVERT: P 203 PHE cc_start: 0.8466 (t80) cc_final: 0.8109 (t80) REVERT: P 206 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6935 (tm-30) REVERT: P 207 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7368 (mm110) outliers start: 100 outliers final: 69 residues processed: 869 average time/residue: 0.2207 time to fit residues: 306.9023 Evaluate side-chains 898 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 824 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 414 GLU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 256 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 204 ASN Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 157 HIS Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 378 optimal weight: 0.8980 chunk 321 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 355 optimal weight: 0.0070 chunk 308 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 406 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS D 242 GLN E 64 GLN E 69 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 129 GLN J 82 ASN J 204 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.239446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.181358 restraints weight = 65690.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.187037 restraints weight = 30724.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187713 restraints weight = 21467.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.189224 restraints weight = 16486.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.189578 restraints weight = 14509.369| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 36753 Z= 0.223 Angle : 0.731 25.058 50271 Z= 0.380 Chirality : 0.048 0.321 5432 Planarity : 0.005 0.052 5969 Dihedral : 16.947 145.401 5791 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.08 % Allowed : 17.59 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3971 helix: 0.75 (0.12), residues: 1892 sheet: -0.11 (0.19), residues: 700 loop : -1.36 (0.15), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 30 TYR 0.031 0.002 TYR I 134 PHE 0.035 0.002 PHE N 99 TRP 0.043 0.002 TRP M 1 HIS 0.030 0.002 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (36705) covalent geometry : angle 0.70644 / 0.38 (50248) hydrogen bonds : bond 0.04918 / 3.30 ( 1694) hydrogen bonds : angle 4.94102 / 3.53 ( 4842) metal coordination : bond 0.02925 / 1.83 ( 48) metal coordination : angle 8.80262 / 6.15 ( 23) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 830 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7169 (t70) cc_final: 0.6695 (t0) REVERT: A 98 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6758 (mm-30) REVERT: A 109 MET cc_start: 0.7253 (tpp) cc_final: 0.6966 (tpp) REVERT: A 138 GLU cc_start: 0.6900 (mp0) cc_final: 0.6486 (mp0) REVERT: A 165 GLU cc_start: 0.7536 (tp30) cc_final: 0.7103 (tp30) REVERT: A 183 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7493 (mt) REVERT: A 223 PHE cc_start: 0.8363 (m-80) cc_final: 0.7492 (m-80) REVERT: A 238 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 254 LYS cc_start: 0.7566 (tppt) cc_final: 0.7252 (ttmt) REVERT: B 124 VAL cc_start: 0.8221 (p) cc_final: 0.7874 (m) REVERT: B 140 THR cc_start: 0.8037 (m) cc_final: 0.7776 (t) REVERT: B 208 GLN cc_start: 0.7850 (tt0) cc_final: 0.7538 (tt0) REVERT: C 9 GLU cc_start: 0.7562 (tp30) cc_final: 0.7307 (tp30) REVERT: C 24 LEU cc_start: 0.8108 (mm) cc_final: 0.7635 (mp) REVERT: C 104 MET cc_start: 0.5433 (ppp) cc_final: 0.4962 (ppp) REVERT: C 107 TYR cc_start: 0.8168 (t80) cc_final: 0.7935 (t80) REVERT: C 198 MET cc_start: 0.7641 (tpt) cc_final: 0.7379 (tpt) REVERT: C 203 PHE cc_start: 0.7035 (t80) cc_final: 0.6476 (t80) REVERT: C 204 ASN cc_start: 0.8120 (p0) cc_final: 0.7829 (p0) REVERT: C 205 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8119 (mmmt) REVERT: C 207 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: C 267 LYS cc_start: 0.8238 (pttp) cc_final: 0.7893 (pttp) REVERT: D 103 THR cc_start: 0.6577 (t) cc_final: 0.5854 (p) REVERT: D 104 MET cc_start: 0.6910 (mmp) cc_final: 0.6031 (mmp) REVERT: D 220 LYS cc_start: 0.5750 (mmtm) cc_final: 0.5454 (mmtm) REVERT: D 236 GLU cc_start: 0.6945 (mp0) cc_final: 0.6589 (mp0) REVERT: D 238 GLN cc_start: 0.8271 (mt0) cc_final: 0.7995 (mt0) REVERT: D 260 ARG cc_start: 0.6638 (mmm-85) cc_final: 0.6388 (mmm-85) REVERT: E 38 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7178 (mm-40) REVERT: E 129 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7369 (mm-40) REVERT: E 155 ARG cc_start: 0.7358 (mtt180) cc_final: 0.7135 (mtt180) REVERT: E 157 HIS cc_start: 0.8397 (m-70) cc_final: 0.7163 (m-70) REVERT: E 158 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7436 (mm-40) REVERT: E 161 LYS cc_start: 0.8540 (mttt) cc_final: 0.7942 (mttt) REVERT: E 195 THR cc_start: 0.8043 (m) cc_final: 0.7506 (t) REVERT: E 208 GLN cc_start: 0.7676 (tp40) cc_final: 0.7251 (tm-30) REVERT: E 212 GLN cc_start: 0.7559 (mp10) cc_final: 0.6529 (mp10) REVERT: E 213 GLN cc_start: 0.7011 (pp30) cc_final: 0.6522 (pp30) REVERT: E 225 TYR cc_start: 0.6151 (t80) cc_final: 0.5561 (t80) REVERT: E 270 LYS cc_start: 0.6792 (mtpt) cc_final: 0.6444 (mtpt) REVERT: E 271 PHE cc_start: 0.6832 (m-80) cc_final: 0.6594 (m-80) REVERT: F 110 PHE cc_start: 0.7815 (m-10) cc_final: 0.7291 (m-80) REVERT: F 254 LYS cc_start: 0.8127 (tptt) cc_final: 0.7924 (tptt) REVERT: H 63 TRP cc_start: 0.6592 (m100) cc_final: 0.5674 (m100) REVERT: H 87 TYR cc_start: 0.6904 (t80) cc_final: 0.6267 (t80) REVERT: H 110 PHE cc_start: 0.7914 (m-10) cc_final: 0.7612 (m-10) REVERT: H 201 PHE cc_start: 0.8129 (t80) cc_final: 0.7582 (t80) REVERT: H 205 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7557 (mmmm) REVERT: H 251 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6306 (mp) REVERT: R 418 MET cc_start: 0.7416 (ppp) cc_final: 0.6864 (ppp) REVERT: Q 360 LYS cc_start: 0.6111 (ptpp) cc_final: 0.5694 (ptpp) REVERT: Q 413 MET cc_start: 0.6501 (mmt) cc_final: 0.5969 (mmt) REVERT: Q 418 MET cc_start: 0.7526 (ppp) cc_final: 0.6955 (ppp) REVERT: I 10 GLU cc_start: 0.6877 (tp30) cc_final: 0.6587 (tp30) REVERT: I 72 ASP cc_start: 0.7113 (t70) cc_final: 0.6839 (t0) REVERT: I 165 GLU cc_start: 0.7304 (tp30) cc_final: 0.6917 (tp30) REVERT: I 183 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7367 (mt) REVERT: I 238 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7232 (tm-30) REVERT: J 86 ILE cc_start: 0.7905 (mp) cc_final: 0.7685 (mt) REVERT: J 94 GLU cc_start: 0.6712 (pp20) cc_final: 0.6324 (pp20) REVERT: J 98 GLU cc_start: 0.7022 (tp30) cc_final: 0.6710 (tp30) REVERT: J 129 GLN cc_start: 0.7744 (tt0) cc_final: 0.7342 (mt0) REVERT: J 206 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7349 (tp30) REVERT: L 80 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6373 (tm-30) REVERT: L 104 MET cc_start: 0.5367 (mmp) cc_final: 0.5002 (mmp) REVERT: L 220 LYS cc_start: 0.6020 (mmtm) cc_final: 0.5675 (mmtm) REVERT: L 256 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6606 (mtp85) REVERT: L 259 ASP cc_start: 0.7790 (p0) cc_final: 0.7561 (p0) REVERT: L 268 ASP cc_start: 0.7259 (p0) cc_final: 0.6921 (p0) REVERT: M 35 ASP cc_start: 0.6989 (m-30) cc_final: 0.6633 (m-30) REVERT: M 38 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7507 (tm-30) REVERT: M 44 GLN cc_start: 0.5854 (tp40) cc_final: 0.5629 (tp-100) REVERT: M 61 ASP cc_start: 0.7666 (t70) cc_final: 0.7189 (t0) REVERT: M 63 TRP cc_start: 0.5811 (m100) cc_final: 0.5553 (m100) REVERT: M 99 PHE cc_start: 0.7656 (m-80) cc_final: 0.6908 (m-80) REVERT: M 155 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7288 (mtt180) REVERT: M 195 THR cc_start: 0.8153 (m) cc_final: 0.7692 (t) REVERT: M 259 ASP cc_start: 0.7727 (t0) cc_final: 0.7477 (t0) REVERT: M 267 LYS cc_start: 0.7754 (tptt) cc_final: 0.7419 (tppt) REVERT: M 271 PHE cc_start: 0.7031 (m-80) cc_final: 0.6432 (m-80) REVERT: N 64 GLN cc_start: 0.6359 (tp-100) cc_final: 0.6071 (tp-100) REVERT: N 105 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8130 (mtmm) REVERT: N 107 TYR cc_start: 0.8495 (t80) cc_final: 0.8153 (t80) REVERT: N 113 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7603 (mmtm) REVERT: N 213 GLN cc_start: 0.7843 (pp30) cc_final: 0.7444 (pp30) REVERT: N 241 THR cc_start: 0.8370 (t) cc_final: 0.8138 (p) REVERT: N 254 LYS cc_start: 0.7711 (tptt) cc_final: 0.7477 (tptt) REVERT: N 260 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.6431 (mtm-85) REVERT: O 11 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7695 (mm-30) REVERT: O 132 MET cc_start: 0.8249 (mpp) cc_final: 0.7742 (mpp) REVERT: O 201 PHE cc_start: 0.8069 (t80) cc_final: 0.7811 (t80) REVERT: P 87 TYR cc_start: 0.6042 (t80) cc_final: 0.5712 (t80) REVERT: P 130 LEU cc_start: 0.8481 (mt) cc_final: 0.8236 (mt) REVERT: P 132 MET cc_start: 0.8063 (tpt) cc_final: 0.7211 (tpt) REVERT: P 201 PHE cc_start: 0.8335 (t80) cc_final: 0.7906 (t80) outliers start: 109 outliers final: 81 residues processed: 871 average time/residue: 0.2130 time to fit residues: 295.9576 Evaluate side-chains 910 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 824 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 157 HIS Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 414 GLU Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 256 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 204 ASN Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 190 LYS Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 325 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 214 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 chunk 319 optimal weight: 0.7980 chunk 385 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 213 optimal weight: 0.5980 chunk 287 optimal weight: 40.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 GLN B 82 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.270515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.251015 restraints weight = 84316.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.249476 restraints weight = 112600.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.248932 restraints weight = 78502.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.248664 restraints weight = 69952.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.248111 restraints weight = 74297.501| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36753 Z= 0.159 Angle : 0.719 21.300 50271 Z= 0.369 Chirality : 0.047 0.286 5432 Planarity : 0.004 0.053 5969 Dihedral : 16.962 145.912 5791 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.11 % Allowed : 18.63 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3971 helix: 0.84 (0.12), residues: 1890 sheet: -0.10 (0.20), residues: 692 loop : -1.27 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 155 TYR 0.030 0.002 TYR P 134 PHE 0.037 0.001 PHE N 99 TRP 0.024 0.002 TRP F 106 HIS 0.032 0.001 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (36705) covalent geometry : angle 0.69856 / 0.37 (50248) hydrogen bonds : bond 0.04341 / 2.90 ( 1694) hydrogen bonds : angle 4.82883 / 3.44 ( 4842) metal coordination : bond 0.02567 / 1.65 ( 48) metal coordination : angle 8.05396 / 5.46 ( 23) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 831 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7263 (t70) cc_final: 0.6725 (t0) REVERT: A 98 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 113 LYS cc_start: 0.7713 (mmmm) cc_final: 0.6884 (mmmm) REVERT: A 138 GLU cc_start: 0.7000 (mp0) cc_final: 0.6499 (mp0) REVERT: A 165 GLU cc_start: 0.7521 (tp30) cc_final: 0.7102 (tp30) REVERT: A 183 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7245 (mt) REVERT: A 223 PHE cc_start: 0.8316 (m-80) cc_final: 0.7489 (m-80) REVERT: A 238 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 254 LYS cc_start: 0.7650 (tppt) cc_final: 0.7299 (ttmt) REVERT: B 124 VAL cc_start: 0.8301 (p) cc_final: 0.7975 (m) REVERT: B 140 THR cc_start: 0.8029 (m) cc_final: 0.7783 (t) REVERT: B 208 GLN cc_start: 0.7851 (tt0) cc_final: 0.7551 (tt0) REVERT: C 9 GLU cc_start: 0.7510 (tp30) cc_final: 0.7258 (tp30) REVERT: C 24 LEU cc_start: 0.8133 (mm) cc_final: 0.7631 (mp) REVERT: C 203 PHE cc_start: 0.6597 (t80) cc_final: 0.6241 (t80) REVERT: C 204 ASN cc_start: 0.7751 (p0) cc_final: 0.7479 (p0) REVERT: C 207 GLN cc_start: 0.6091 (OUTLIER) cc_final: 0.5798 (pm20) REVERT: C 267 LYS cc_start: 0.8033 (pttp) cc_final: 0.7615 (pttp) REVERT: D 103 THR cc_start: 0.5467 (t) cc_final: 0.5155 (p) REVERT: D 104 MET cc_start: 0.5980 (mmp) cc_final: 0.5330 (mmp) REVERT: D 132 MET cc_start: 0.7846 (ppp) cc_final: 0.7433 (ppp) REVERT: D 220 LYS cc_start: 0.5704 (mmtm) cc_final: 0.5446 (mmtm) REVERT: D 236 GLU cc_start: 0.7054 (mp0) cc_final: 0.6645 (mp0) REVERT: D 238 GLN cc_start: 0.8436 (mt0) cc_final: 0.8082 (mt0) REVERT: D 260 ARG cc_start: 0.6798 (mmm-85) cc_final: 0.6444 (mmm-85) REVERT: E 157 HIS cc_start: 0.7924 (m-70) cc_final: 0.7030 (m-70) REVERT: E 158 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7196 (mm-40) REVERT: E 161 LYS cc_start: 0.8371 (mttt) cc_final: 0.7881 (mttt) REVERT: E 181 THR cc_start: 0.8192 (p) cc_final: 0.7988 (t) REVERT: E 195 THR cc_start: 0.8001 (m) cc_final: 0.7482 (t) REVERT: E 208 GLN cc_start: 0.7454 (tp40) cc_final: 0.7119 (tm-30) REVERT: E 212 GLN cc_start: 0.7471 (mp10) cc_final: 0.6348 (mp10) REVERT: E 225 TYR cc_start: 0.5249 (t80) cc_final: 0.4966 (t80) REVERT: F 103 THR cc_start: 0.7574 (t) cc_final: 0.7328 (p) REVERT: F 110 PHE cc_start: 0.7716 (m-10) cc_final: 0.7253 (m-80) REVERT: F 213 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7767 (pp30) REVERT: F 241 THR cc_start: 0.8298 (t) cc_final: 0.7964 (p) REVERT: F 254 LYS cc_start: 0.8097 (tptt) cc_final: 0.7794 (tptt) REVERT: H 166 LYS cc_start: 0.7322 (tptp) cc_final: 0.7120 (tptp) REVERT: H 201 PHE cc_start: 0.7473 (t80) cc_final: 0.7022 (t80) REVERT: H 205 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7016 (mmmm) REVERT: R 418 MET cc_start: 0.6741 (ppp) cc_final: 0.6321 (ppp) REVERT: Q 360 LYS cc_start: 0.6483 (ptpp) cc_final: 0.6124 (ptpp) REVERT: Q 387 MET cc_start: 0.5192 (OUTLIER) cc_final: 0.4853 (tpp) REVERT: Q 413 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.4981 (mmt) REVERT: Q 418 MET cc_start: 0.6877 (ppp) cc_final: 0.6407 (ppp) REVERT: I 10 GLU cc_start: 0.6867 (tp30) cc_final: 0.6493 (tp30) REVERT: I 39 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7840 (mp10) REVERT: I 72 ASP cc_start: 0.7224 (t70) cc_final: 0.6874 (t0) REVERT: I 165 GLU cc_start: 0.7373 (tp30) cc_final: 0.6972 (tp30) REVERT: I 183 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7042 (mt) REVERT: I 199 ASP cc_start: 0.6402 (t0) cc_final: 0.6102 (t0) REVERT: I 238 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7208 (tm-30) REVERT: J 86 ILE cc_start: 0.7910 (mp) cc_final: 0.7675 (mt) REVERT: J 94 GLU cc_start: 0.6749 (pp20) cc_final: 0.6329 (pp20) REVERT: J 98 GLU cc_start: 0.6843 (tp30) cc_final: 0.6549 (tp30) REVERT: J 129 GLN cc_start: 0.7777 (tt0) cc_final: 0.7376 (mt0) REVERT: J 206 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7301 (tp30) REVERT: L 104 MET cc_start: 0.4913 (mmp) cc_final: 0.4625 (mmp) REVERT: L 220 LYS cc_start: 0.6064 (mmtm) cc_final: 0.5695 (mmtm) REVERT: L 256 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6773 (mtp85) REVERT: L 268 ASP cc_start: 0.7370 (p0) cc_final: 0.6592 (p0) REVERT: M 15 TRP cc_start: 0.7361 (m100) cc_final: 0.6911 (m-10) REVERT: M 35 ASP cc_start: 0.6975 (m-30) cc_final: 0.6525 (m-30) REVERT: M 38 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7417 (tm-30) REVERT: M 61 ASP cc_start: 0.7514 (t70) cc_final: 0.7233 (t0) REVERT: M 63 TRP cc_start: 0.5401 (m100) cc_final: 0.5176 (m100) REVERT: M 99 PHE cc_start: 0.7052 (m-80) cc_final: 0.6549 (m-80) REVERT: M 155 ARG cc_start: 0.7285 (mtt180) cc_final: 0.7017 (mtt180) REVERT: M 195 THR cc_start: 0.7922 (m) cc_final: 0.7435 (t) REVERT: M 259 ASP cc_start: 0.6912 (t0) cc_final: 0.6611 (t0) REVERT: M 267 LYS cc_start: 0.7526 (tptt) cc_final: 0.7214 (tppt) REVERT: N 213 GLN cc_start: 0.7785 (pp30) cc_final: 0.7446 (pp30) REVERT: N 241 THR cc_start: 0.8434 (t) cc_final: 0.8087 (p) REVERT: N 254 LYS cc_start: 0.7743 (tptt) cc_final: 0.7432 (tptt) REVERT: N 260 ARG cc_start: 0.6778 (mtm-85) cc_final: 0.6345 (mtm-85) REVERT: O 36 ILE cc_start: 0.7215 (mm) cc_final: 0.6978 (mm) REVERT: P 132 MET cc_start: 0.6457 (tpt) cc_final: 0.6174 (tpt) REVERT: P 201 PHE cc_start: 0.7637 (t80) cc_final: 0.7370 (t80) REVERT: P 230 LYS cc_start: 0.4938 (OUTLIER) cc_final: 0.4250 (mmmt) outliers start: 110 outliers final: 87 residues processed: 869 average time/residue: 0.2135 time to fit residues: 295.1970 Evaluate side-chains 916 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 821 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain Q residue 387 MET Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 256 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 75 optimal weight: 50.0000 chunk 275 optimal weight: 0.0570 chunk 254 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN J 204 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** 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 = 0.4750 r_free = 0.4750 target = 0.240409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182569 restraints weight = 66057.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.187868 restraints weight = 30753.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189426 restraints weight = 20326.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.190926 restraints weight = 16596.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.191587 restraints weight = 14590.325| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 36753 Z= 0.206 Angle : 0.749 21.742 50271 Z= 0.387 Chirality : 0.048 0.298 5432 Planarity : 0.005 0.051 5969 Dihedral : 17.046 146.392 5791 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.14 % Allowed : 19.54 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 3971 helix: 0.76 (0.12), residues: 1890 sheet: -0.08 (0.19), residues: 692 loop : -1.34 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 155 TYR 0.054 0.002 TYR B 70 PHE 0.039 0.002 PHE N 99 TRP 0.042 0.002 TRP P 106 HIS 0.039 0.001 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (36705) covalent geometry : angle 0.73084 / 0.39 (50248) hydrogen bonds : bond 0.04671 / 3.12 ( 1694) hydrogen bonds : angle 4.88050 / 3.49 ( 4842) metal coordination : bond 0.02312 / 1.44 ( 48) metal coordination : angle 7.71395 / 5.27 ( 23) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 842 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7228 (t70) cc_final: 0.6723 (t0) REVERT: A 98 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6743 (mm-30) REVERT: A 113 LYS cc_start: 0.7569 (mmmm) cc_final: 0.6875 (mmmm) REVERT: A 138 GLU cc_start: 0.6891 (mp0) cc_final: 0.6492 (mp0) REVERT: A 165 GLU cc_start: 0.7375 (tp30) cc_final: 0.6995 (tp30) REVERT: A 183 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7510 (mt) REVERT: A 223 PHE cc_start: 0.8285 (m-80) cc_final: 0.7408 (m-80) REVERT: A 238 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 254 LYS cc_start: 0.7603 (tppt) cc_final: 0.7262 (ttmt) REVERT: B 124 VAL cc_start: 0.8334 (p) cc_final: 0.8009 (m) REVERT: B 140 THR cc_start: 0.8028 (m) cc_final: 0.7773 (t) REVERT: B 208 GLN cc_start: 0.7843 (tt0) cc_final: 0.7610 (tt0) REVERT: C 9 GLU cc_start: 0.7546 (tp30) cc_final: 0.7316 (tp30) REVERT: C 24 LEU cc_start: 0.8145 (mm) cc_final: 0.7662 (mp) REVERT: C 203 PHE cc_start: 0.7061 (t80) cc_final: 0.6515 (t80) REVERT: C 204 ASN cc_start: 0.8193 (p0) cc_final: 0.7861 (p0) REVERT: C 207 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6084 (pm20) REVERT: C 267 LYS cc_start: 0.8233 (pttp) cc_final: 0.7844 (pttp) REVERT: D 103 THR cc_start: 0.6622 (t) cc_final: 0.5892 (p) REVERT: D 104 MET cc_start: 0.6784 (mmp) cc_final: 0.5895 (mmp) REVERT: D 132 MET cc_start: 0.8449 (ppp) cc_final: 0.8079 (ppp) REVERT: D 162 ASN cc_start: 0.7145 (m110) cc_final: 0.6816 (p0) REVERT: D 220 LYS cc_start: 0.5735 (mmtm) cc_final: 0.5497 (mmtm) REVERT: D 236 GLU cc_start: 0.6953 (mp0) cc_final: 0.6518 (mp0) REVERT: D 260 ARG cc_start: 0.6629 (mmm-85) cc_final: 0.6394 (mmm-85) REVERT: E 157 HIS cc_start: 0.8325 (m-70) cc_final: 0.7171 (m-70) REVERT: E 158 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7405 (mm-40) REVERT: E 161 LYS cc_start: 0.8506 (mttt) cc_final: 0.7956 (mttt) REVERT: E 195 THR cc_start: 0.7978 (m) cc_final: 0.7444 (t) REVERT: E 208 GLN cc_start: 0.7616 (tp40) cc_final: 0.7102 (tm-30) REVERT: E 270 LYS cc_start: 0.6795 (mtpt) cc_final: 0.6360 (mtmt) REVERT: F 64 GLN cc_start: 0.5776 (tp40) cc_final: 0.5212 (tp40) REVERT: F 110 PHE cc_start: 0.7871 (m-10) cc_final: 0.7387 (m-80) REVERT: F 213 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7821 (pp30) REVERT: F 254 LYS cc_start: 0.8101 (tptt) cc_final: 0.7806 (tptt) REVERT: G 150 GLN cc_start: 0.7944 (mm110) cc_final: 0.7543 (mm110) REVERT: H 86 ILE cc_start: 0.6500 (mp) cc_final: 0.6214 (mp) REVERT: H 201 PHE cc_start: 0.8095 (t80) cc_final: 0.7510 (t80) REVERT: H 205 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7549 (mmmm) REVERT: H 242 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7641 (tp-100) REVERT: R 368 LEU cc_start: 0.4857 (OUTLIER) cc_final: 0.4590 (mm) REVERT: R 418 MET cc_start: 0.7408 (ppp) cc_final: 0.6845 (ppp) REVERT: Q 360 LYS cc_start: 0.6148 (ptpp) cc_final: 0.5728 (ptpp) REVERT: Q 413 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5839 (mmt) REVERT: Q 418 MET cc_start: 0.7527 (ppp) cc_final: 0.6943 (ppp) REVERT: I 10 GLU cc_start: 0.6921 (tp30) cc_final: 0.6586 (tp30) REVERT: I 39 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7878 (mp10) REVERT: I 72 ASP cc_start: 0.7136 (t70) cc_final: 0.6840 (t0) REVERT: I 165 GLU cc_start: 0.7320 (tp30) cc_final: 0.6940 (tp30) REVERT: I 183 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7386 (mt) REVERT: I 199 ASP cc_start: 0.6558 (t0) cc_final: 0.6245 (t0) REVERT: I 238 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7287 (tm-30) REVERT: J 86 ILE cc_start: 0.7841 (mp) cc_final: 0.7619 (mt) REVERT: J 94 GLU cc_start: 0.6789 (pp20) cc_final: 0.6386 (pp20) REVERT: J 98 GLU cc_start: 0.6954 (tp30) cc_final: 0.6698 (tp30) REVERT: J 105 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7756 (mtpt) REVERT: J 129 GLN cc_start: 0.7768 (tt0) cc_final: 0.7407 (mt0) REVERT: L 80 GLU cc_start: 0.7420 (tp30) cc_final: 0.7112 (tp30) REVERT: L 104 MET cc_start: 0.5436 (mmp) cc_final: 0.5076 (mmp) REVERT: L 220 LYS cc_start: 0.6061 (mmtm) cc_final: 0.5794 (mmtm) REVERT: L 256 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6297 (mtp85) REVERT: M 35 ASP cc_start: 0.7025 (m-30) cc_final: 0.6611 (m-30) REVERT: M 38 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7473 (tm-30) REVERT: M 61 ASP cc_start: 0.7678 (t70) cc_final: 0.7206 (t0) REVERT: M 63 TRP cc_start: 0.5578 (m100) cc_final: 0.5229 (m100) REVERT: M 99 PHE cc_start: 0.7618 (m-80) cc_final: 0.6852 (m-80) REVERT: M 195 THR cc_start: 0.7945 (m) cc_final: 0.7423 (t) REVERT: M 208 GLN cc_start: 0.7129 (tm-30) cc_final: 0.6735 (tm-30) REVERT: M 211 GLN cc_start: 0.7405 (pp30) cc_final: 0.7132 (pp30) REVERT: M 212 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7697 (mm-40) REVERT: M 245 TRP cc_start: 0.7630 (t60) cc_final: 0.6846 (t-100) REVERT: M 259 ASP cc_start: 0.7662 (t0) cc_final: 0.7391 (t0) REVERT: M 267 LYS cc_start: 0.7754 (tptt) cc_final: 0.7412 (tppt) REVERT: M 271 PHE cc_start: 0.7040 (m-80) cc_final: 0.6388 (m-80) REVERT: N 213 GLN cc_start: 0.7829 (pp30) cc_final: 0.7459 (pp30) REVERT: N 241 THR cc_start: 0.8401 (t) cc_final: 0.8127 (p) REVERT: N 254 LYS cc_start: 0.7642 (tptt) cc_final: 0.7387 (tptt) REVERT: N 260 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6425 (mtm-85) REVERT: P 106 TRP cc_start: 0.5562 (t60) cc_final: 0.5165 (t60) REVERT: P 132 MET cc_start: 0.8014 (tpt) cc_final: 0.7167 (tpt) REVERT: P 201 PHE cc_start: 0.8309 (t80) cc_final: 0.7947 (t80) REVERT: P 230 LYS cc_start: 0.6174 (OUTLIER) cc_final: 0.5053 (mmmt) outliers start: 111 outliers final: 92 residues processed: 887 average time/residue: 0.2200 time to fit residues: 311.3279 Evaluate side-chains 928 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 829 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain Q residue 387 MET Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain J residue 211 GLN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 256 ARG Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 321 optimal weight: 0.0010 chunk 383 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 389 optimal weight: 0.7980 chunk 62 optimal weight: 0.0670 chunk 348 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.242158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.187922 restraints weight = 66403.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.190254 restraints weight = 36064.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.190336 restraints weight = 23176.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.191251 restraints weight = 21801.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.191518 restraints weight = 19934.502| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36753 Z= 0.145 Angle : 0.735 19.538 50271 Z= 0.375 Chirality : 0.046 0.278 5432 Planarity : 0.004 0.067 5969 Dihedral : 17.018 146.255 5791 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.08 % Allowed : 19.96 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 3971 helix: 0.85 (0.12), residues: 1892 sheet: -0.04 (0.20), residues: 680 loop : -1.22 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 155 TYR 0.017 0.001 TYR O 87 PHE 0.040 0.001 PHE N 99 TRP 0.032 0.001 TRP P 106 HIS 0.017 0.001 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (36705) covalent geometry : angle 0.71790 / 0.37 (50248) hydrogen bonds : bond 0.04111 / 2.74 ( 1694) hydrogen bonds : angle 4.77967 / 3.42 ( 4842) metal coordination : bond 0.02013 / 1.26 ( 48) metal coordination : angle 7.48324 / 5.22 ( 23) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 829 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7216 (t70) cc_final: 0.6760 (t0) REVERT: A 138 GLU cc_start: 0.6893 (mp0) cc_final: 0.6475 (mp0) REVERT: A 165 GLU cc_start: 0.7391 (tp30) cc_final: 0.7043 (tp30) REVERT: A 183 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7521 (mt) REVERT: A 223 PHE cc_start: 0.8320 (m-80) cc_final: 0.7576 (m-80) REVERT: A 238 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7462 (tm-30) REVERT: B 124 VAL cc_start: 0.8279 (p) cc_final: 0.7971 (m) REVERT: B 140 THR cc_start: 0.8023 (m) cc_final: 0.7751 (t) REVERT: B 208 GLN cc_start: 0.7773 (tt0) cc_final: 0.7499 (tt0) REVERT: C 9 GLU cc_start: 0.7548 (tp30) cc_final: 0.7311 (tp30) REVERT: C 24 LEU cc_start: 0.8137 (mm) cc_final: 0.7638 (mp) REVERT: C 203 PHE cc_start: 0.6996 (t80) cc_final: 0.6460 (t80) REVERT: C 204 ASN cc_start: 0.8180 (p0) cc_final: 0.7767 (p0) REVERT: C 207 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: C 208 GLN cc_start: 0.6675 (pp30) cc_final: 0.6266 (pp30) REVERT: C 267 LYS cc_start: 0.8190 (pttp) cc_final: 0.7777 (pttp) REVERT: D 103 THR cc_start: 0.6531 (t) cc_final: 0.5802 (p) REVERT: D 104 MET cc_start: 0.6731 (mmp) cc_final: 0.5803 (mmp) REVERT: D 132 MET cc_start: 0.8368 (ppp) cc_final: 0.8010 (ppp) REVERT: D 162 ASN cc_start: 0.7237 (m110) cc_final: 0.6911 (p0) REVERT: D 220 LYS cc_start: 0.5649 (mmtm) cc_final: 0.5391 (mmtm) REVERT: D 236 GLU cc_start: 0.7026 (mp0) cc_final: 0.6569 (mp0) REVERT: D 260 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.6361 (mmm-85) REVERT: E 35 ASP cc_start: 0.6753 (m-30) cc_final: 0.6227 (m-30) REVERT: E 157 HIS cc_start: 0.8186 (m-70) cc_final: 0.7066 (m-70) REVERT: E 158 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7411 (mm-40) REVERT: E 161 LYS cc_start: 0.8510 (mttt) cc_final: 0.7946 (mttt) REVERT: E 195 THR cc_start: 0.7860 (m) cc_final: 0.7365 (t) REVERT: E 208 GLN cc_start: 0.7525 (tp40) cc_final: 0.7063 (tm-30) REVERT: E 213 GLN cc_start: 0.6843 (pp30) cc_final: 0.6317 (pp30) REVERT: E 270 LYS cc_start: 0.6780 (mtpt) cc_final: 0.6317 (mtmt) REVERT: F 110 PHE cc_start: 0.7761 (m-10) cc_final: 0.7145 (m-80) REVERT: F 213 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7759 (pp30) REVERT: F 254 LYS cc_start: 0.8132 (tptt) cc_final: 0.7829 (tptt) REVERT: G 150 GLN cc_start: 0.7845 (mm110) cc_final: 0.7423 (mm110) REVERT: G 155 ARG cc_start: 0.7891 (pmt170) cc_final: 0.7640 (tpt170) REVERT: H 86 ILE cc_start: 0.6342 (mp) cc_final: 0.6072 (mp) REVERT: H 201 PHE cc_start: 0.8049 (t80) cc_final: 0.7485 (t80) REVERT: H 205 LYS cc_start: 0.8140 (mmmm) cc_final: 0.7468 (mmmm) REVERT: H 225 TYR cc_start: 0.5111 (m-80) cc_final: 0.4906 (m-80) REVERT: H 242 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7782 (tp-100) REVERT: H 272 ILE cc_start: 0.8044 (mp) cc_final: 0.7680 (mp) REVERT: R 368 LEU cc_start: 0.4788 (OUTLIER) cc_final: 0.4569 (mm) REVERT: R 418 MET cc_start: 0.7388 (ppp) cc_final: 0.6811 (ppp) REVERT: Q 360 LYS cc_start: 0.6108 (ptpp) cc_final: 0.5669 (ptpp) REVERT: Q 413 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.5821 (mmt) REVERT: Q 418 MET cc_start: 0.7497 (ppp) cc_final: 0.6941 (ppp) REVERT: I 37 VAL cc_start: 0.8234 (p) cc_final: 0.8000 (t) REVERT: I 39 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7851 (mp10) REVERT: I 52 LEU cc_start: 0.8279 (mp) cc_final: 0.8017 (mt) REVERT: I 72 ASP cc_start: 0.7115 (t70) cc_final: 0.6813 (t70) REVERT: I 165 GLU cc_start: 0.7307 (tp30) cc_final: 0.6970 (tp30) REVERT: I 183 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7341 (mt) REVERT: I 199 ASP cc_start: 0.6346 (t0) cc_final: 0.6010 (t0) REVERT: I 238 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7201 (tm-30) REVERT: J 86 ILE cc_start: 0.7834 (mp) cc_final: 0.7601 (mt) REVERT: J 94 GLU cc_start: 0.6781 (pp20) cc_final: 0.6368 (pp20) REVERT: J 98 GLU cc_start: 0.6938 (tp30) cc_final: 0.6678 (tp30) REVERT: J 129 GLN cc_start: 0.7703 (tt0) cc_final: 0.7347 (mt0) REVERT: K 11 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6420 (mt-10) REVERT: L 104 MET cc_start: 0.5355 (mmp) cc_final: 0.4991 (mmp) REVERT: L 220 LYS cc_start: 0.5944 (mmtm) cc_final: 0.5622 (mmtm) REVERT: M 35 ASP cc_start: 0.6892 (m-30) cc_final: 0.6464 (m-30) REVERT: M 38 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7552 (tm-30) REVERT: M 61 ASP cc_start: 0.7615 (t70) cc_final: 0.7149 (t0) REVERT: M 63 TRP cc_start: 0.5619 (m100) cc_final: 0.5348 (m100) REVERT: M 99 PHE cc_start: 0.7684 (m-80) cc_final: 0.6838 (m-80) REVERT: M 164 LEU cc_start: 0.8129 (mt) cc_final: 0.7391 (pp) REVERT: M 195 THR cc_start: 0.7821 (m) cc_final: 0.7349 (t) REVERT: M 245 TRP cc_start: 0.7588 (t60) cc_final: 0.6874 (t-100) REVERT: M 259 ASP cc_start: 0.7699 (t0) cc_final: 0.7437 (t0) REVERT: M 267 LYS cc_start: 0.7757 (tptt) cc_final: 0.7412 (tppt) REVERT: N 105 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8126 (mtmm) REVERT: N 213 GLN cc_start: 0.7727 (pp30) cc_final: 0.7353 (pp30) REVERT: N 241 THR cc_start: 0.8477 (t) cc_final: 0.8177 (p) REVERT: N 254 LYS cc_start: 0.7669 (tptt) cc_final: 0.7388 (tptt) REVERT: N 260 ARG cc_start: 0.6792 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: P 106 TRP cc_start: 0.5502 (t60) cc_final: 0.5102 (t60) REVERT: P 132 MET cc_start: 0.7976 (tpt) cc_final: 0.7200 (tpt) REVERT: P 201 PHE cc_start: 0.8275 (t80) cc_final: 0.7924 (t80) REVERT: P 230 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5210 (tptm) REVERT: P 276 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7675 (mmtt) outliers start: 109 outliers final: 86 residues processed: 875 average time/residue: 0.2186 time to fit residues: 305.7424 Evaluate side-chains 915 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 822 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain Q residue 387 MET Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 323 optimal weight: 0.0270 chunk 307 optimal weight: 0.9980 chunk 342 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 264 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 285 optimal weight: 0.6980 chunk 400 optimal weight: 0.0670 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.242291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.188123 restraints weight = 66880.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190621 restraints weight = 43685.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190965 restraints weight = 25479.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191704 restraints weight = 23833.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.192217 restraints weight = 21397.184| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36753 Z= 0.144 Angle : 0.742 18.900 50271 Z= 0.378 Chirality : 0.046 0.263 5432 Planarity : 0.004 0.062 5969 Dihedral : 17.021 146.029 5791 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 20.87 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 3971 helix: 0.90 (0.12), residues: 1889 sheet: -0.12 (0.19), residues: 734 loop : -1.21 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 155 TYR 0.020 0.001 TYR O 87 PHE 0.041 0.001 PHE N 99 TRP 0.032 0.001 TRP H 78 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (36705) covalent geometry : angle 0.72644 / 0.38 (50248) hydrogen bonds : bond 0.04046 / 2.69 ( 1694) hydrogen bonds : angle 4.76006 / 3.40 ( 4842) metal coordination : bond 0.01893 / 1.17 ( 48) metal coordination : angle 7.12121 / 4.95 ( 23) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 837 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7242 (t70) cc_final: 0.6755 (t0) REVERT: A 113 LYS cc_start: 0.7585 (mmmm) cc_final: 0.6857 (mmmm) REVERT: A 138 GLU cc_start: 0.6916 (mp0) cc_final: 0.6488 (mp0) REVERT: A 165 GLU cc_start: 0.7405 (tp30) cc_final: 0.7053 (tp30) REVERT: A 183 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (mt) REVERT: A 223 PHE cc_start: 0.8328 (m-80) cc_final: 0.7633 (m-80) REVERT: A 238 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 124 VAL cc_start: 0.8336 (p) cc_final: 0.8042 (m) REVERT: B 140 THR cc_start: 0.7995 (m) cc_final: 0.7723 (t) REVERT: B 208 GLN cc_start: 0.7778 (tt0) cc_final: 0.7522 (tt0) REVERT: C 9 GLU cc_start: 0.7536 (tp30) cc_final: 0.7316 (tp30) REVERT: C 24 LEU cc_start: 0.8138 (mm) cc_final: 0.7623 (mp) REVERT: C 203 PHE cc_start: 0.7002 (t80) cc_final: 0.6546 (t80) REVERT: C 204 ASN cc_start: 0.8164 (p0) cc_final: 0.7786 (p0) REVERT: C 207 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.6032 (pm20) REVERT: C 267 LYS cc_start: 0.8181 (pttp) cc_final: 0.7765 (pttp) REVERT: D 103 THR cc_start: 0.6420 (t) cc_final: 0.5730 (p) REVERT: D 104 MET cc_start: 0.6673 (mmp) cc_final: 0.5759 (mmp) REVERT: D 132 MET cc_start: 0.8326 (ppp) cc_final: 0.7976 (ppp) REVERT: D 162 ASN cc_start: 0.7232 (m110) cc_final: 0.6764 (p0) REVERT: D 220 LYS cc_start: 0.5685 (mmtm) cc_final: 0.5439 (mmtm) REVERT: D 236 GLU cc_start: 0.6906 (mp0) cc_final: 0.6407 (mp0) REVERT: D 260 ARG cc_start: 0.6824 (mmm-85) cc_final: 0.6536 (mmm-85) REVERT: E 25 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6006 (mm-30) REVERT: E 35 ASP cc_start: 0.7004 (m-30) cc_final: 0.6494 (m-30) REVERT: E 157 HIS cc_start: 0.8182 (m-70) cc_final: 0.7336 (m-70) REVERT: E 158 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7397 (mm-40) REVERT: E 161 LYS cc_start: 0.8469 (mttt) cc_final: 0.7914 (mttt) REVERT: E 195 THR cc_start: 0.7855 (m) cc_final: 0.7360 (t) REVERT: E 202 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7631 (mm) REVERT: E 208 GLN cc_start: 0.7441 (tp40) cc_final: 0.7108 (tm-30) REVERT: E 212 GLN cc_start: 0.7584 (mp10) cc_final: 0.6380 (mp10) REVERT: E 213 GLN cc_start: 0.6870 (pp30) cc_final: 0.6412 (pp30) REVERT: E 270 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6459 (mtmt) REVERT: F 64 GLN cc_start: 0.5717 (tp40) cc_final: 0.5369 (tp40) REVERT: F 110 PHE cc_start: 0.7691 (m-10) cc_final: 0.7101 (m-80) REVERT: F 213 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7575 (pp30) REVERT: F 254 LYS cc_start: 0.8119 (tptt) cc_final: 0.7808 (tptt) REVERT: G 150 GLN cc_start: 0.7772 (mm110) cc_final: 0.7392 (mm110) REVERT: G 205 LYS cc_start: 0.6556 (mmtm) cc_final: 0.5927 (mmtm) REVERT: H 86 ILE cc_start: 0.6161 (mp) cc_final: 0.5900 (mp) REVERT: H 201 PHE cc_start: 0.7939 (t80) cc_final: 0.7344 (t80) REVERT: H 205 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7363 (mmmm) REVERT: H 242 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7184 (tp-100) REVERT: H 272 ILE cc_start: 0.7972 (mp) cc_final: 0.7607 (mp) REVERT: R 368 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4613 (mm) REVERT: R 418 MET cc_start: 0.7364 (ppp) cc_final: 0.6784 (ppp) REVERT: Q 360 LYS cc_start: 0.6209 (ptpp) cc_final: 0.5775 (ptpp) REVERT: Q 413 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5737 (mmt) REVERT: Q 418 MET cc_start: 0.7469 (ppp) cc_final: 0.6902 (ppp) REVERT: I 37 VAL cc_start: 0.8268 (p) cc_final: 0.8004 (t) REVERT: I 39 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7834 (mp10) REVERT: I 52 LEU cc_start: 0.8277 (mp) cc_final: 0.7979 (mt) REVERT: I 72 ASP cc_start: 0.7131 (t70) cc_final: 0.6830 (t70) REVERT: I 165 GLU cc_start: 0.7313 (tp30) cc_final: 0.6979 (tp30) REVERT: I 183 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7356 (mt) REVERT: I 199 ASP cc_start: 0.6446 (t0) cc_final: 0.6146 (t0) REVERT: I 238 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7124 (tm-30) REVERT: J 86 ILE cc_start: 0.7833 (mp) cc_final: 0.7591 (mt) REVERT: J 94 GLU cc_start: 0.6778 (pp20) cc_final: 0.6366 (pp20) REVERT: J 98 GLU cc_start: 0.6916 (tp30) cc_final: 0.6658 (tp30) REVERT: J 129 GLN cc_start: 0.7665 (tt0) cc_final: 0.7208 (mt0) REVERT: L 104 MET cc_start: 0.5345 (mmp) cc_final: 0.4991 (mmp) REVERT: L 220 LYS cc_start: 0.5927 (mmtm) cc_final: 0.5650 (mmtm) REVERT: M 15 TRP cc_start: 0.7320 (m100) cc_final: 0.6345 (m-10) REVERT: M 28 ILE cc_start: 0.6981 (pt) cc_final: 0.6759 (mm) REVERT: M 35 ASP cc_start: 0.6887 (m-30) cc_final: 0.6441 (m-30) REVERT: M 38 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7534 (tm-30) REVERT: M 61 ASP cc_start: 0.7567 (t70) cc_final: 0.7129 (t0) REVERT: M 63 TRP cc_start: 0.5575 (m100) cc_final: 0.5362 (m100) REVERT: M 99 PHE cc_start: 0.7566 (m-80) cc_final: 0.6733 (m-80) REVERT: M 195 THR cc_start: 0.7788 (m) cc_final: 0.7329 (t) REVERT: M 245 TRP cc_start: 0.7512 (t60) cc_final: 0.6878 (t-100) REVERT: M 259 ASP cc_start: 0.7655 (t0) cc_final: 0.7390 (t0) REVERT: M 267 LYS cc_start: 0.7750 (tptt) cc_final: 0.7404 (tppt) REVERT: N 105 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8134 (mtmm) REVERT: N 213 GLN cc_start: 0.7746 (pp30) cc_final: 0.7367 (pp30) REVERT: N 241 THR cc_start: 0.8466 (t) cc_final: 0.8172 (p) REVERT: N 254 LYS cc_start: 0.7664 (tptt) cc_final: 0.7405 (tptt) REVERT: N 260 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: P 106 TRP cc_start: 0.5398 (t60) cc_final: 0.4963 (t60) REVERT: P 132 MET cc_start: 0.7847 (tpt) cc_final: 0.7016 (tpt) REVERT: P 201 PHE cc_start: 0.8203 (t80) cc_final: 0.7895 (t80) REVERT: P 203 PHE cc_start: 0.8420 (t80) cc_final: 0.7954 (t80) REVERT: P 230 LYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5130 (tptm) outliers start: 91 outliers final: 79 residues processed: 875 average time/residue: 0.2253 time to fit residues: 314.8896 Evaluate side-chains 911 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 824 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 82 ASN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain Q residue 387 MET Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 130 LEU Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain M residue 224 CYS Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 230 LYS Chi-restraints excluded: chain P residue 251 ILE Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 77 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 379 optimal weight: 7.9990 chunk 310 optimal weight: 0.2980 chunk 169 optimal weight: 0.7980 chunk 350 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 299 optimal weight: 0.7980 chunk 271 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.240835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183822 restraints weight = 64077.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.188751 restraints weight = 29165.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.191701 restraints weight = 17942.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.193538 restraints weight = 13665.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.194286 restraints weight = 11734.160| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36753 Z= 0.157 Angle : 0.761 19.207 50271 Z= 0.387 Chirality : 0.047 0.261 5432 Planarity : 0.005 0.093 5969 Dihedral : 17.044 146.057 5791 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.60 % Allowed : 21.09 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 3971 helix: 0.88 (0.12), residues: 1883 sheet: -0.03 (0.19), residues: 714 loop : -1.25 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 231 TYR 0.037 0.002 TYR B 70 PHE 0.041 0.001 PHE N 99 TRP 0.042 0.002 TRP M 15 HIS 0.032 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (36705) covalent geometry : angle 0.74620 / 0.39 (50248) hydrogen bonds : bond 0.04112 / 2.72 ( 1694) hydrogen bonds : angle 4.77058 / 3.42 ( 4842) metal coordination : bond 0.01924 / 1.19 ( 48) metal coordination : angle 7.00387 / 4.86 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.19 seconds wall clock time: 133 minutes 38.84 seconds (8018.84 seconds total)