Starting phenix.real_space_refine on Fri Mar 6 23:19:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1z_14453/03_2026/7z1z_14453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1z_14453/03_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_14453/03_2026/7z1z_14453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1z_14453/03_2026/7z1z_14453.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1z_14453/03_2026/7z1z_14453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1z_14453/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.04, per 1000 atoms: 0.25 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 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: 4.27 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: 7.67 Time building geometry restraints manager: 4.09 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=" C ILE H 168 " pdb=" N PRO H 169 " ideal model delta sigma weight residual 1.336 1.365 -0.029 1.20e-02 6.94e+03 5.66e+00 bond pdb=" C ILE P 168 " pdb=" N PRO P 169 " ideal model delta sigma weight residual 1.336 1.364 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C ILE E 168 " pdb=" N PRO E 169 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.50e-01 bond pdb=" CB GLN A 211 " pdb=" CG GLN A 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.36e-01 bond pdb=" CB GLN I 211 " pdb=" CG GLN I 211 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.18e-01 ... (remaining 36700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 49096 1.39 - 2.77: 891 2.77 - 4.16: 184 4.16 - 5.54: 43 5.54 - 6.93: 34 Bond angle restraints: 50248 Sorted by residual: angle pdb=" CA GLY L 247 " pdb=" C GLY L 247 " pdb=" N ASP L 248 " ideal model delta sigma weight residual 114.65 117.17 -2.52 9.20e-01 1.18e+00 7.49e+00 angle pdb=" CA GLY D 247 " pdb=" C GLY D 247 " pdb=" N ASP D 248 " ideal model delta sigma weight residual 114.65 117.14 -2.49 9.20e-01 1.18e+00 7.35e+00 angle pdb=" N ILE D 168 " pdb=" CA ILE D 168 " pdb=" C ILE D 168 " ideal model delta sigma weight residual 108.88 114.48 -5.60 2.16e+00 2.14e-01 6.73e+00 angle pdb=" N ILE L 168 " pdb=" CA ILE L 168 " pdb=" C ILE L 168 " ideal model delta sigma weight residual 108.88 114.47 -5.59 2.16e+00 2.14e-01 6.70e+00 angle pdb=" CA GLN I 211 " pdb=" CB GLN I 211 " pdb=" CG GLN I 211 " ideal model delta sigma weight residual 114.10 119.21 -5.11 2.00e+00 2.50e-01 6.52e+00 ... (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: 3805 0.034 - 0.069: 1108 0.069 - 0.103: 368 0.103 - 0.137: 139 0.137 - 0.172: 12 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: 2.930 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 39.740 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 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= 0.117 Angle : 1.170 75.246 50271 Z= 0.340 Chirality : 0.040 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 covalent geometry : bond 0.00218 (36705) covalent geometry : angle 0.51033 (50248) hydrogen bonds : bond 0.21904 ( 1694) hydrogen bonds : angle 7.66322 ( 4842) metal coordination : bond 0.05432 ( 48) metal coordination : angle 49.21018 ( 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 : 1.274 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: 0.2222 time to fit residues: 329.0099 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 : 1.064 ------------------------------------------------------------------------------- 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 139 HIS ** 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 129 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 39 GLN 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** O 82 ASN O 212 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.246948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.191290 restraints weight = 64686.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.196839 restraints weight = 30375.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.198710 restraints weight = 18933.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.200269 restraints weight = 15013.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.200928 restraints weight = 12373.591| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 36753 Z= 0.164 Angle : 0.690 23.455 50271 Z= 0.347 Chirality : 0.045 0.156 5432 Planarity : 0.005 0.072 5969 Dihedral : 16.225 140.909 5791 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.30 % Allowed : 9.22 % Favored : 89.48 % 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: 0.28 (0.13), residues: 3971 helix: 1.23 (0.12), residues: 1880 sheet: 0.08 (0.19), residues: 754 loop : -1.19 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 222 TYR 0.022 0.002 TYR N 134 PHE 0.023 0.001 PHE E 203 TRP 0.033 0.001 TRP P 245 HIS 0.019 0.002 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00340 (36705) covalent geometry : angle 0.64351 (50248) hydrogen bonds : bond 0.05725 ( 1694) hydrogen bonds : angle 5.24190 ( 4842) metal coordination : bond 0.04301 ( 48) metal coordination : angle 11.66887 ( 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 919 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 873 time to evaluate : 1.095 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 34 GLU cc_start: 0.6287 (OUTLIER) cc_final: 0.6081 (tp30) REVERT: A 76 LEU cc_start: 0.8193 (tp) cc_final: 0.7986 (tp) REVERT: A 98 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6948 (mm-30) REVERT: A 162 ASN cc_start: 0.8165 (t0) cc_final: 0.7696 (t0) REVERT: A 199 ASP cc_start: 0.6859 (t0) cc_final: 0.6528 (t0) REVERT: A 206 GLU cc_start: 0.6708 (tp30) cc_final: 0.6327 (tm-30) REVERT: A 223 PHE cc_start: 0.8184 (m-80) cc_final: 0.7566 (m-80) REVERT: A 238 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 140 THR cc_start: 0.8052 (m) cc_final: 0.7814 (t) REVERT: B 185 LEU cc_start: 0.7566 (mt) cc_final: 0.6997 (mp) REVERT: B 206 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6974 (tp30) REVERT: B 208 GLN cc_start: 0.7546 (tt0) cc_final: 0.7225 (tt0) REVERT: C 9 GLU cc_start: 0.7772 (tp30) cc_final: 0.7552 (tp30) REVERT: C 24 LEU cc_start: 0.8184 (mm) cc_final: 0.7755 (mp) REVERT: C 186 ASN cc_start: 0.8207 (m-40) cc_final: 0.7979 (t0) REVERT: C 203 PHE cc_start: 0.7070 (t80) cc_final: 0.6692 (t80) REVERT: C 205 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8088 (mmmt) REVERT: C 245 TRP cc_start: 0.7871 (m-90) cc_final: 0.7466 (m-90) REVERT: C 267 LYS cc_start: 0.8286 (pttp) cc_final: 0.7887 (pttp) REVERT: D 70 TYR cc_start: 0.6745 (t80) cc_final: 0.6521 (t80) REVERT: D 103 THR cc_start: 0.6670 (t) cc_final: 0.5995 (p) REVERT: D 104 MET cc_start: 0.6755 (mmp) cc_final: 0.5764 (mmp) REVERT: D 205 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7326 (tppt) REVERT: D 212 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6673 (tm-30) REVERT: D 236 GLU cc_start: 0.6928 (mp0) cc_final: 0.6626 (mp0) REVERT: D 238 GLN cc_start: 0.8434 (mt0) cc_final: 0.8143 (mt0) REVERT: D 268 ASP cc_start: 0.7035 (p0) cc_final: 0.6434 (p0) REVERT: E 61 ASP cc_start: 0.7699 (t70) cc_final: 0.7442 (t0) REVERT: E 99 PHE cc_start: 0.7284 (m-80) cc_final: 0.6783 (m-80) REVERT: E 129 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7407 (mm110) REVERT: E 153 VAL cc_start: 0.8762 (t) cc_final: 0.7556 (p) REVERT: E 163 THR cc_start: 0.7565 (p) cc_final: 0.7091 (p) REVERT: E 181 THR cc_start: 0.8303 (p) cc_final: 0.7805 (t) REVERT: E 202 ILE cc_start: 0.7987 (tp) cc_final: 0.7762 (tp) REVERT: E 212 GLN cc_start: 0.7579 (mp10) cc_final: 0.7234 (mm-40) REVERT: E 225 TYR cc_start: 0.5074 (t80) cc_final: 0.4362 (t80) REVERT: E 270 LYS cc_start: 0.7055 (mtpt) cc_final: 0.6577 (mtpt) REVERT: E 271 PHE cc_start: 0.7090 (m-80) cc_final: 0.6561 (m-80) REVERT: F 230 LYS cc_start: 0.8241 (tppp) cc_final: 0.7838 (tppp) REVERT: F 254 LYS cc_start: 0.7987 (tmtt) cc_final: 0.7755 (tptt) REVERT: G 110 PHE cc_start: 0.7373 (m-80) cc_final: 0.6968 (m-10) REVERT: G 155 ARG cc_start: 0.8060 (pmt170) cc_final: 0.7681 (tpt170) REVERT: G 211 GLN cc_start: 0.6156 (mm-40) cc_final: 0.5946 (tp40) REVERT: H 132 MET cc_start: 0.7517 (tpt) cc_final: 0.6939 (tpt) REVERT: H 201 PHE cc_start: 0.8000 (t80) cc_final: 0.7598 (t80) REVERT: H 205 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7819 (mmmm) REVERT: H 206 GLU cc_start: 0.6758 (pp20) cc_final: 0.6471 (pp20) REVERT: H 262 LEU cc_start: 0.6736 (mm) cc_final: 0.6487 (mm) REVERT: R 413 MET cc_start: 0.6409 (mmm) cc_final: 0.6037 (mmm) REVERT: R 418 MET cc_start: 0.7407 (ppp) cc_final: 0.6821 (ppp) REVERT: Q 360 LYS cc_start: 0.5521 (ptpp) cc_final: 0.5266 (ptpp) REVERT: Q 418 MET cc_start: 0.7450 (ppp) cc_final: 0.6856 (ppp) REVERT: I 35 ASP cc_start: 0.7299 (t70) cc_final: 0.7090 (t70) REVERT: I 72 ASP cc_start: 0.7100 (t70) cc_final: 0.6814 (t70) REVERT: I 98 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6633 (mm-30) REVERT: J 129 GLN cc_start: 0.7568 (tt0) cc_final: 0.7054 (mt0) REVERT: J 190 LYS cc_start: 0.8092 (mttp) cc_final: 0.7877 (mtpp) REVERT: J 206 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7472 (tp30) REVERT: J 211 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6771 (tm-30) REVERT: K 109 MET cc_start: 0.7609 (tpp) cc_final: 0.7291 (pmm) REVERT: L 104 MET cc_start: 0.5347 (mmp) cc_final: 0.4924 (mmp) REVERT: L 110 PHE cc_start: 0.6985 (m-80) cc_final: 0.6598 (t80) REVERT: L 133 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8124 (mmmt) REVERT: L 221 ILE cc_start: 0.6950 (mt) cc_final: 0.6646 (tt) REVERT: L 260 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.6356 (mmm-85) REVERT: L 268 ASP cc_start: 0.7150 (p0) cc_final: 0.6795 (p0) REVERT: M 7 LEU cc_start: 0.7924 (tt) cc_final: 0.7717 (tt) REVERT: M 35 ASP cc_start: 0.6535 (m-30) cc_final: 0.6092 (m-30) REVERT: M 38 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7229 (tm-30) REVERT: M 61 ASP cc_start: 0.7186 (t70) cc_final: 0.6526 (t0) REVERT: M 99 PHE cc_start: 0.7566 (m-80) cc_final: 0.6955 (m-80) REVERT: M 207 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7543 (mm-40) REVERT: M 208 GLN cc_start: 0.7546 (tm-30) cc_final: 0.6983 (tm-30) REVERT: M 226 TYR cc_start: 0.5218 (p90) cc_final: 0.4917 (p90) REVERT: M 259 ASP cc_start: 0.7469 (t0) cc_final: 0.7266 (t0) REVERT: M 271 PHE cc_start: 0.6771 (m-80) cc_final: 0.6121 (m-80) REVERT: N 213 GLN cc_start: 0.7646 (pp30) cc_final: 0.7186 (pp30) REVERT: N 241 THR cc_start: 0.8122 (t) cc_final: 0.7759 (m) REVERT: N 252 VAL cc_start: 0.8204 (p) cc_final: 0.7956 (m) REVERT: N 260 ARG cc_start: 0.6725 (mtm-85) cc_final: 0.6324 (mtm-85) REVERT: O 104 MET cc_start: 0.7021 (mmp) cc_final: 0.6109 (mmp) REVERT: O 110 PHE cc_start: 0.7256 (m-80) cc_final: 0.6951 (m-80) REVERT: O 132 MET cc_start: 0.8223 (mpp) cc_final: 0.7806 (mpp) REVERT: O 155 ARG cc_start: 0.8447 (pmt170) cc_final: 0.7987 (tpt170) REVERT: O 200 ILE cc_start: 0.8208 (mm) cc_final: 0.7950 (mm) REVERT: O 201 PHE cc_start: 0.8150 (t80) cc_final: 0.7929 (t80) REVERT: O 204 ASN cc_start: 0.8631 (m110) cc_final: 0.8281 (p0) REVERT: O 208 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7260 (tm-30) REVERT: P 63 TRP cc_start: 0.6557 (m100) cc_final: 0.5952 (m100) REVERT: P 110 PHE cc_start: 0.6935 (m-80) cc_final: 0.6624 (m-80) REVERT: P 132 MET cc_start: 0.7810 (tpt) cc_final: 0.7033 (tpt) REVERT: P 187 ILE cc_start: 0.8422 (mt) cc_final: 0.8186 (pt) REVERT: P 201 PHE cc_start: 0.8305 (t80) cc_final: 0.7388 (t80) REVERT: P 202 ILE cc_start: 0.8641 (pt) cc_final: 0.8336 (pt) REVERT: P 205 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7198 (mmmm) REVERT: P 206 GLU cc_start: 0.6691 (pp20) cc_final: 0.6053 (pp20) outliers start: 46 outliers final: 26 residues processed: 883 average time/residue: 0.2148 time to fit residues: 302.4684 Evaluate side-chains 856 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 829 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 372 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 258 optimal weight: 0.0970 chunk 326 optimal weight: 0.9980 chunk 378 optimal weight: 0.4980 chunk 196 optimal weight: 10.0000 chunk 357 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS H 129 GLN J 13 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS ** M 208 GLN ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.272989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.254245 restraints weight = 86156.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.253047 restraints weight = 111574.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.252061 restraints weight = 81303.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.251651 restraints weight = 80858.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.251267 restraints weight = 76610.817| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 36753 Z= 0.166 Angle : 0.674 20.934 50271 Z= 0.343 Chirality : 0.045 0.277 5432 Planarity : 0.004 0.063 5969 Dihedral : 16.469 143.072 5791 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.92 % Allowed : 13.01 % Favored : 85.07 % 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: 0.23 (0.13), residues: 3971 helix: 1.18 (0.12), residues: 1869 sheet: -0.01 (0.19), residues: 746 loop : -1.13 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 155 TYR 0.018 0.002 TYR F 70 PHE 0.032 0.002 PHE N 99 TRP 0.041 0.002 TRP P 245 HIS 0.015 0.002 HIS M 139 Details of bonding type rmsd covalent geometry : bond 0.00354 (36705) covalent geometry : angle 0.64103 (50248) hydrogen bonds : bond 0.04776 ( 1694) hydrogen bonds : angle 4.94488 ( 4842) metal coordination : bond 0.03256 ( 48) metal coordination : angle 9.69132 ( 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 910 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 842 time to evaluate : 1.200 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: 0.7513 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: A 72 ASP cc_start: 0.6946 (t70) cc_final: 0.6701 (t0) REVERT: A 76 LEU cc_start: 0.7729 (tp) cc_final: 0.7476 (tp) REVERT: A 109 MET cc_start: 0.7530 (tpp) cc_final: 0.7276 (tpt) REVERT: A 165 GLU cc_start: 0.7489 (tp30) cc_final: 0.7079 (tp30) REVERT: A 199 ASP cc_start: 0.6528 (t0) cc_final: 0.6114 (t70) REVERT: A 206 GLU cc_start: 0.6680 (tp30) cc_final: 0.6355 (tm-30) REVERT: A 223 PHE cc_start: 0.8295 (m-80) cc_final: 0.7632 (m-80) REVERT: A 255 ASP cc_start: 0.7153 (t0) cc_final: 0.6853 (t0) REVERT: B 118 ASP cc_start: 0.7247 (p0) cc_final: 0.7020 (p0) REVERT: B 124 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7742 (m) REVERT: B 140 THR cc_start: 0.8011 (m) cc_final: 0.7751 (t) REVERT: B 185 LEU cc_start: 0.7654 (mt) cc_final: 0.7019 (mp) REVERT: B 206 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7161 (tp30) REVERT: B 208 GLN cc_start: 0.7719 (tt0) cc_final: 0.7380 (tt0) REVERT: C 24 LEU cc_start: 0.8173 (mm) cc_final: 0.7671 (mp) REVERT: C 203 PHE cc_start: 0.6757 (t80) cc_final: 0.6362 (t80) REVERT: C 222 ARG cc_start: 0.5988 (ptm-80) cc_final: 0.5495 (ptm160) REVERT: C 267 LYS cc_start: 0.7877 (pttp) cc_final: 0.7575 (pttp) REVERT: D 103 THR cc_start: 0.5581 (t) cc_final: 0.5217 (p) REVERT: D 104 MET cc_start: 0.6188 (mmp) cc_final: 0.5353 (mmp) REVERT: D 132 MET cc_start: 0.8100 (ppp) cc_final: 0.7878 (ppp) REVERT: D 208 GLN cc_start: 0.7373 (mt0) cc_final: 0.7050 (mt0) REVERT: D 236 GLU cc_start: 0.7003 (mp0) cc_final: 0.6632 (mp0) REVERT: D 238 GLN cc_start: 0.8479 (mt0) cc_final: 0.8162 (mt0) REVERT: E 61 ASP cc_start: 0.7632 (t70) cc_final: 0.7290 (t70) REVERT: E 157 HIS cc_start: 0.7647 (m-70) cc_final: 0.7371 (m-70) REVERT: E 158 GLN cc_start: 0.7619 (pt0) cc_final: 0.7399 (pt0) REVERT: E 208 GLN cc_start: 0.7132 (tp-100) cc_final: 0.6661 (tm-30) REVERT: E 210 ILE cc_start: 0.8124 (mm) cc_final: 0.7489 (mt) REVERT: E 211 GLN cc_start: 0.6863 (pp30) cc_final: 0.6301 (pp30) REVERT: E 212 GLN cc_start: 0.7276 (mp10) cc_final: 0.6464 (mp10) REVERT: E 270 LYS cc_start: 0.6876 (mtpt) cc_final: 0.6598 (mtpt) REVERT: F 70 TYR cc_start: 0.7470 (t80) cc_final: 0.7185 (t80) REVERT: F 230 LYS cc_start: 0.8274 (tppp) cc_final: 0.7886 (tppp) REVERT: H 205 LYS cc_start: 0.7601 (mmmm) cc_final: 0.7396 (mmmm) REVERT: H 230 LYS cc_start: 0.4833 (pttm) cc_final: 0.4567 (pttm) REVERT: R 418 MET cc_start: 0.6821 (ppp) cc_final: 0.6396 (ppp) REVERT: Q 360 LYS cc_start: 0.6005 (ptpp) cc_final: 0.5754 (ptpp) REVERT: Q 418 MET cc_start: 0.6852 (ppp) cc_final: 0.6371 (ppp) REVERT: I 72 ASP cc_start: 0.7118 (t70) cc_final: 0.6790 (t0) REVERT: I 109 MET cc_start: 0.6840 (ttt) cc_final: 0.6216 (ttt) REVERT: I 165 GLU cc_start: 0.7198 (tp30) cc_final: 0.6928 (tp30) REVERT: I 183 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6890 (mt) REVERT: I 238 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7369 (tp40) REVERT: I 254 LYS cc_start: 0.7847 (tptp) cc_final: 0.7635 (tppt) REVERT: J 94 GLU cc_start: 0.6388 (pp20) cc_final: 0.6089 (pp20) REVERT: J 105 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7655 (ttmt) REVERT: J 129 GLN cc_start: 0.7788 (tt0) cc_final: 0.7400 (mt0) REVERT: J 132 MET cc_start: 0.7814 (tpp) cc_final: 0.7386 (mmt) REVERT: J 190 LYS cc_start: 0.8337 (mttp) cc_final: 0.8134 (mtpp) REVERT: J 206 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7485 (tp30) REVERT: J 211 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6985 (tm-30) REVERT: K 222 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4181 (ptp90) REVERT: L 104 MET cc_start: 0.4861 (mmp) cc_final: 0.4559 (mmp) REVERT: L 220 LYS cc_start: 0.5735 (mmtm) cc_final: 0.5311 (mmtm) REVERT: L 221 ILE cc_start: 0.7129 (mt) cc_final: 0.6798 (tt) REVERT: L 248 ASP cc_start: 0.6809 (p0) cc_final: 0.6537 (p0) REVERT: L 260 ARG cc_start: 0.6881 (mmm-85) cc_final: 0.6598 (mmm-85) REVERT: L 268 ASP cc_start: 0.7354 (p0) cc_final: 0.6744 (p0) REVERT: M 35 ASP cc_start: 0.6806 (m-30) cc_final: 0.6438 (m-30) REVERT: M 61 ASP cc_start: 0.7319 (t70) cc_final: 0.6658 (t0) REVERT: M 62 HIS cc_start: 0.5683 (t70) cc_final: 0.5436 (t70) REVERT: M 82 ASN cc_start: 0.7775 (p0) cc_final: 0.7419 (p0) REVERT: M 87 TYR cc_start: 0.7316 (t80) cc_final: 0.7107 (t80) REVERT: M 99 PHE cc_start: 0.6936 (m-80) cc_final: 0.6582 (m-80) REVERT: M 155 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6916 (mtt180) REVERT: M 164 LEU cc_start: 0.7581 (mt) cc_final: 0.7137 (pp) REVERT: M 215 LYS cc_start: 0.8032 (pttt) cc_final: 0.7787 (pttt) REVERT: M 271 PHE cc_start: 0.6050 (m-80) cc_final: 0.5805 (m-80) REVERT: N 64 GLN cc_start: 0.5981 (tp40) cc_final: 0.5600 (tp-100) REVERT: N 105 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8204 (mtmm) REVERT: N 186 ASN cc_start: 0.4573 (m110) cc_final: 0.4209 (m-40) REVERT: N 213 GLN cc_start: 0.7911 (pp30) cc_final: 0.7493 (pp30) REVERT: N 241 THR cc_start: 0.8317 (t) cc_final: 0.7981 (m) REVERT: N 252 VAL cc_start: 0.8282 (p) cc_final: 0.8039 (m) REVERT: N 260 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.6336 (mtm-85) REVERT: P 201 PHE cc_start: 0.7503 (t80) cc_final: 0.7141 (t80) REVERT: P 203 PHE cc_start: 0.7680 (t80) cc_final: 0.7030 (t80) REVERT: P 206 GLU cc_start: 0.5793 (pp20) cc_final: 0.4810 (tm-30) outliers start: 68 outliers final: 45 residues processed: 856 average time/residue: 0.2209 time to fit residues: 300.1524 Evaluate side-chains 870 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 821 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 34 GLU 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 D residue 258 THR 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 139 HIS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 101 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 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE 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 I residue 14 LYS 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 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 75 ILE Chi-restraints excluded: chain M residue 139 HIS 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 199 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 264 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 365 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 291 optimal weight: 5.9990 chunk 360 optimal weight: 1.9990 chunk 257 optimal weight: 0.0770 chunk 186 optimal weight: 0.7980 chunk 406 optimal weight: 3.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 157 HIS D 242 GLN ** E 139 HIS ** 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 64 GLN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN H 129 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** P 186 ASN ** 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 = 0.4974 r_free = 0.4974 target = 0.271941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.253634 restraints weight = 85133.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.251413 restraints weight = 107603.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.250115 restraints weight = 87014.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.249861 restraints weight = 83986.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.249532 restraints weight = 77613.419| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 36753 Z= 0.162 Angle : 0.667 18.693 50271 Z= 0.341 Chirality : 0.045 0.243 5432 Planarity : 0.004 0.057 5969 Dihedral : 16.590 143.675 5791 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.52 % Allowed : 15.18 % Favored : 82.30 % 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: 0.13 (0.13), residues: 3971 helix: 1.08 (0.12), residues: 1877 sheet: -0.01 (0.19), residues: 754 loop : -1.22 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 155 TYR 0.020 0.002 TYR N 134 PHE 0.032 0.002 PHE N 99 TRP 0.040 0.002 TRP P 245 HIS 0.017 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00356 (36705) covalent geometry : angle 0.64143 (50248) hydrogen bonds : bond 0.04373 ( 1694) hydrogen bonds : angle 4.84702 ( 4842) metal coordination : bond 0.03235 ( 48) metal coordination : angle 8.52668 ( 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 923 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 834 time to evaluate : 1.139 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 38 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7126 (mt0) REVERT: A 52 LEU cc_start: 0.8054 (mm) cc_final: 0.7798 (mt) REVERT: A 72 ASP cc_start: 0.7091 (t70) cc_final: 0.6684 (t0) REVERT: A 76 LEU cc_start: 0.7847 (tp) cc_final: 0.7610 (tp) REVERT: A 165 GLU cc_start: 0.7477 (tp30) cc_final: 0.7019 (tp30) REVERT: A 183 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7178 (mt) REVERT: A 199 ASP cc_start: 0.6575 (t0) cc_final: 0.6138 (t0) REVERT: A 223 PHE cc_start: 0.8335 (m-80) cc_final: 0.7594 (m-80) REVERT: A 254 LYS cc_start: 0.7583 (tppt) cc_final: 0.7289 (ttmt) REVERT: A 255 ASP cc_start: 0.7083 (t0) cc_final: 0.6872 (t0) REVERT: B 118 ASP cc_start: 0.7258 (p0) cc_final: 0.7041 (p0) REVERT: B 124 VAL cc_start: 0.8188 (p) cc_final: 0.7800 (m) REVERT: B 140 THR cc_start: 0.8003 (m) cc_final: 0.7698 (t) REVERT: B 185 LEU cc_start: 0.7713 (mt) cc_final: 0.7054 (mp) REVERT: B 206 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7225 (tp30) REVERT: B 208 GLN cc_start: 0.7740 (tt0) cc_final: 0.7400 (tt0) REVERT: C 9 GLU cc_start: 0.7630 (tp30) cc_final: 0.7356 (tp30) REVERT: C 24 LEU cc_start: 0.8172 (mm) cc_final: 0.7665 (mp) REVERT: C 104 MET cc_start: 0.4383 (ppp) cc_final: 0.4059 (ppp) REVERT: C 186 ASN cc_start: 0.8012 (t0) cc_final: 0.7321 (t0) REVERT: C 198 MET cc_start: 0.6544 (pmm) cc_final: 0.6141 (pmm) REVERT: C 203 PHE cc_start: 0.6615 (t80) cc_final: 0.6298 (t80) REVERT: C 222 ARG cc_start: 0.6073 (ptm-80) cc_final: 0.5601 (ptm160) REVERT: C 267 LYS cc_start: 0.7919 (pttp) cc_final: 0.7549 (pttp) REVERT: D 103 THR cc_start: 0.5589 (t) cc_final: 0.5204 (p) REVERT: D 104 MET cc_start: 0.6253 (mmp) cc_final: 0.5455 (mmp) REVERT: D 236 GLU cc_start: 0.7028 (mp0) cc_final: 0.6622 (mp0) REVERT: D 238 GLN cc_start: 0.8463 (mt0) cc_final: 0.8114 (mt0) REVERT: E 61 ASP cc_start: 0.7482 (t70) cc_final: 0.7280 (t70) REVERT: E 157 HIS cc_start: 0.7591 (m-70) cc_final: 0.6847 (m-70) REVERT: E 161 LYS cc_start: 0.8242 (mttt) cc_final: 0.7894 (mttt) REVERT: E 208 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6828 (tm-30) REVERT: E 212 GLN cc_start: 0.7435 (mp10) cc_final: 0.6630 (mp10) REVERT: E 213 GLN cc_start: 0.6805 (pp30) cc_final: 0.6417 (pp30) REVERT: E 225 TYR cc_start: 0.4618 (t80) cc_final: 0.4038 (t80) REVERT: F 230 LYS cc_start: 0.8316 (tppp) cc_final: 0.7920 (tppp) REVERT: H 230 LYS cc_start: 0.4717 (pttm) cc_final: 0.4467 (pttm) REVERT: R 418 MET cc_start: 0.6840 (ppp) cc_final: 0.6402 (ppp) REVERT: Q 360 LYS cc_start: 0.6048 (ptpp) cc_final: 0.5734 (ptpp) REVERT: Q 418 MET cc_start: 0.6906 (ppp) cc_final: 0.6389 (ppp) REVERT: I 72 ASP cc_start: 0.7129 (t70) cc_final: 0.6818 (t0) REVERT: I 109 MET cc_start: 0.7066 (ttt) cc_final: 0.6614 (ttt) REVERT: I 165 GLU cc_start: 0.7187 (tp30) cc_final: 0.6904 (tp30) REVERT: I 183 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6929 (mt) REVERT: I 238 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7442 (tm-30) REVERT: J 94 GLU cc_start: 0.6395 (pp20) cc_final: 0.6027 (pp20) REVERT: J 97 GLN cc_start: 0.7461 (tp40) cc_final: 0.7048 (tp40) REVERT: J 105 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7692 (ttmt) REVERT: J 129 GLN cc_start: 0.7771 (tt0) cc_final: 0.7255 (mt0) REVERT: J 206 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7407 (tp30) REVERT: J 211 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7159 (tm-30) REVERT: K 222 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.3941 (ttt90) REVERT: L 104 MET cc_start: 0.4800 (mmp) cc_final: 0.4529 (mmp) REVERT: L 220 LYS cc_start: 0.5866 (mmtm) cc_final: 0.5488 (mmtm) REVERT: L 248 ASP cc_start: 0.6901 (p0) cc_final: 0.6593 (p0) REVERT: L 259 ASP cc_start: 0.7720 (p0) cc_final: 0.7304 (p0) REVERT: L 268 ASP cc_start: 0.7370 (p0) cc_final: 0.6733 (p0) REVERT: M 1 TRP cc_start: 0.6083 (t-100) cc_final: 0.5881 (t-100) REVERT: M 35 ASP cc_start: 0.6814 (m-30) cc_final: 0.6358 (m-30) REVERT: M 61 ASP cc_start: 0.7355 (t70) cc_final: 0.6933 (t0) REVERT: M 99 PHE cc_start: 0.6951 (m-80) cc_final: 0.6562 (m-80) REVERT: M 155 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7012 (mtt180) REVERT: M 161 LYS cc_start: 0.8763 (mttt) cc_final: 0.8532 (mttt) REVERT: M 195 THR cc_start: 0.8140 (m) cc_final: 0.7545 (t) REVERT: M 259 ASP cc_start: 0.7137 (t0) cc_final: 0.6778 (t0) REVERT: M 271 PHE cc_start: 0.6113 (m-80) cc_final: 0.5883 (m-80) REVERT: N 105 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8178 (mtmm) REVERT: N 107 TYR cc_start: 0.8193 (t80) cc_final: 0.7754 (t80) REVERT: N 213 GLN cc_start: 0.7953 (pp30) cc_final: 0.7551 (pp30) REVERT: N 241 THR cc_start: 0.8386 (t) cc_final: 0.7991 (m) REVERT: N 252 VAL cc_start: 0.8335 (p) cc_final: 0.8078 (m) REVERT: N 260 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6340 (mtm-85) REVERT: O 132 MET cc_start: 0.7455 (mpp) cc_final: 0.7220 (mpp) REVERT: P 201 PHE cc_start: 0.7526 (t80) cc_final: 0.7142 (t80) outliers start: 89 outliers final: 67 residues processed: 863 average time/residue: 0.2191 time to fit residues: 300.5846 Evaluate side-chains 896 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 825 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 95 THR 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 13 ASN Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU 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 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 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 156 THR 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 128 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE 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 164 LEU Chi-restraints excluded: chain H residue 203 PHE 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 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 L residue 208 GLN Chi-restraints excluded: chain L residue 253 VAL 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 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 P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 196 SER 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: 3.9990 chunk 145 optimal weight: 0.9990 chunk 246 optimal weight: 0.5980 chunk 197 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 273 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 chunk 164 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 208 GLN D 242 GLN E 139 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN J 13 ASN J 82 ASN J 204 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS ** 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** N 148 GLN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.240293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182402 restraints weight = 64121.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.188075 restraints weight = 29624.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.189741 restraints weight = 19031.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.191005 restraints weight = 14770.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.191554 restraints weight = 12544.027| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 36753 Z= 0.226 Angle : 0.717 18.353 50271 Z= 0.370 Chirality : 0.047 0.206 5432 Planarity : 0.005 0.060 5969 Dihedral : 16.795 144.543 5791 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.25 % Allowed : 16.40 % Favored : 80.35 % 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: -0.09 (0.13), residues: 3971 helix: 0.92 (0.12), residues: 1884 sheet: -0.14 (0.19), residues: 740 loop : -1.33 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 155 TYR 0.032 0.002 TYR I 134 PHE 0.035 0.002 PHE N 99 TRP 0.042 0.002 TRP M 63 HIS 0.021 0.002 HIS M 139 Details of bonding type rmsd covalent geometry : bond 0.00506 (36705) covalent geometry : angle 0.69354 (50248) hydrogen bonds : bond 0.04781 ( 1694) hydrogen bonds : angle 4.88289 ( 4842) metal coordination : bond 0.03023 ( 48) metal coordination : angle 8.55328 ( 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 946 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 831 time to evaluate : 1.179 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: A 38 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7228 (mt0) REVERT: A 52 LEU cc_start: 0.8185 (mm) cc_final: 0.7938 (mt) REVERT: A 72 ASP cc_start: 0.7187 (t70) cc_final: 0.6750 (t0) REVERT: A 98 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 113 LYS cc_start: 0.7662 (mmmm) cc_final: 0.6751 (mmmm) REVERT: A 138 GLU cc_start: 0.7003 (mp0) cc_final: 0.6545 (mp0) REVERT: A 165 GLU cc_start: 0.7552 (tp30) cc_final: 0.7114 (tp30) REVERT: A 183 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7333 (mt) REVERT: A 223 PHE cc_start: 0.8300 (m-80) cc_final: 0.7432 (m-80) REVERT: A 238 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 255 ASP cc_start: 0.7337 (t0) cc_final: 0.7135 (t0) REVERT: B 124 VAL cc_start: 0.8226 (p) cc_final: 0.7890 (m) REVERT: B 140 THR cc_start: 0.8117 (m) cc_final: 0.7742 (t) REVERT: B 185 LEU cc_start: 0.7785 (mt) cc_final: 0.7451 (mt) REVERT: B 208 GLN cc_start: 0.7843 (tt0) cc_final: 0.7475 (tt0) REVERT: C 9 GLU cc_start: 0.7587 (tp30) cc_final: 0.7300 (tp30) REVERT: C 24 LEU cc_start: 0.8101 (mm) cc_final: 0.7626 (mp) REVERT: C 30 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6858 (tpp80) REVERT: C 104 MET cc_start: 0.5572 (ppp) cc_final: 0.4955 (ppp) REVERT: C 203 PHE cc_start: 0.7246 (t80) cc_final: 0.6677 (t80) REVERT: C 267 LYS cc_start: 0.8224 (pttp) cc_final: 0.7893 (pttp) REVERT: D 103 THR cc_start: 0.6555 (t) cc_final: 0.5881 (p) REVERT: D 104 MET cc_start: 0.6764 (mmp) cc_final: 0.5876 (mmp) REVERT: D 132 MET cc_start: 0.8427 (ppp) cc_final: 0.8101 (ppp) REVERT: D 220 LYS cc_start: 0.5709 (mmtm) cc_final: 0.5331 (mmtm) REVERT: D 236 GLU cc_start: 0.7041 (mp0) cc_final: 0.6637 (mp0) REVERT: D 238 GLN cc_start: 0.8398 (mt0) cc_final: 0.8085 (mt0) REVERT: D 260 ARG cc_start: 0.6730 (mmm-85) cc_final: 0.6406 (mmm-85) REVERT: E 61 ASP cc_start: 0.7765 (t70) cc_final: 0.7308 (t70) REVERT: E 89 GLU cc_start: 0.4947 (tm-30) cc_final: 0.4703 (tm-30) REVERT: E 129 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7621 (mm-40) REVERT: E 157 HIS cc_start: 0.8172 (m-70) cc_final: 0.7305 (m-70) REVERT: E 161 LYS cc_start: 0.8491 (mttt) cc_final: 0.7902 (mttt) REVERT: E 195 THR cc_start: 0.8257 (m) cc_final: 0.7620 (t) REVERT: E 206 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6861 (tm-30) REVERT: E 208 GLN cc_start: 0.7639 (tp40) cc_final: 0.7143 (tm-30) REVERT: E 213 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6277 (pp30) REVERT: E 225 TYR cc_start: 0.6331 (t80) cc_final: 0.5975 (t80) REVERT: E 270 LYS cc_start: 0.6787 (mtpt) cc_final: 0.6218 (pttt) REVERT: F 110 PHE cc_start: 0.7875 (m-10) cc_final: 0.7514 (m-10) REVERT: F 113 LYS cc_start: 0.7535 (mmtm) cc_final: 0.7334 (mmtm) REVERT: F 254 LYS cc_start: 0.8135 (tptt) cc_final: 0.7876 (tptt) REVERT: G 11 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7700 (mm-30) REVERT: G 201 PHE cc_start: 0.8152 (t80) cc_final: 0.7816 (t80) REVERT: H 87 TYR cc_start: 0.7137 (t80) cc_final: 0.6225 (t80) REVERT: H 110 PHE cc_start: 0.7838 (m-10) cc_final: 0.7377 (m-10) REVERT: H 199 ASP cc_start: 0.7210 (m-30) cc_final: 0.6909 (t0) REVERT: H 201 PHE cc_start: 0.8089 (t80) cc_final: 0.7802 (t80) REVERT: H 205 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7585 (mmmm) REVERT: R 418 MET cc_start: 0.7401 (ppp) cc_final: 0.6854 (ppp) REVERT: Q 360 LYS cc_start: 0.6088 (ptpp) cc_final: 0.5653 (ptpp) REVERT: Q 418 MET cc_start: 0.7502 (ppp) cc_final: 0.6909 (ppp) REVERT: I 72 ASP cc_start: 0.7194 (t70) cc_final: 0.6893 (t0) REVERT: I 109 MET cc_start: 0.7013 (ttt) cc_final: 0.6450 (ttt) REVERT: I 238 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7219 (tm-30) REVERT: I 254 LYS cc_start: 0.7959 (tppt) cc_final: 0.7633 (tppt) REVERT: J 94 GLU cc_start: 0.6717 (pp20) cc_final: 0.6307 (pp20) REVERT: J 105 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7662 (mtpt) REVERT: J 109 MET cc_start: 0.6410 (mtm) cc_final: 0.6144 (mtm) REVERT: J 129 GLN cc_start: 0.7726 (tt0) cc_final: 0.7285 (mt0) REVERT: J 206 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7256 (tp30) REVERT: K 109 MET cc_start: 0.7842 (tpp) cc_final: 0.7477 (pmm) REVERT: L 80 GLU cc_start: 0.7260 (tm-30) cc_final: 0.6453 (tm-30) REVERT: L 104 MET cc_start: 0.5325 (mmp) cc_final: 0.4959 (mmp) REVERT: L 133 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7618 (mmmt) REVERT: L 220 LYS cc_start: 0.5916 (mmtm) cc_final: 0.5530 (mmtm) REVERT: L 238 GLN cc_start: 0.8266 (mt0) cc_final: 0.8000 (mt0) REVERT: L 248 ASP cc_start: 0.7006 (p0) cc_final: 0.6730 (p0) REVERT: L 256 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6653 (mtp85) REVERT: L 259 ASP cc_start: 0.7875 (p0) cc_final: 0.7529 (p0) REVERT: L 268 ASP cc_start: 0.7373 (p0) cc_final: 0.6606 (p0) REVERT: M 35 ASP cc_start: 0.7055 (m-30) cc_final: 0.6676 (m-30) REVERT: M 61 ASP cc_start: 0.7555 (t70) cc_final: 0.6669 (t0) REVERT: M 62 HIS cc_start: 0.6204 (t70) cc_final: 0.5616 (t70) REVERT: M 99 PHE cc_start: 0.7666 (m-80) cc_final: 0.6939 (m-80) REVERT: M 158 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7608 (mm-40) REVERT: M 161 LYS cc_start: 0.8990 (mttt) cc_final: 0.8483 (mttt) REVERT: M 164 LEU cc_start: 0.8079 (mt) cc_final: 0.7402 (pp) REVERT: M 195 THR cc_start: 0.8281 (m) cc_final: 0.7733 (t) REVERT: M 208 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7309 (tm-30) REVERT: M 211 GLN cc_start: 0.7005 (pp30) cc_final: 0.6231 (pp30) REVERT: M 212 GLN cc_start: 0.8101 (mm110) cc_final: 0.7840 (mm-40) REVERT: M 259 ASP cc_start: 0.7574 (t0) cc_final: 0.7216 (t0) REVERT: M 271 PHE cc_start: 0.7031 (m-80) cc_final: 0.6438 (m-80) REVERT: N 64 GLN cc_start: 0.6388 (tp-100) cc_final: 0.6060 (tp-100) REVERT: N 104 MET cc_start: 0.7749 (tpt) cc_final: 0.7447 (tpt) REVERT: N 105 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8233 (mtmm) REVERT: N 113 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7427 (mmtm) REVERT: N 213 GLN cc_start: 0.7976 (pp30) cc_final: 0.7580 (pp30) REVERT: N 241 THR cc_start: 0.8467 (t) cc_final: 0.8135 (p) REVERT: N 254 LYS cc_start: 0.7789 (tptt) cc_final: 0.7500 (tptt) REVERT: N 260 ARG cc_start: 0.6734 (mtm-85) cc_final: 0.6352 (mtm-85) REVERT: O 11 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7747 (mm-30) REVERT: O 132 MET cc_start: 0.8233 (mpp) cc_final: 0.7708 (mpp) REVERT: O 198 MET cc_start: 0.7870 (tpt) cc_final: 0.7652 (tpt) REVERT: P 87 TYR cc_start: 0.6258 (t80) cc_final: 0.5942 (t80) REVERT: P 201 PHE cc_start: 0.8352 (t80) cc_final: 0.7928 (t80) outliers start: 115 outliers final: 83 residues processed: 870 average time/residue: 0.2169 time to fit residues: 300.5803 Evaluate side-chains 910 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 823 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR 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 13 ASN 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 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 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 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 GLN 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 109 MET Chi-restraints excluded: chain F residue 128 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 G residue 204 ASN 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 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 269 VAL 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 J residue 172 ASN Chi-restraints excluded: chain J residue 193 LEU 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 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 85 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 196 SER Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 251 ILE 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: 0.0060 chunk 321 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 355 optimal weight: 0.9980 chunk 308 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 406 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 242 GLN E 69 HIS E 139 HIS ** 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 146 ASN ** 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 44 GLN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.241971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.185659 restraints weight = 63783.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.190539 restraints weight = 31607.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192196 restraints weight = 18155.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.192972 restraints weight = 15319.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.193323 restraints weight = 13582.986| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 0.121 36753 Z= 0.155 Angle : 0.670 17.057 50271 Z= 0.342 Chirality : 0.045 0.237 5432 Planarity : 0.004 0.052 5969 Dihedral : 16.815 145.648 5791 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % Favored : 79.36 % 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: -0.00 (0.13), residues: 3971 helix: 0.98 (0.12), residues: 1886 sheet: -0.05 (0.19), residues: 732 loop : -1.32 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 155 TYR 0.023 0.001 TYR N 134 PHE 0.035 0.001 PHE N 99 TRP 0.040 0.001 TRP M 63 HIS 0.021 0.001 HIS N 16 Details of bonding type rmsd covalent geometry : bond 0.00343 (36705) covalent geometry : angle 0.65016 (50248) hydrogen bonds : bond 0.04021 ( 1694) hydrogen bonds : angle 4.71135 ( 4842) metal coordination : bond 0.02602 ( 48) metal coordination : angle 7.54828 ( 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 937 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 835 time to evaluate : 1.155 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: A 72 ASP cc_start: 0.7266 (t70) cc_final: 0.6822 (t0) REVERT: A 98 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 138 GLU cc_start: 0.7035 (mp0) cc_final: 0.6536 (mp0) REVERT: A 148 GLN cc_start: 0.8834 (tt0) cc_final: 0.8622 (mt0) REVERT: A 165 GLU cc_start: 0.7535 (tp30) cc_final: 0.7146 (tp30) REVERT: A 183 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7352 (mt) REVERT: A 223 PHE cc_start: 0.8372 (m-80) cc_final: 0.7565 (m-80) REVERT: A 238 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 254 LYS cc_start: 0.7699 (tppt) cc_final: 0.7363 (ttmt) REVERT: A 255 ASP cc_start: 0.7358 (t0) cc_final: 0.7111 (t0) REVERT: B 124 VAL cc_start: 0.8332 (p) cc_final: 0.7980 (m) REVERT: B 140 THR cc_start: 0.8083 (m) cc_final: 0.7753 (t) REVERT: B 185 LEU cc_start: 0.7786 (mt) cc_final: 0.7582 (mp) REVERT: B 208 GLN cc_start: 0.7795 (tt0) cc_final: 0.7449 (tt0) REVERT: C 9 GLU cc_start: 0.7551 (tp30) cc_final: 0.7265 (tp30) REVERT: C 24 LEU cc_start: 0.8129 (mm) cc_final: 0.7667 (mp) REVERT: C 104 MET cc_start: 0.5685 (ppp) cc_final: 0.5108 (ppp) REVERT: C 203 PHE cc_start: 0.7138 (t80) cc_final: 0.6561 (t80) REVERT: C 204 ASN cc_start: 0.8479 (m-40) cc_final: 0.8265 (m-40) REVERT: C 267 LYS cc_start: 0.8230 (pttp) cc_final: 0.7879 (pttp) REVERT: D 103 THR cc_start: 0.6521 (t) cc_final: 0.5841 (p) REVERT: D 104 MET cc_start: 0.6848 (mmp) cc_final: 0.5906 (mmp) REVERT: D 132 MET cc_start: 0.8466 (ppp) cc_final: 0.8254 (ppp) REVERT: D 220 LYS cc_start: 0.5695 (mmtm) cc_final: 0.5378 (mmtm) REVERT: D 236 GLU cc_start: 0.7026 (mp0) cc_final: 0.6604 (mp0) REVERT: D 238 GLN cc_start: 0.8347 (mt0) cc_final: 0.7983 (mt0) REVERT: D 260 ARG cc_start: 0.6734 (mmm-85) cc_final: 0.6406 (mmm-85) REVERT: E 15 TRP cc_start: 0.7046 (m-10) cc_final: 0.4709 (m-10) REVERT: E 24 LEU cc_start: 0.7305 (mp) cc_final: 0.6990 (mp) REVERT: E 25 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6149 (mm-30) REVERT: E 61 ASP cc_start: 0.7775 (t70) cc_final: 0.7271 (t70) REVERT: E 129 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7644 (mm-40) REVERT: E 157 HIS cc_start: 0.8265 (m-70) cc_final: 0.7493 (m-70) REVERT: E 161 LYS cc_start: 0.8406 (mttt) cc_final: 0.7755 (mttt) REVERT: E 181 THR cc_start: 0.8355 (p) cc_final: 0.8032 (t) REVERT: E 195 THR cc_start: 0.8181 (m) cc_final: 0.7566 (t) REVERT: E 208 GLN cc_start: 0.7529 (tp40) cc_final: 0.7016 (tm-30) REVERT: E 213 GLN cc_start: 0.7448 (pp30) cc_final: 0.6799 (pp30) REVERT: E 225 TYR cc_start: 0.6443 (t80) cc_final: 0.5820 (t80) REVERT: E 270 LYS cc_start: 0.6767 (mtpt) cc_final: 0.6121 (pttt) REVERT: F 103 THR cc_start: 0.7655 (t) cc_final: 0.7395 (p) REVERT: F 110 PHE cc_start: 0.7744 (m-10) cc_final: 0.7182 (m-80) REVERT: F 241 THR cc_start: 0.8235 (t) cc_final: 0.7892 (m) REVERT: G 110 PHE cc_start: 0.7338 (m-10) cc_final: 0.7130 (m-80) REVERT: G 198 MET cc_start: 0.8089 (tpt) cc_final: 0.7879 (tpt) REVERT: H 87 TYR cc_start: 0.7300 (t80) cc_final: 0.7010 (t80) REVERT: H 110 PHE cc_start: 0.7903 (m-10) cc_final: 0.7638 (m-10) REVERT: H 199 ASP cc_start: 0.7161 (m-30) cc_final: 0.6776 (t0) REVERT: H 205 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7981 (mmmm) REVERT: H 262 LEU cc_start: 0.7028 (mm) cc_final: 0.6736 (mm) REVERT: R 418 MET cc_start: 0.7398 (ppp) cc_final: 0.6849 (ppp) REVERT: Q 360 LYS cc_start: 0.6039 (ptpp) cc_final: 0.5617 (ptpp) REVERT: Q 413 MET cc_start: 0.6414 (mtt) cc_final: 0.6175 (mmt) REVERT: Q 418 MET cc_start: 0.7500 (ppp) cc_final: 0.6908 (ppp) REVERT: I 72 ASP cc_start: 0.7270 (t70) cc_final: 0.6958 (t70) REVERT: I 109 MET cc_start: 0.7073 (ttt) cc_final: 0.6408 (ttt) REVERT: I 183 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7182 (mt) REVERT: I 199 ASP cc_start: 0.6467 (t0) cc_final: 0.6203 (t0) REVERT: I 238 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7141 (tm-30) REVERT: I 254 LYS cc_start: 0.7978 (tppt) cc_final: 0.7593 (tppt) REVERT: J 94 GLU cc_start: 0.6743 (pp20) cc_final: 0.6313 (pp20) REVERT: J 98 GLU cc_start: 0.6886 (tp30) cc_final: 0.6611 (tp30) REVERT: J 105 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7777 (ttpt) REVERT: J 129 GLN cc_start: 0.7765 (tt0) cc_final: 0.7365 (mt0) REVERT: J 206 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7180 (tp30) REVERT: K 109 MET cc_start: 0.7671 (tpp) cc_final: 0.7414 (pmm) REVERT: L 80 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6420 (tm-30) REVERT: L 104 MET cc_start: 0.5312 (mmp) cc_final: 0.4950 (mmp) REVERT: L 133 LYS cc_start: 0.7935 (mmmt) cc_final: 0.7709 (mmmt) REVERT: L 220 LYS cc_start: 0.5862 (mmtm) cc_final: 0.5487 (mmtm) REVERT: L 248 ASP cc_start: 0.6959 (p0) cc_final: 0.6616 (p0) REVERT: L 268 ASP cc_start: 0.7303 (p0) cc_final: 0.6541 (p0) REVERT: M 15 TRP cc_start: 0.7310 (m100) cc_final: 0.6947 (m-10) REVERT: M 35 ASP cc_start: 0.6927 (m-30) cc_final: 0.6450 (m-30) REVERT: M 61 ASP cc_start: 0.7609 (t70) cc_final: 0.6845 (t0) REVERT: M 63 TRP cc_start: 0.6414 (m100) cc_final: 0.5175 (m100) REVERT: M 80 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7375 (tm-30) REVERT: M 99 PHE cc_start: 0.7644 (m-80) cc_final: 0.6863 (m-80) REVERT: M 158 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7741 (mm-40) REVERT: M 161 LYS cc_start: 0.8991 (mttt) cc_final: 0.8501 (mttt) REVERT: M 195 THR cc_start: 0.8129 (m) cc_final: 0.7588 (t) REVERT: M 211 GLN cc_start: 0.7096 (pp30) cc_final: 0.6729 (pp30) REVERT: M 259 ASP cc_start: 0.7604 (t0) cc_final: 0.7243 (t0) REVERT: N 64 GLN cc_start: 0.6372 (tp-100) cc_final: 0.5976 (tp-100) REVERT: N 105 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8166 (mtmm) REVERT: N 113 LYS cc_start: 0.7766 (mmtm) cc_final: 0.7396 (mmtm) REVERT: N 213 GLN cc_start: 0.7930 (pp30) cc_final: 0.7543 (pp30) REVERT: N 241 THR cc_start: 0.8389 (t) cc_final: 0.8040 (p) REVERT: N 260 ARG cc_start: 0.6742 (mtm-85) cc_final: 0.6335 (mtm-85) REVERT: O 11 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7738 (mm-30) REVERT: O 110 PHE cc_start: 0.6853 (m-10) cc_final: 0.6650 (m-10) REVERT: O 132 MET cc_start: 0.8241 (mpp) cc_final: 0.7709 (mpp) REVERT: O 198 MET cc_start: 0.7697 (tpt) cc_final: 0.7480 (tpt) REVERT: P 85 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5882 (mm) REVERT: P 87 TYR cc_start: 0.6249 (t80) cc_final: 0.5970 (t80) REVERT: P 201 PHE cc_start: 0.8318 (t80) cc_final: 0.7942 (t80) REVERT: P 203 PHE cc_start: 0.8565 (t80) cc_final: 0.8300 (t80) REVERT: P 206 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6543 (pp20) outliers start: 102 outliers final: 79 residues processed: 868 average time/residue: 0.2195 time to fit residues: 302.9768 Evaluate side-chains 899 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 816 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 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 13 ASN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU 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 D residue 264 ILE 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 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 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 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 231 ARG 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 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 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 J residue 172 ASN 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 258 THR Chi-restraints excluded: chain M residue 10 GLU 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 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 85 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU 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: 1.9990 chunk 29 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 319 optimal weight: 0.2980 chunk 385 optimal weight: 0.0670 chunk 57 optimal weight: 20.0000 chunk 310 optimal weight: 0.0870 chunk 213 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN C 186 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 242 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** ** 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 ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN J 172 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS M 157 HIS ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.270979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.252730 restraints weight = 84627.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.250283 restraints weight = 103743.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.248681 restraints weight = 84851.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.248193 restraints weight = 85099.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.248002 restraints weight = 75576.269| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 36753 Z= 0.140 Angle : 0.679 16.939 50271 Z= 0.346 Chirality : 0.044 0.252 5432 Planarity : 0.004 0.069 5969 Dihedral : 16.818 145.639 5791 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.97 % Allowed : 18.69 % Favored : 78.34 % 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: 1.00 (0.12), residues: 1888 sheet: 0.01 (0.19), residues: 706 loop : -1.23 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG L 231 TYR 0.016 0.001 TYR A 134 PHE 0.037 0.001 PHE N 99 TRP 0.027 0.001 TRP H 245 HIS 0.017 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00308 (36705) covalent geometry : angle 0.66230 (50248) hydrogen bonds : bond 0.03866 ( 1694) hydrogen bonds : angle 4.65321 ( 4842) metal coordination : bond 0.02284 ( 48) metal coordination : angle 7.01566 ( 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 945 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 840 time to evaluate : 1.232 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: A 72 ASP cc_start: 0.7198 (t70) cc_final: 0.6764 (t0) REVERT: A 98 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6665 (mm-30) REVERT: A 138 GLU cc_start: 0.7062 (mp0) cc_final: 0.6517 (mp0) REVERT: A 148 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: A 165 GLU cc_start: 0.7531 (tp30) cc_final: 0.7137 (tp30) REVERT: A 183 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7200 (mt) REVERT: A 223 PHE cc_start: 0.8276 (m-80) cc_final: 0.7567 (m-80) REVERT: A 238 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 254 LYS cc_start: 0.7695 (tppt) cc_final: 0.7343 (ttmt) REVERT: A 255 ASP cc_start: 0.7382 (t0) cc_final: 0.7150 (t0) REVERT: B 124 VAL cc_start: 0.8390 (p) cc_final: 0.8057 (m) REVERT: B 140 THR cc_start: 0.8052 (m) cc_final: 0.7734 (t) REVERT: B 185 LEU cc_start: 0.7722 (mt) cc_final: 0.7276 (mp) REVERT: B 208 GLN cc_start: 0.7855 (tt0) cc_final: 0.7517 (tt0) REVERT: C 9 GLU cc_start: 0.7510 (tp30) cc_final: 0.7266 (tp30) REVERT: C 24 LEU cc_start: 0.8148 (mm) cc_final: 0.7642 (mp) REVERT: C 203 PHE cc_start: 0.6612 (t80) cc_final: 0.6234 (t80) REVERT: C 267 LYS cc_start: 0.8065 (pttp) cc_final: 0.7640 (pttp) REVERT: D 103 THR cc_start: 0.5547 (t) cc_final: 0.5241 (p) REVERT: D 104 MET cc_start: 0.6244 (mmp) cc_final: 0.5469 (mmp) REVERT: D 220 LYS cc_start: 0.5743 (mmtm) cc_final: 0.5483 (mmtm) REVERT: D 236 GLU cc_start: 0.7030 (mp0) cc_final: 0.6582 (mp0) REVERT: D 238 GLN cc_start: 0.8441 (mt0) cc_final: 0.8024 (mt0) REVERT: D 260 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.6525 (mmm-85) REVERT: E 61 ASP cc_start: 0.7593 (t70) cc_final: 0.7299 (t70) REVERT: E 129 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7203 (mm110) REVERT: E 139 HIS cc_start: 0.6139 (OUTLIER) cc_final: 0.5710 (p-80) REVERT: E 157 HIS cc_start: 0.7735 (m-70) cc_final: 0.7337 (m-70) REVERT: E 158 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7152 (mm-40) REVERT: E 161 LYS cc_start: 0.8196 (mttt) cc_final: 0.7675 (mttt) REVERT: E 174 PHE cc_start: 0.7357 (t80) cc_final: 0.7003 (t80) REVERT: E 181 THR cc_start: 0.8154 (p) cc_final: 0.7908 (t) REVERT: E 195 THR cc_start: 0.8089 (m) cc_final: 0.7496 (t) REVERT: E 208 GLN cc_start: 0.7211 (tp40) cc_final: 0.6901 (tm-30) REVERT: E 225 TYR cc_start: 0.5407 (t80) cc_final: 0.5074 (t80) REVERT: E 270 LYS cc_start: 0.6534 (mtpt) cc_final: 0.6073 (pttt) REVERT: F 64 GLN cc_start: 0.5694 (tp40) cc_final: 0.5265 (tp40) REVERT: F 208 GLN cc_start: 0.7546 (mp10) cc_final: 0.7307 (mp10) REVERT: F 213 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: F 241 THR cc_start: 0.8342 (t) cc_final: 0.8009 (m) REVERT: F 254 LYS cc_start: 0.8079 (tptt) cc_final: 0.7845 (tptt) REVERT: H 166 LYS cc_start: 0.7253 (tptp) cc_final: 0.7019 (tptp) REVERT: H 201 PHE cc_start: 0.7461 (t80) cc_final: 0.7216 (t80) REVERT: H 205 LYS cc_start: 0.7558 (mmmm) cc_final: 0.7056 (mmmm) REVERT: H 272 ILE cc_start: 0.7761 (mp) cc_final: 0.7417 (mp) REVERT: R 418 MET cc_start: 0.6799 (ppp) cc_final: 0.6363 (ppp) REVERT: Q 360 LYS cc_start: 0.6477 (ptpp) cc_final: 0.6094 (ptpp) REVERT: Q 418 MET cc_start: 0.6913 (ppp) cc_final: 0.6443 (ppp) REVERT: I 72 ASP cc_start: 0.7163 (t70) cc_final: 0.6815 (t70) REVERT: I 109 MET cc_start: 0.7164 (ttt) cc_final: 0.6436 (ttt) REVERT: I 183 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.7005 (mt) REVERT: I 238 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7173 (tm-30) REVERT: I 254 LYS cc_start: 0.7861 (tppt) cc_final: 0.7522 (tppt) REVERT: J 94 GLU cc_start: 0.6739 (pp20) cc_final: 0.6315 (pp20) REVERT: J 98 GLU cc_start: 0.6706 (tp30) cc_final: 0.6442 (tp30) REVERT: J 105 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7792 (ttpt) REVERT: J 129 GLN cc_start: 0.7711 (tt0) cc_final: 0.7281 (mt0) REVERT: J 176 SER cc_start: 0.7896 (p) cc_final: 0.7687 (m) REVERT: J 206 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7283 (tp30) REVERT: L 80 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5630 (tm-30) REVERT: L 104 MET cc_start: 0.4946 (mmp) cc_final: 0.4655 (mmp) REVERT: L 220 LYS cc_start: 0.6032 (mmtm) cc_final: 0.5726 (mmtm) REVERT: L 238 GLN cc_start: 0.8195 (mt0) cc_final: 0.7974 (mt0) REVERT: L 248 ASP cc_start: 0.6890 (p0) cc_final: 0.6557 (p0) REVERT: L 268 ASP cc_start: 0.7337 (p0) cc_final: 0.6587 (p0) REVERT: M 15 TRP cc_start: 0.7422 (m100) cc_final: 0.7189 (m-10) REVERT: M 35 ASP cc_start: 0.6930 (m-30) cc_final: 0.6472 (m-30) REVERT: M 38 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7252 (tm-30) REVERT: M 61 ASP cc_start: 0.7384 (t70) cc_final: 0.7030 (t0) REVERT: M 63 TRP cc_start: 0.5839 (m100) cc_final: 0.5110 (m100) REVERT: M 99 PHE cc_start: 0.7007 (m-80) cc_final: 0.6491 (m-80) REVERT: M 195 THR cc_start: 0.8014 (m) cc_final: 0.7561 (t) REVERT: M 259 ASP cc_start: 0.7023 (t0) cc_final: 0.6642 (t0) REVERT: N 78 TRP cc_start: 0.7095 (m100) cc_final: 0.6396 (m100) REVERT: N 113 LYS cc_start: 0.7580 (mmtm) cc_final: 0.7255 (mmtm) REVERT: N 213 GLN cc_start: 0.7881 (pp30) cc_final: 0.7549 (pp30) REVERT: N 241 THR cc_start: 0.8396 (t) cc_final: 0.8072 (p) REVERT: N 254 LYS cc_start: 0.7755 (tptt) cc_final: 0.7491 (tptt) REVERT: N 260 ARG cc_start: 0.6691 (mtm-85) cc_final: 0.6332 (mtm-85) REVERT: P 201 PHE cc_start: 0.7629 (t80) cc_final: 0.7340 (t80) outliers start: 105 outliers final: 88 residues processed: 873 average time/residue: 0.2151 time to fit residues: 300.0627 Evaluate side-chains 909 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 816 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN 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 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 10 GLU Chi-restraints excluded: chain C residue 199 ASP 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 10 GLU 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 156 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 69 HIS 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 129 GLN Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 20 VAL 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 132 MET 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 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 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 258 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 30 ARG 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 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 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 132 MET 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 206 GLU 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: 20.0000 chunk 275 optimal weight: 0.0010 chunk 254 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 266 optimal weight: 0.9990 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 359 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN B 82 ASN C 186 ASN C 204 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS ** 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 69 HIS ** 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 212 GLN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.270612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.252208 restraints weight = 84398.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.250292 restraints weight = 105027.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.249089 restraints weight = 92846.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.248824 restraints weight = 85409.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.248131 restraints weight = 85391.534| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36753 Z= 0.153 Angle : 0.697 16.108 50271 Z= 0.354 Chirality : 0.045 0.271 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.849 145.490 5791 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.36 % Allowed : 19.31 % 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: 0.05 (0.13), residues: 3971 helix: 0.99 (0.12), residues: 1890 sheet: -0.03 (0.19), residues: 710 loop : -1.22 (0.15), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 155 TYR 0.018 0.001 TYR I 134 PHE 0.039 0.001 PHE N 99 TRP 0.027 0.001 TRP H 245 HIS 0.018 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00342 (36705) covalent geometry : angle 0.68236 (50248) hydrogen bonds : bond 0.03887 ( 1694) hydrogen bonds : angle 4.66613 ( 4842) metal coordination : bond 0.02115 ( 48) metal coordination : angle 6.67486 ( 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 934 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 815 time to evaluate : 1.326 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: A 72 ASP cc_start: 0.7208 (t70) cc_final: 0.6788 (t0) REVERT: A 98 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6617 (mm-30) REVERT: A 138 GLU cc_start: 0.6973 (mp0) cc_final: 0.6483 (mp0) REVERT: A 148 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: A 165 GLU cc_start: 0.7422 (tp30) cc_final: 0.7052 (tp30) REVERT: A 183 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7194 (mt) REVERT: A 223 PHE cc_start: 0.8234 (m-80) cc_final: 0.7522 (m-80) REVERT: A 238 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 94 GLU cc_start: 0.6619 (pp20) cc_final: 0.6207 (pp20) REVERT: B 124 VAL cc_start: 0.8417 (p) cc_final: 0.8107 (m) REVERT: B 140 THR cc_start: 0.8049 (m) cc_final: 0.7731 (t) REVERT: B 185 LEU cc_start: 0.7767 (mt) cc_final: 0.7328 (mp) REVERT: B 208 GLN cc_start: 0.7894 (tt0) cc_final: 0.7549 (tt0) REVERT: C 9 GLU cc_start: 0.7487 (tp30) cc_final: 0.7262 (tp30) REVERT: C 24 LEU cc_start: 0.8148 (mm) cc_final: 0.7648 (mp) REVERT: C 203 PHE cc_start: 0.6590 (t80) cc_final: 0.6118 (t80) REVERT: C 267 LYS cc_start: 0.8031 (pttp) cc_final: 0.7598 (pttp) REVERT: D 103 THR cc_start: 0.5507 (t) cc_final: 0.5256 (p) REVERT: D 104 MET cc_start: 0.6233 (mmp) cc_final: 0.5487 (mmp) REVERT: D 220 LYS cc_start: 0.5807 (mmtm) cc_final: 0.5538 (mmtm) REVERT: D 236 GLU cc_start: 0.7043 (mp0) cc_final: 0.6573 (mp0) REVERT: D 260 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.6561 (mmm-85) REVERT: E 61 ASP cc_start: 0.7525 (t70) cc_final: 0.7312 (t70) REVERT: E 139 HIS cc_start: 0.5722 (OUTLIER) cc_final: 0.5165 (p90) REVERT: E 157 HIS cc_start: 0.7680 (m-70) cc_final: 0.7313 (m-70) REVERT: E 158 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7094 (mm-40) REVERT: E 161 LYS cc_start: 0.8175 (mttt) cc_final: 0.7655 (mttt) REVERT: E 174 PHE cc_start: 0.7332 (t80) cc_final: 0.7015 (t80) REVERT: E 181 THR cc_start: 0.8174 (p) cc_final: 0.7917 (t) REVERT: E 195 THR cc_start: 0.8068 (m) cc_final: 0.7499 (t) REVERT: E 208 GLN cc_start: 0.7192 (tp40) cc_final: 0.6937 (tm-30) REVERT: E 225 TYR cc_start: 0.5406 (t80) cc_final: 0.5167 (t80) REVERT: E 270 LYS cc_start: 0.6534 (mtpt) cc_final: 0.6157 (pttt) REVERT: F 64 GLN cc_start: 0.5525 (tp40) cc_final: 0.5060 (tp-100) REVERT: F 103 THR cc_start: 0.7395 (t) cc_final: 0.7178 (p) REVERT: F 129 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: F 241 THR cc_start: 0.8391 (t) cc_final: 0.8158 (m) REVERT: F 254 LYS cc_start: 0.8058 (tptt) cc_final: 0.7767 (tptt) REVERT: H 201 PHE cc_start: 0.7401 (t80) cc_final: 0.7154 (t80) REVERT: H 205 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7062 (mmmm) REVERT: R 368 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4664 (mm) REVERT: R 418 MET cc_start: 0.6735 (ppp) cc_final: 0.6319 (ppp) REVERT: Q 360 LYS cc_start: 0.6511 (ptpp) cc_final: 0.6135 (ptpp) REVERT: Q 418 MET cc_start: 0.6877 (ppp) cc_final: 0.6425 (ppp) REVERT: I 72 ASP cc_start: 0.7117 (t70) cc_final: 0.6778 (t70) REVERT: I 109 MET cc_start: 0.7291 (ttt) cc_final: 0.6502 (ttt) REVERT: I 148 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mt0) REVERT: I 183 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7081 (mt) REVERT: I 199 ASP cc_start: 0.6249 (t0) cc_final: 0.5900 (t0) REVERT: I 238 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7129 (tm-30) REVERT: I 254 LYS cc_start: 0.7848 (tppt) cc_final: 0.7527 (tppt) REVERT: J 80 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6104 (tt0) REVERT: J 94 GLU cc_start: 0.6714 (pp20) cc_final: 0.6276 (pp20) REVERT: J 98 GLU cc_start: 0.6701 (tp30) cc_final: 0.6438 (tp30) REVERT: J 105 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7636 (ttpt) REVERT: J 129 GLN cc_start: 0.7642 (tt0) cc_final: 0.7286 (mt0) REVERT: J 206 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7413 (tp30) REVERT: K 203 PHE cc_start: 0.6580 (t80) cc_final: 0.6084 (t80) REVERT: L 104 MET cc_start: 0.4956 (mmp) cc_final: 0.4687 (mmp) REVERT: L 220 LYS cc_start: 0.6051 (mmtm) cc_final: 0.5733 (mmtm) REVERT: L 248 ASP cc_start: 0.6893 (p0) cc_final: 0.6536 (p0) REVERT: L 260 ARG cc_start: 0.6684 (mmm-85) cc_final: 0.6457 (mmm-85) REVERT: M 15 TRP cc_start: 0.7436 (m100) cc_final: 0.7218 (m-10) REVERT: M 35 ASP cc_start: 0.6943 (m-30) cc_final: 0.6535 (m-30) REVERT: M 61 ASP cc_start: 0.7536 (t70) cc_final: 0.7151 (t0) REVERT: M 63 TRP cc_start: 0.5948 (m100) cc_final: 0.5408 (m100) REVERT: M 99 PHE cc_start: 0.6970 (m-80) cc_final: 0.6476 (m-80) REVERT: M 195 THR cc_start: 0.8019 (m) cc_final: 0.7592 (t) REVERT: M 259 ASP cc_start: 0.6958 (t0) cc_final: 0.6609 (t0) REVERT: N 78 TRP cc_start: 0.7013 (m100) cc_final: 0.6322 (m100) REVERT: N 213 GLN cc_start: 0.7848 (pp30) cc_final: 0.7529 (pp30) REVERT: N 230 LYS cc_start: 0.8313 (tppp) cc_final: 0.8025 (tppp) REVERT: N 236 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6586 (mm-30) REVERT: N 241 THR cc_start: 0.8395 (t) cc_final: 0.8088 (p) REVERT: N 254 LYS cc_start: 0.7762 (tptt) cc_final: 0.7514 (tptt) REVERT: N 260 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.6338 (mtm-85) REVERT: P 201 PHE cc_start: 0.7579 (t80) cc_final: 0.7369 (t80) outliers start: 119 outliers final: 88 residues processed: 860 average time/residue: 0.2193 time to fit residues: 301.0227 Evaluate side-chains 901 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 805 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN 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 A residue 264 ILE Chi-restraints excluded: chain B residue 13 ASN 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 10 GLU 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 D residue 264 ILE 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 156 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 69 HIS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 129 GLN Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 212 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 20 VAL 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 132 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU 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 148 GLN 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 80 GLU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 156 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 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 10 GLU 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 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 O residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 132 MET 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 206 GLU 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: 1.9990 chunk 383 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 389 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 348 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 129 GLN ** 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 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** 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 ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** 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 = 0.4763 r_free = 0.4763 target = 0.241826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.185897 restraints weight = 66277.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.191480 restraints weight = 32241.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.191147 restraints weight = 19293.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.192077 restraints weight = 18809.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.192537 restraints weight = 17383.256| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36753 Z= 0.162 Angle : 0.728 17.709 50271 Z= 0.368 Chirality : 0.046 0.228 5432 Planarity : 0.004 0.050 5969 Dihedral : 16.880 145.481 5791 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.00 % Allowed : 20.05 % 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: 0.02 (0.13), residues: 3971 helix: 0.98 (0.12), residues: 1884 sheet: -0.03 (0.19), residues: 712 loop : -1.24 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 155 TYR 0.020 0.001 TYR O 87 PHE 0.045 0.001 PHE N 99 TRP 0.027 0.002 TRP G 78 HIS 0.009 0.001 HIS F 69 Details of bonding type rmsd covalent geometry : bond 0.00364 (36705) covalent geometry : angle 0.71450 (50248) hydrogen bonds : bond 0.03966 ( 1694) hydrogen bonds : angle 4.69639 ( 4842) metal coordination : bond 0.02047 ( 48) metal coordination : angle 6.49019 ( 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 925 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 819 time to evaluate : 1.214 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: A 72 ASP cc_start: 0.7217 (t70) cc_final: 0.6785 (t0) REVERT: A 98 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6642 (mm-30) REVERT: A 138 GLU cc_start: 0.6884 (mp0) cc_final: 0.6430 (mp0) REVERT: A 148 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: A 183 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7479 (mt) REVERT: A 223 PHE cc_start: 0.8327 (m-80) cc_final: 0.7618 (m-80) REVERT: A 238 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 94 GLU cc_start: 0.6568 (pp20) cc_final: 0.6167 (pp20) REVERT: B 124 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (m) REVERT: B 140 THR cc_start: 0.8009 (m) cc_final: 0.7671 (t) REVERT: B 185 LEU cc_start: 0.7865 (mt) cc_final: 0.7419 (mp) REVERT: B 208 GLN cc_start: 0.7652 (tt0) cc_final: 0.7368 (tt0) REVERT: C 9 GLU cc_start: 0.7603 (tp30) cc_final: 0.7366 (tp30) REVERT: C 24 LEU cc_start: 0.8170 (mm) cc_final: 0.7684 (mp) REVERT: C 201 PHE cc_start: 0.8100 (t80) cc_final: 0.7889 (t80) REVERT: C 203 PHE cc_start: 0.7447 (t80) cc_final: 0.6846 (t80) REVERT: C 267 LYS cc_start: 0.8192 (pttp) cc_final: 0.7869 (pttp) REVERT: D 80 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7079 (tp30) REVERT: D 103 THR cc_start: 0.6740 (t) cc_final: 0.6051 (p) REVERT: D 104 MET cc_start: 0.6883 (mmp) cc_final: 0.5974 (mmp) REVERT: D 132 MET cc_start: 0.8282 (ppp) cc_final: 0.7841 (ppp) REVERT: D 220 LYS cc_start: 0.5779 (mmtm) cc_final: 0.5528 (mmtm) REVERT: D 236 GLU cc_start: 0.6926 (mp0) cc_final: 0.6500 (mp0) REVERT: E 35 ASP cc_start: 0.7031 (m-30) cc_final: 0.6517 (m-30) REVERT: E 61 ASP cc_start: 0.7670 (t70) cc_final: 0.7249 (t70) REVERT: E 97 GLN cc_start: 0.8247 (pm20) cc_final: 0.7956 (pm20) REVERT: E 157 HIS cc_start: 0.8260 (m-70) cc_final: 0.7514 (m-70) REVERT: E 158 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7475 (mm-40) REVERT: E 161 LYS cc_start: 0.8385 (mttt) cc_final: 0.7712 (mttt) REVERT: E 195 THR cc_start: 0.7985 (m) cc_final: 0.7491 (t) REVERT: E 208 GLN cc_start: 0.7385 (tp40) cc_final: 0.7001 (tm-30) REVERT: E 270 LYS cc_start: 0.6823 (mtpt) cc_final: 0.6245 (pttt) REVERT: F 64 GLN cc_start: 0.5805 (tp40) cc_final: 0.5286 (tp-100) REVERT: F 241 THR cc_start: 0.8351 (t) cc_final: 0.8147 (m) REVERT: F 254 LYS cc_start: 0.8083 (tptt) cc_final: 0.7786 (tptt) REVERT: H 201 PHE cc_start: 0.8110 (t80) cc_final: 0.7769 (t80) REVERT: H 205 LYS cc_start: 0.8210 (mmmm) cc_final: 0.7540 (mmmm) REVERT: H 242 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7087 (tp-100) REVERT: R 368 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.4562 (mm) REVERT: R 418 MET cc_start: 0.7434 (ppp) cc_final: 0.6892 (ppp) REVERT: Q 360 LYS cc_start: 0.6053 (ptpp) cc_final: 0.5617 (ptpp) REVERT: Q 413 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6324 (mmt) REVERT: Q 418 MET cc_start: 0.7541 (ppp) cc_final: 0.7003 (ppp) REVERT: I 72 ASP cc_start: 0.7073 (t70) cc_final: 0.6774 (t70) REVERT: I 109 MET cc_start: 0.7153 (ttt) cc_final: 0.6601 (ttt) REVERT: I 148 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: I 183 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7382 (mt) REVERT: I 199 ASP cc_start: 0.6471 (t0) cc_final: 0.6082 (t0) REVERT: I 238 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7129 (tm-30) REVERT: J 80 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6131 (tt0) REVERT: J 94 GLU cc_start: 0.6726 (pp20) cc_final: 0.6284 (pp20) REVERT: J 98 GLU cc_start: 0.6780 (tp30) cc_final: 0.6565 (tp30) REVERT: J 105 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7818 (ttpt) REVERT: J 129 GLN cc_start: 0.7663 (tt0) cc_final: 0.7279 (mt0) REVERT: K 203 PHE cc_start: 0.6866 (t80) cc_final: 0.6395 (t80) REVERT: L 80 GLU cc_start: 0.7454 (tp30) cc_final: 0.7166 (tp30) REVERT: L 104 MET cc_start: 0.5409 (mmp) cc_final: 0.5064 (mmp) REVERT: L 220 LYS cc_start: 0.6003 (mmtm) cc_final: 0.5703 (mmtm) REVERT: L 248 ASP cc_start: 0.6874 (p0) cc_final: 0.6490 (p0) REVERT: L 260 ARG cc_start: 0.6573 (mmm-85) cc_final: 0.6354 (mmm-85) REVERT: M 28 ILE cc_start: 0.6945 (pt) cc_final: 0.6740 (mm) REVERT: M 35 ASP cc_start: 0.7028 (m-30) cc_final: 0.6632 (m-30) REVERT: M 61 ASP cc_start: 0.7705 (t70) cc_final: 0.7088 (t0) REVERT: M 63 TRP cc_start: 0.6534 (m100) cc_final: 0.5420 (m100) REVERT: M 99 PHE cc_start: 0.7660 (m-80) cc_final: 0.6807 (m-80) REVERT: M 195 THR cc_start: 0.8080 (m) cc_final: 0.7602 (t) REVERT: M 212 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7991 (mm-40) REVERT: M 259 ASP cc_start: 0.7775 (t0) cc_final: 0.7455 (t0) REVERT: M 267 LYS cc_start: 0.7742 (tptt) cc_final: 0.7493 (tppt) REVERT: N 78 TRP cc_start: 0.7413 (m100) cc_final: 0.6157 (m100) REVERT: N 87 TYR cc_start: 0.7148 (t80) cc_final: 0.6903 (t80) REVERT: N 213 GLN cc_start: 0.7869 (pp30) cc_final: 0.7495 (pp30) REVERT: N 236 GLU cc_start: 0.6781 (mm-30) cc_final: 0.6549 (mm-30) REVERT: N 241 THR cc_start: 0.8446 (t) cc_final: 0.8167 (p) REVERT: N 254 LYS cc_start: 0.7685 (tptt) cc_final: 0.7435 (tptt) REVERT: N 260 ARG cc_start: 0.6704 (mtm-85) cc_final: 0.6373 (mtm-85) REVERT: P 201 PHE cc_start: 0.8323 (t80) cc_final: 0.8041 (t80) outliers start: 106 outliers final: 87 residues processed: 864 average time/residue: 0.2167 time to fit residues: 298.3048 Evaluate side-chains 900 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 805 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN 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 A residue 264 ILE Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 10 GLU 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 D residue 264 ILE 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 156 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 102 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 20 VAL 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 203 PHE Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU 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 95 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 148 GLN 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 80 GLU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 156 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 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 10 GLU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 ARG 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 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 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 206 GLU 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: 0.8980 chunk 307 optimal weight: 0.9980 chunk 342 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 264 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 400 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN ** E 139 HIS ** 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** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 82 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.270022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.250976 restraints weight = 84592.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.248855 restraints weight = 109452.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.247609 restraints weight = 85536.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.247344 restraints weight = 77941.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.247257 restraints weight = 67158.534| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.258 36753 Z= 0.228 Angle : 0.871 59.199 50271 Z= 0.473 Chirality : 0.046 0.387 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.879 145.479 5791 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 20.30 % Favored : 76.87 % Cbeta Deviations : 0.05 % 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: 0.99 (0.12), residues: 1874 sheet: 0.00 (0.19), residues: 708 loop : -1.23 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 155 TYR 0.020 0.001 TYR I 134 PHE 0.040 0.001 PHE N 99 TRP 0.024 0.001 TRP G 78 HIS 0.013 0.001 HIS G 69 Details of bonding type rmsd covalent geometry : bond 0.00511 (36705) covalent geometry : angle 0.86113 (50248) hydrogen bonds : bond 0.04008 ( 1694) hydrogen bonds : angle 4.70350 ( 4842) metal coordination : bond 0.02006 ( 48) metal coordination : angle 6.30639 ( 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 905 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 805 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7251 (t70) cc_final: 0.6801 (t0) REVERT: A 98 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6597 (mm-30) REVERT: A 138 GLU cc_start: 0.6957 (mp0) cc_final: 0.6452 (mp0) REVERT: A 148 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8587 (mt0) REVERT: A 223 PHE cc_start: 0.8223 (m-80) cc_final: 0.7505 (m-80) REVERT: A 238 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 94 GLU cc_start: 0.6656 (pp20) cc_final: 0.6229 (pp20) REVERT: B 124 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 140 THR cc_start: 0.8037 (m) cc_final: 0.7703 (t) REVERT: B 185 LEU cc_start: 0.7753 (mt) cc_final: 0.7300 (mp) REVERT: B 208 GLN cc_start: 0.7735 (tt0) cc_final: 0.7454 (tt0) REVERT: C 9 GLU cc_start: 0.7539 (tp30) cc_final: 0.7271 (tp30) REVERT: C 24 LEU cc_start: 0.8163 (mm) cc_final: 0.7665 (mp) REVERT: C 203 PHE cc_start: 0.7170 (t80) cc_final: 0.6603 (t80) REVERT: C 267 LYS cc_start: 0.8028 (pttp) cc_final: 0.7592 (pttp) REVERT: D 103 THR cc_start: 0.5560 (t) cc_final: 0.5293 (p) REVERT: D 104 MET cc_start: 0.6239 (mmp) cc_final: 0.5495 (mmp) REVERT: D 132 MET cc_start: 0.7709 (ppp) cc_final: 0.7263 (ppp) REVERT: D 220 LYS cc_start: 0.5848 (mmtm) cc_final: 0.5615 (mmtm) REVERT: D 236 GLU cc_start: 0.7040 (mp0) cc_final: 0.6559 (mp0) REVERT: E 35 ASP cc_start: 0.7073 (m-30) cc_final: 0.6576 (m-30) REVERT: E 61 ASP cc_start: 0.7535 (t70) cc_final: 0.7303 (t70) REVERT: E 157 HIS cc_start: 0.7695 (m-70) cc_final: 0.7353 (m-70) REVERT: E 158 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7156 (mm-40) REVERT: E 161 LYS cc_start: 0.8158 (mttt) cc_final: 0.7646 (mttt) REVERT: E 195 THR cc_start: 0.8044 (m) cc_final: 0.7548 (t) REVERT: E 208 GLN cc_start: 0.7222 (tp40) cc_final: 0.6977 (tm-30) REVERT: E 270 LYS cc_start: 0.6555 (mtpt) cc_final: 0.6125 (pttt) REVERT: F 64 GLN cc_start: 0.5515 (tp40) cc_final: 0.5069 (tp-100) REVERT: F 241 THR cc_start: 0.8361 (t) cc_final: 0.8148 (m) REVERT: F 254 LYS cc_start: 0.8050 (tptt) cc_final: 0.7756 (tptt) REVERT: H 201 PHE cc_start: 0.7425 (t80) cc_final: 0.7133 (t80) REVERT: H 205 LYS cc_start: 0.7581 (mmmm) cc_final: 0.7050 (mmmm) REVERT: H 242 GLN cc_start: 0.7383 (tp-100) cc_final: 0.6849 (tp-100) REVERT: R 368 LEU cc_start: 0.4926 (OUTLIER) cc_final: 0.4700 (mm) REVERT: R 418 MET cc_start: 0.6729 (ppp) cc_final: 0.6312 (ppp) REVERT: Q 360 LYS cc_start: 0.6516 (ptpp) cc_final: 0.6140 (ptpp) REVERT: Q 418 MET cc_start: 0.6853 (ppp) cc_final: 0.6421 (ppp) REVERT: I 72 ASP cc_start: 0.7158 (t70) cc_final: 0.6819 (t70) REVERT: I 109 MET cc_start: 0.7229 (ttt) cc_final: 0.6626 (ttt) REVERT: I 148 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8726 (mt0) REVERT: I 183 ILE cc_start: 0.7435 (OUTLIER) cc_final: 0.7123 (mt) REVERT: I 199 ASP cc_start: 0.6281 (t0) cc_final: 0.5935 (t0) REVERT: I 238 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7159 (tm-30) REVERT: J 80 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6178 (tt0) REVERT: J 94 GLU cc_start: 0.6774 (pp20) cc_final: 0.6328 (pp20) REVERT: J 98 GLU cc_start: 0.6685 (tp30) cc_final: 0.6441 (tp30) REVERT: J 129 GLN cc_start: 0.7668 (tt0) cc_final: 0.7277 (mt0) REVERT: K 203 PHE cc_start: 0.6507 (t80) cc_final: 0.6016 (t80) REVERT: L 104 MET cc_start: 0.4973 (mmp) cc_final: 0.4668 (mmp) REVERT: L 220 LYS cc_start: 0.6085 (mmtm) cc_final: 0.5857 (mmtm) REVERT: L 248 ASP cc_start: 0.6916 (p0) cc_final: 0.6511 (p0) REVERT: L 260 ARG cc_start: 0.6697 (mmm-85) cc_final: 0.6458 (mmm-85) REVERT: M 28 ILE cc_start: 0.6968 (pt) cc_final: 0.6746 (mm) REVERT: M 35 ASP cc_start: 0.7106 (m-30) cc_final: 0.6704 (m-30) REVERT: M 61 ASP cc_start: 0.7565 (t70) cc_final: 0.7162 (t0) REVERT: M 63 TRP cc_start: 0.5923 (m100) cc_final: 0.5239 (m100) REVERT: M 99 PHE cc_start: 0.6986 (m-80) cc_final: 0.6481 (m-80) REVERT: M 195 THR cc_start: 0.8057 (m) cc_final: 0.7617 (t) REVERT: M 212 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7705 (mm-40) REVERT: M 259 ASP cc_start: 0.7131 (t0) cc_final: 0.6830 (t0) REVERT: M 267 LYS cc_start: 0.7450 (tptt) cc_final: 0.7234 (tppt) REVERT: N 78 TRP cc_start: 0.7035 (m100) cc_final: 0.6117 (m100) REVERT: N 213 GLN cc_start: 0.7842 (pp30) cc_final: 0.7527 (pp30) REVERT: N 236 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6602 (mm-30) REVERT: N 241 THR cc_start: 0.8464 (t) cc_final: 0.8156 (p) REVERT: N 254 LYS cc_start: 0.7679 (tptt) cc_final: 0.7407 (tptt) REVERT: N 260 ARG cc_start: 0.6703 (mtm-85) cc_final: 0.6342 (mtm-85) REVERT: P 201 PHE cc_start: 0.7565 (t80) cc_final: 0.7351 (t80) outliers start: 100 outliers final: 88 residues processed: 850 average time/residue: 0.2260 time to fit residues: 305.6815 Evaluate side-chains 898 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 804 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 124 VAL 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 167 LEU Chi-restraints excluded: chain C residue 204 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 D residue 264 ILE 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 156 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 102 GLN Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 20 VAL 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 206 GLU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU 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 95 THR Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 148 GLN 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 80 GLU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 156 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 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 10 GLU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 ARG 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 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 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 206 GLU 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: 0.9990 chunk 27 optimal weight: 0.0770 chunk 379 optimal weight: 8.9990 chunk 310 optimal weight: 0.3980 chunk 169 optimal weight: 0.1980 chunk 350 optimal weight: 0.3980 chunk 124 optimal weight: 50.0000 chunk 299 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 129 GLN ** E 139 HIS ** 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** 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 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** 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 = 0.4953 r_free = 0.4953 target = 0.270012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.251127 restraints weight = 84026.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.249219 restraints weight = 108897.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.248263 restraints weight = 86612.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.247854 restraints weight = 87031.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.247287 restraints weight = 80090.747| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.258 36753 Z= 0.228 Angle : 0.871 59.199 50271 Z= 0.473 Chirality : 0.046 0.387 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.879 145.479 5791 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.69 % Allowed : 20.50 % Favored : 76.82 % Cbeta Deviations : 0.05 % 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: 0.99 (0.12), residues: 1874 sheet: 0.00 (0.19), residues: 708 loop : -1.23 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 155 TYR 0.020 0.001 TYR I 134 PHE 0.040 0.001 PHE N 99 TRP 0.024 0.001 TRP G 78 HIS 0.013 0.001 HIS G 69 Details of bonding type rmsd covalent geometry : bond 0.00511 (36705) covalent geometry : angle 0.86114 (50248) hydrogen bonds : bond 0.04008 ( 1694) hydrogen bonds : angle 4.70350 ( 4842) metal coordination : bond 0.02006 ( 48) metal coordination : angle 6.30639 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7418.60 seconds wall clock time: 128 minutes 19.70 seconds (7699.70 seconds total)