Starting phenix.real_space_refine on Tue Sep 15 03:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1z_14453/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1z_14453/09_2026/7z1z_14453.map" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35605 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "B" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "D" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 Chain: "E" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "F" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "G" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "H" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 674 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "Q" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 667 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "X" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "W" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "U" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "I" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2235 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain: "J" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1639 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2130 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 249} Chain breaks: 1 Chain: "L" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2051 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 Chain: "M" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2116 Classifications: {'peptide': 260} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Chain: "N" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2115 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 247} Chain breaks: 1 Chain: "O" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1647 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 1 Chain: "P" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1761 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 11, 'TRANS': 205} Chain: "Y" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Z" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "a" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 252 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 40 52.555 98.275 57.044 1.00 82.30 S ATOM 350 SG CYS A 43 55.029 100.117 57.886 1.00 80.20 S ATOM 2550 SG CYS B 40 141.347 77.147 78.894 1.00234.54 S ATOM 2571 SG CYS B 43 140.373 75.690 76.304 1.00237.78 S ATOM 4203 SG CYS C 40 112.859 55.219 47.405 1.00165.74 S ATOM 4224 SG CYS C 43 115.169 57.021 48.375 1.00154.11 S ATOM 8384 SG CYS E 40 35.028 89.415 83.743 1.00201.72 S ATOM 8405 SG CYS E 43 36.217 86.876 85.415 1.00192.57 S ATOM 10469 SG CYS F 40 51.442 57.845 50.351 1.00254.89 S ATOM 10490 SG CYS F 43 49.499 55.856 51.548 1.00254.39 S ATOM 12615 SG CYS G 40 27.432 33.168 82.886 1.00236.12 S ATOM 12636 SG CYS G 43 28.446 35.251 80.527 1.00234.83 S ATOM 18796 SG CYS I 40 112.929 111.593 57.211 1.00 82.30 S ATOM 18817 SG CYS I 43 110.445 109.764 58.051 1.00 80.20 S ATOM 21017 SG CYS J 40 23.984 133.086 78.061 1.00234.54 S ATOM 21038 SG CYS J 43 24.983 134.515 75.464 1.00237.78 S ATOM 22670 SG CYS K 40 52.782 154.640 46.597 1.00165.74 S ATOM 22691 SG CYS K 43 50.461 152.852 47.564 1.00154.11 S ATOM 26851 SG CYS M 40 130.237 120.704 83.969 1.00201.72 S ATOM 26872 SG CYS M 43 129.036 123.262 85.604 1.00192.57 S ATOM 28936 SG CYS N 40 114.167 151.949 50.107 1.00254.89 S ATOM 28957 SG CYS N 43 116.103 153.948 51.301 1.00254.39 S ATOM 31082 SG CYS O 40 137.932 176.928 82.593 1.00236.12 S ATOM 31103 SG CYS O 43 136.935 174.822 80.247 1.00234.83 S Time building chain proxies: 8.26, per 1000 atoms: 0.23 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: 3.04 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: 4.01 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: 7.86 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10707 1.34 - 1.46: 6374 1.46 - 1.57: 19126 1.57 - 1.69: 272 1.69 - 1.81: 226 Bond restraints: 36705 Sorted by residual: bond pdb=" C3' DC Y 17 " pdb=" C2' DC Y 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC Z 28 " pdb=" C2' DC Z 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC X 17 " pdb=" C2' DC X 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC W 28 " pdb=" C2' DC W 28 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC X 14 " pdb=" C2' DC X 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 36700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 48772 1.39 - 2.77: 1211 2.77 - 4.16: 188 4.16 - 5.54: 43 5.54 - 6.93: 34 Bond angle restraints: 50248 Sorted by residual: angle pdb=" N3 DT W 34 " pdb=" C4 DT W 34 " pdb=" O4 DT W 34 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT a 9 " pdb=" C4 DT a 9 " pdb=" O4 DT a 9 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT U 10 " pdb=" C4 DT U 10 " pdb=" O4 DT U 10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT Y 15 " pdb=" C4 DT Y 15 " pdb=" O4 DT Y 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 50243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.60: 20355 27.60 - 55.20: 1066 55.20 - 82.79: 117 82.79 - 110.39: 12 110.39 - 137.99: 2 Dihedral angle restraints: 21552 sinusoidal: 9895 harmonic: 11657 Sorted by residual: dihedral pdb=" C4' DG W 20 " pdb=" C3' DG W 20 " pdb=" O3' DG W 20 " pdb=" P DT W 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.01 137.99 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DG Z 20 " pdb=" C3' DG Z 20 " pdb=" O3' DG Z 20 " pdb=" P DT Z 21 " ideal model delta sinusoidal sigma weight residual 220.00 82.02 137.98 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU H 219 " pdb=" C GLU H 219 " pdb=" N LYS H 220 " pdb=" CA LYS H 220 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3605 0.034 - 0.069: 1198 0.069 - 0.103: 469 0.103 - 0.137: 146 0.137 - 0.172: 14 Chirality restraints: 5432 Sorted by residual: chirality pdb=" CA VAL H 79 " pdb=" N VAL H 79 " pdb=" C VAL H 79 " pdb=" CB VAL H 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA VAL P 79 " pdb=" N VAL P 79 " pdb=" C VAL P 79 " pdb=" CB VAL P 79 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA GLN D 218 " pdb=" N GLN D 218 " pdb=" C GLN D 218 " pdb=" CB GLN D 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 5429 not shown) Planarity restraints: 5969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO I 273 " -0.064 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO I 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 273 " -0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A 274 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 272 " 0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 273 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " 0.046 5.00e-02 4.00e+02 ... (remaining 5966 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5048 2.76 - 3.29: 34919 3.29 - 3.83: 59506 3.83 - 4.36: 67800 4.36 - 4.90: 111512 Nonbonded interactions: 278785 Sorted by model distance: nonbonded pdb=" OG1 THR M 95 " pdb=" OE1 GLU M 98 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR E 95 " pdb=" OE1 GLU E 98 " model vdw 2.225 3.040 nonbonded pdb=" O ASP L 61 " pdb=" OG SER L 114 " model vdw 2.225 3.040 nonbonded pdb=" O ASP D 61 " pdb=" OG SER D 114 " model vdw 2.226 3.040 nonbonded pdb=" O ASP C 18 " pdb=" OG SER C 21 " model vdw 2.227 3.040 ... (remaining 278780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'C' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'D' and resid 4 through 272) selection = (chain 'E' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'F' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'I' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'K' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'L' and resid 4 through 272) selection = (chain 'M' and (resid 4 through 36 or resid 61 through 272)) selection = (chain 'N' and (resid 4 through 36 or resid 61 through 272)) } ncs_group { reference = (chain 'B' and (resid 2 through 215 or resid 301)) selection = (chain 'G' and resid 2 through 301) selection = (chain 'J' and (resid 2 through 215 or resid 301)) selection = (chain 'O' and resid 2 through 301) } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and resid 348 through 428) } ncs_group { reference = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 39.230 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.263 36753 Z= 0.237 Angle : 1.184 75.246 50271 Z= 0.406 Chirality : 0.042 0.172 5432 Planarity : 0.004 0.097 5969 Dihedral : 15.201 137.992 14014 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 3971 helix: 1.14 (0.12), residues: 1808 sheet: 0.22 (0.21), residues: 694 loop : -1.02 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 155 TYR 0.014 0.001 TYR M 225 PHE 0.020 0.001 PHE N 203 TRP 0.017 0.001 TRP C 245 HIS 0.004 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.23 (36705) covalent geometry : angle 0.54331 / 0.35 (50248) hydrogen bonds : bond 0.21904 / 14.64 ( 1694) hydrogen bonds : angle 7.66322 / 5.51 ( 4842) metal coordination : bond 0.05432 / 3.63 ( 48) metal coordination : angle 49.21018 / 35.23 ( 23) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 929 time to evaluate : 1.779 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: 0.2363 time to fit residues: 350.0111 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 : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.0870 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN B 13 ASN B 82 ASN C 39 GLN C 233 HIS ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 62 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 148 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 ASN G 212 GLN H 162 ASN H 266 ASN I 4 ASN I 17 GLN I 38 GLN ** I 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN K 233 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 GLN M 139 HIS M 157 HIS M 204 ASN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN O 82 ASN O 212 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.247024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.191547 restraints weight = 64765.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.197296 restraints weight = 30262.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.199062 restraints weight = 18479.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.200447 restraints weight = 14793.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201258 restraints weight = 12314.090| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 36753 Z= 0.176 Angle : 0.730 22.252 50271 Z= 0.373 Chirality : 0.047 0.270 5432 Planarity : 0.005 0.071 5969 Dihedral : 16.196 141.220 5791 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.50 % Allowed : 9.16 % Favored : 89.34 % 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: 0.28 (0.13), residues: 3971 helix: 1.19 (0.12), residues: 1866 sheet: 0.24 (0.20), residues: 720 loop : -1.18 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 222 TYR 0.020 0.002 TYR N 134 PHE 0.022 0.001 PHE E 203 TRP 0.034 0.001 TRP P 245 HIS 0.026 0.002 HIS K 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (36705) covalent geometry : angle 0.68483 / 0.37 (50248) hydrogen bonds : bond 0.06442 / 4.28 ( 1694) hydrogen bonds : angle 5.39979 / 3.86 ( 4842) metal coordination : bond 0.05858 / 4.33 ( 48) metal coordination : angle 11.81643 / 8.44 ( 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 925 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 872 time to evaluate : 1.257 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: A 76 LEU cc_start: 0.8185 (tp) cc_final: 0.7973 (tp) REVERT: A 98 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6739 (mm-30) REVERT: A 162 ASN cc_start: 0.8168 (t0) cc_final: 0.7724 (t0) REVERT: A 199 ASP cc_start: 0.6879 (t0) cc_final: 0.6563 (t0) REVERT: A 206 GLU cc_start: 0.6705 (tp30) cc_final: 0.6314 (tm-30) REVERT: A 223 PHE cc_start: 0.8158 (m-80) cc_final: 0.7522 (m-80) REVERT: A 238 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 129 GLN cc_start: 0.7381 (tt0) cc_final: 0.7173 (mt0) REVERT: B 140 THR cc_start: 0.8046 (m) cc_final: 0.7785 (t) REVERT: B 206 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6960 (tp30) REVERT: B 208 GLN cc_start: 0.7500 (tt0) cc_final: 0.7191 (tt0) REVERT: C 9 GLU cc_start: 0.7766 (tp30) cc_final: 0.7501 (tp30) REVERT: C 24 LEU cc_start: 0.8200 (mm) cc_final: 0.7742 (mp) REVERT: C 105 LYS cc_start: 0.7616 (ttpp) cc_final: 0.7415 (ttpp) REVERT: C 186 ASN cc_start: 0.8213 (m-40) cc_final: 0.7899 (t0) REVERT: C 198 MET cc_start: 0.6996 (pmm) cc_final: 0.6170 (pmm) REVERT: C 203 PHE cc_start: 0.7049 (t80) cc_final: 0.6688 (t80) REVERT: C 204 ASN cc_start: 0.8128 (m-40) cc_final: 0.7917 (m110) REVERT: C 205 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7904 (mmmt) REVERT: C 222 ARG cc_start: 0.5531 (ptm160) cc_final: 0.4842 (ptm160) REVERT: C 245 TRP cc_start: 0.7649 (m-90) cc_final: 0.7299 (m-90) REVERT: C 267 LYS cc_start: 0.8237 (pttp) cc_final: 0.7870 (pttp) REVERT: D 70 TYR cc_start: 0.6731 (t80) cc_final: 0.6480 (t80) REVERT: D 103 THR cc_start: 0.6653 (t) cc_final: 0.6005 (p) REVERT: D 104 MET cc_start: 0.6737 (mmp) cc_final: 0.5773 (mmp) REVERT: D 205 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7392 (tppt) REVERT: D 212 GLN cc_start: 0.6880 (tm-30) cc_final: 0.6629 (tm-30) REVERT: D 236 GLU cc_start: 0.6921 (mp0) cc_final: 0.6614 (mp0) REVERT: D 238 GLN cc_start: 0.8442 (mt0) cc_final: 0.8169 (mt0) REVERT: D 268 ASP cc_start: 0.7027 (p0) cc_final: 0.6432 (p0) REVERT: E 99 PHE cc_start: 0.7241 (m-80) cc_final: 0.6757 (m-80) REVERT: E 153 VAL cc_start: 0.8770 (t) cc_final: 0.7629 (p) REVERT: E 163 THR cc_start: 0.7575 (p) cc_final: 0.7124 (p) REVERT: E 181 THR cc_start: 0.8322 (p) cc_final: 0.7838 (t) REVERT: E 202 ILE cc_start: 0.7979 (tp) cc_final: 0.7749 (tp) REVERT: E 225 TYR cc_start: 0.5050 (t80) cc_final: 0.4352 (t80) REVERT: E 270 LYS cc_start: 0.7041 (mtpt) cc_final: 0.6566 (mtpt) REVERT: E 271 PHE cc_start: 0.7180 (m-80) cc_final: 0.6628 (m-80) REVERT: F 62 HIS cc_start: 0.6791 (m170) cc_final: 0.6359 (m170) REVERT: F 213 GLN cc_start: 0.7804 (pp30) cc_final: 0.7553 (pp30) REVERT: F 230 LYS cc_start: 0.8221 (tppp) cc_final: 0.7828 (tppp) REVERT: F 254 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7674 (tmtt) REVERT: G 110 PHE cc_start: 0.7348 (m-80) cc_final: 0.7049 (m-80) REVERT: G 155 ARG cc_start: 0.8046 (pmt170) cc_final: 0.7680 (tpt170) REVERT: G 198 MET cc_start: 0.8151 (tpt) cc_final: 0.7823 (tpt) REVERT: H 132 MET cc_start: 0.7506 (tpt) cc_final: 0.6945 (tpt) REVERT: H 196 SER cc_start: 0.4990 (p) cc_final: 0.4784 (t) REVERT: H 198 MET cc_start: 0.7638 (mpp) cc_final: 0.7322 (mpp) REVERT: H 201 PHE cc_start: 0.8007 (t80) cc_final: 0.7615 (t80) REVERT: H 205 LYS cc_start: 0.8256 (mmmm) cc_final: 0.7778 (mmmm) REVERT: H 206 GLU cc_start: 0.6856 (pp20) cc_final: 0.5532 (pp20) REVERT: H 262 LEU cc_start: 0.6725 (mm) cc_final: 0.6494 (mm) REVERT: R 413 MET cc_start: 0.6479 (mmm) cc_final: 0.6113 (mmm) REVERT: R 418 MET cc_start: 0.7351 (ppp) cc_final: 0.6795 (ppp) REVERT: Q 360 LYS cc_start: 0.5522 (ptpp) cc_final: 0.5293 (ptpp) REVERT: Q 387 MET cc_start: 0.7295 (tpp) cc_final: 0.7049 (mmm) REVERT: Q 418 MET cc_start: 0.7431 (ppp) cc_final: 0.6849 (ppp) REVERT: I 72 ASP cc_start: 0.7082 (t70) cc_final: 0.6807 (t70) REVERT: I 98 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6627 (mm-30) REVERT: J 129 GLN cc_start: 0.7562 (tt0) cc_final: 0.7077 (mt0) REVERT: J 206 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7473 (tp30) REVERT: J 211 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6744 (tm-30) REVERT: K 109 MET cc_start: 0.7595 (tpp) cc_final: 0.7280 (pmm) REVERT: L 104 MET cc_start: 0.5324 (mmp) cc_final: 0.4908 (mmp) REVERT: L 110 PHE cc_start: 0.7106 (m-80) cc_final: 0.6680 (t80) REVERT: L 221 ILE cc_start: 0.6951 (mt) cc_final: 0.6641 (tt) REVERT: L 260 ARG cc_start: 0.6700 (mmm-85) cc_final: 0.6357 (mmm-85) REVERT: L 268 ASP cc_start: 0.7119 (p0) cc_final: 0.6768 (p0) REVERT: M 35 ASP cc_start: 0.6502 (m-30) cc_final: 0.6070 (m-30) REVERT: M 38 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7222 (tm-30) REVERT: M 61 ASP cc_start: 0.7140 (t70) cc_final: 0.6517 (t0) REVERT: M 99 PHE cc_start: 0.7550 (m-80) cc_final: 0.6943 (m-80) REVERT: M 157 HIS cc_start: 0.8162 (m170) cc_final: 0.7941 (m-70) REVERT: M 161 LYS cc_start: 0.8697 (mttt) cc_final: 0.8441 (mttt) REVERT: M 207 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7487 (mm-40) REVERT: M 208 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6975 (tm-30) REVERT: M 259 ASP cc_start: 0.7524 (t0) cc_final: 0.7323 (t0) REVERT: M 271 PHE cc_start: 0.6775 (m-80) cc_final: 0.6131 (m-80) REVERT: N 186 ASN cc_start: 0.4958 (m110) cc_final: 0.4568 (m-40) REVERT: N 213 GLN cc_start: 0.7640 (pp30) cc_final: 0.7136 (pp30) REVERT: N 241 THR cc_start: 0.8097 (t) cc_final: 0.7744 (m) REVERT: N 252 VAL cc_start: 0.8199 (p) cc_final: 0.7950 (m) REVERT: N 260 ARG cc_start: 0.6745 (mtm-85) cc_final: 0.6387 (mtm-85) REVERT: O 104 MET cc_start: 0.7061 (mmp) cc_final: 0.6164 (mmp) REVERT: O 110 PHE cc_start: 0.7322 (m-80) cc_final: 0.7014 (m-80) REVERT: O 132 MET cc_start: 0.8216 (mpp) cc_final: 0.7805 (mpp) REVERT: O 200 ILE cc_start: 0.8082 (mm) cc_final: 0.7801 (mm) REVERT: O 201 PHE cc_start: 0.8158 (t80) cc_final: 0.7946 (t80) REVERT: O 204 ASN cc_start: 0.8666 (m110) cc_final: 0.8288 (p0) REVERT: O 208 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7197 (tm-30) REVERT: P 63 TRP cc_start: 0.6551 (m100) cc_final: 0.5943 (m100) REVERT: P 110 PHE cc_start: 0.6956 (m-80) cc_final: 0.6620 (m-80) REVERT: P 132 MET cc_start: 0.7814 (tpt) cc_final: 0.7033 (tpt) REVERT: P 187 ILE cc_start: 0.8420 (mt) cc_final: 0.8160 (pt) REVERT: P 201 PHE cc_start: 0.8305 (t80) cc_final: 0.7442 (t80) REVERT: P 202 ILE cc_start: 0.8677 (pt) cc_final: 0.8448 (pt) REVERT: P 205 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7169 (mmmm) outliers start: 53 outliers final: 30 residues processed: 882 average time/residue: 0.2293 time to fit residues: 323.7399 Evaluate side-chains 857 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 826 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 309 optimal weight: 0.4980 chunk 372 optimal weight: 0.9980 chunk 297 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 326 optimal weight: 0.8980 chunk 378 optimal weight: 0.0070 chunk 196 optimal weight: 9.9990 chunk 357 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 242 GLN E 69 HIS ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS I 207 GLN J 13 ASN J 172 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.245682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189245 restraints weight = 65251.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.194157 restraints weight = 30267.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197124 restraints weight = 18670.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.198930 restraints weight = 14227.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.199863 restraints weight = 12214.335| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 36753 Z= 0.169 Angle : 0.704 22.400 50271 Z= 0.362 Chirality : 0.046 0.320 5432 Planarity : 0.004 0.061 5969 Dihedral : 16.499 141.963 5791 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.04 % Allowed : 12.55 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.13), residues: 3971 helix: 1.10 (0.12), residues: 1878 sheet: -0.07 (0.19), residues: 770 loop : -1.14 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 209 TYR 0.017 0.002 TYR A 134 PHE 0.030 0.002 PHE N 99 TRP 0.041 0.002 TRP P 245 HIS 0.032 0.002 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (36705) covalent geometry : angle 0.66928 / 0.36 (50248) hydrogen bonds : bond 0.05359 / 3.59 ( 1694) hydrogen bonds : angle 5.10082 / 3.65 ( 4842) metal coordination : bond 0.03789 / 2.70 ( 48) metal coordination : angle 10.29635 / 6.98 ( 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 914 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 842 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.6982 (t70) cc_final: 0.6677 (t0) REVERT: A 76 LEU cc_start: 0.8146 (tp) cc_final: 0.7933 (tp) REVERT: A 98 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6675 (mm-30) REVERT: A 162 ASN cc_start: 0.8169 (t0) cc_final: 0.7657 (t0) REVERT: A 165 GLU cc_start: 0.7491 (tp30) cc_final: 0.7066 (tp30) REVERT: A 199 ASP cc_start: 0.6830 (t0) cc_final: 0.6402 (t0) REVERT: A 223 PHE cc_start: 0.8259 (m-80) cc_final: 0.7523 (m-80) REVERT: A 238 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 124 VAL cc_start: 0.8174 (p) cc_final: 0.7666 (m) REVERT: B 140 THR cc_start: 0.8033 (m) cc_final: 0.7776 (t) REVERT: B 206 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7017 (tp30) REVERT: B 208 GLN cc_start: 0.7542 (tt0) cc_final: 0.7236 (tt0) REVERT: C 9 GLU cc_start: 0.7722 (tp30) cc_final: 0.7470 (tp30) REVERT: C 24 LEU cc_start: 0.8153 (mm) cc_final: 0.7707 (mp) REVERT: C 186 ASN cc_start: 0.8174 (m-40) cc_final: 0.7931 (t0) REVERT: C 198 MET cc_start: 0.6922 (pmm) cc_final: 0.6197 (pmm) REVERT: C 203 PHE cc_start: 0.6973 (t80) cc_final: 0.6653 (t80) REVERT: C 222 ARG cc_start: 0.6069 (ptm160) cc_final: 0.5321 (ptm160) REVERT: C 245 TRP cc_start: 0.7832 (m-90) cc_final: 0.7504 (m-90) REVERT: C 267 LYS cc_start: 0.8238 (pttp) cc_final: 0.7854 (pttp) REVERT: D 70 TYR cc_start: 0.6726 (t80) cc_final: 0.6524 (t80) REVERT: D 103 THR cc_start: 0.6531 (t) cc_final: 0.5860 (p) REVERT: D 104 MET cc_start: 0.6744 (mmp) cc_final: 0.5763 (mmp) REVERT: D 208 GLN cc_start: 0.7612 (mt0) cc_final: 0.7238 (mt0) REVERT: D 212 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6660 (tm-30) REVERT: D 236 GLU cc_start: 0.6929 (mp0) cc_final: 0.6628 (mp0) REVERT: D 238 GLN cc_start: 0.8404 (mt0) cc_final: 0.8121 (mt0) REVERT: D 268 ASP cc_start: 0.7040 (p0) cc_final: 0.6442 (p0) REVERT: E 34 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6470 (mm-30) REVERT: E 85 LEU cc_start: 0.8123 (tt) cc_final: 0.7915 (tp) REVERT: E 89 GLU cc_start: 0.4622 (tm-30) cc_final: 0.4405 (tm-30) REVERT: E 157 HIS cc_start: 0.7906 (m-70) cc_final: 0.7292 (m90) REVERT: E 181 THR cc_start: 0.8287 (p) cc_final: 0.7822 (t) REVERT: E 208 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6914 (tm-30) REVERT: E 210 ILE cc_start: 0.8244 (mm) cc_final: 0.7576 (mm) REVERT: E 271 PHE cc_start: 0.7133 (m-80) cc_final: 0.6629 (m-80) REVERT: F 158 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6859 (tm-30) REVERT: F 213 GLN cc_start: 0.7896 (pp30) cc_final: 0.7595 (pp30) REVERT: F 230 LYS cc_start: 0.8296 (tppp) cc_final: 0.7900 (tppp) REVERT: G 110 PHE cc_start: 0.7397 (m-80) cc_final: 0.7016 (m-10) REVERT: G 211 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5985 (tp40) REVERT: H 63 TRP cc_start: 0.6355 (m100) cc_final: 0.5418 (m100) REVERT: H 87 TYR cc_start: 0.7014 (t80) cc_final: 0.6536 (t80) REVERT: H 132 MET cc_start: 0.7373 (tpt) cc_final: 0.6871 (tpt) REVERT: H 196 SER cc_start: 0.5021 (p) cc_final: 0.4638 (p) REVERT: H 201 PHE cc_start: 0.8009 (t80) cc_final: 0.7586 (t80) REVERT: H 205 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7746 (mmmm) REVERT: R 418 MET cc_start: 0.7304 (ppp) cc_final: 0.6716 (ppp) REVERT: Q 360 LYS cc_start: 0.5746 (ptpp) cc_final: 0.5472 (ptpp) REVERT: Q 413 MET cc_start: 0.5994 (mmt) cc_final: 0.5689 (mmt) REVERT: Q 418 MET cc_start: 0.7393 (ppp) cc_final: 0.6762 (ppp) REVERT: I 72 ASP cc_start: 0.7123 (t70) cc_final: 0.6809 (t0) REVERT: I 165 GLU cc_start: 0.7131 (tp30) cc_final: 0.6795 (tp30) REVERT: I 238 GLN cc_start: 0.7574 (tm-30) cc_final: 0.6876 (tm-30) REVERT: J 94 GLU cc_start: 0.6284 (pp20) cc_final: 0.5999 (pp20) REVERT: J 98 GLU cc_start: 0.7307 (tp30) cc_final: 0.7074 (tp30) REVERT: J 129 GLN cc_start: 0.7636 (tt0) cc_final: 0.7205 (mt0) REVERT: J 132 MET cc_start: 0.7777 (tpp) cc_final: 0.7345 (mmt) REVERT: J 206 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7462 (tp30) REVERT: J 211 GLN cc_start: 0.7182 (tm-30) cc_final: 0.6913 (tm-30) REVERT: K 109 MET cc_start: 0.7596 (tpp) cc_final: 0.7244 (pmm) REVERT: K 186 ASN cc_start: 0.7874 (t0) cc_final: 0.7658 (t0) REVERT: K 222 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.4084 (ttt90) REVERT: L 104 MET cc_start: 0.5374 (mmp) cc_final: 0.5046 (mmp) REVERT: L 110 PHE cc_start: 0.7080 (m-80) cc_final: 0.6714 (t80) REVERT: L 221 ILE cc_start: 0.7086 (mt) cc_final: 0.6765 (tt) REVERT: L 248 ASP cc_start: 0.6764 (p0) cc_final: 0.6519 (p0) REVERT: L 268 ASP cc_start: 0.7204 (p0) cc_final: 0.6633 (p0) REVERT: M 7 LEU cc_start: 0.7906 (tt) cc_final: 0.7657 (tt) REVERT: M 35 ASP cc_start: 0.6751 (m-30) cc_final: 0.6356 (m-30) REVERT: M 38 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7268 (tm-30) REVERT: M 61 ASP cc_start: 0.7525 (t70) cc_final: 0.6780 (t0) REVERT: M 99 PHE cc_start: 0.7431 (m-80) cc_final: 0.6862 (m-80) REVERT: M 155 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7298 (mtt180) REVERT: M 259 ASP cc_start: 0.7353 (t0) cc_final: 0.7148 (t0) REVERT: M 271 PHE cc_start: 0.6778 (m-80) cc_final: 0.6152 (m-80) REVERT: N 64 GLN cc_start: 0.6440 (tp40) cc_final: 0.5998 (tp-100) REVERT: N 105 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8178 (mtmm) REVERT: N 213 GLN cc_start: 0.7915 (pp30) cc_final: 0.7387 (pp30) REVERT: N 241 THR cc_start: 0.8212 (t) cc_final: 0.7835 (m) REVERT: N 252 VAL cc_start: 0.8267 (p) cc_final: 0.8030 (m) REVERT: N 260 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.6292 (mtm-85) REVERT: O 11 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7578 (mm-30) REVERT: O 36 ILE cc_start: 0.6506 (mm) cc_final: 0.6223 (mm) REVERT: O 104 MET cc_start: 0.6953 (mmp) cc_final: 0.6057 (mmp) REVERT: O 110 PHE cc_start: 0.7243 (m-80) cc_final: 0.7000 (m-80) REVERT: O 132 MET cc_start: 0.8202 (mpp) cc_final: 0.7659 (mpp) REVERT: O 201 PHE cc_start: 0.8053 (t80) cc_final: 0.7722 (t80) REVERT: O 208 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7306 (tm-30) REVERT: P 63 TRP cc_start: 0.6614 (m100) cc_final: 0.5460 (m100) REVERT: P 132 MET cc_start: 0.7718 (tpt) cc_final: 0.6982 (tpt) REVERT: P 186 ASN cc_start: 0.8545 (m-40) cc_final: 0.8278 (t0) REVERT: P 198 MET cc_start: 0.7146 (mpp) cc_final: 0.6832 (mpp) REVERT: P 201 PHE cc_start: 0.8272 (t80) cc_final: 0.7718 (t80) REVERT: P 276 LYS cc_start: 0.7791 (mmtt) cc_final: 0.7372 (mmtt) outliers start: 72 outliers final: 49 residues processed: 856 average time/residue: 0.2372 time to fit residues: 324.4054 Evaluate side-chains 868 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 818 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 THR Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 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 104 MET Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain Q residue 426 MET Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 266 ASN Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 204 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 264 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 365 optimal weight: 10.0000 chunk 0 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 360 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 406 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS E 139 HIS ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN M 139 HIS ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 ASN ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 HIS N 211 GLN ** P 129 GLN ** 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 = 0.4975 r_free = 0.4975 target = 0.272049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.253899 restraints weight = 85407.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.251782 restraints weight = 108200.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.250408 restraints weight = 84857.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.249938 restraints weight = 81138.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.249534 restraints weight = 78803.159| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 36753 Z= 0.178 Angle : 0.701 20.456 50271 Z= 0.362 Chirality : 0.046 0.304 5432 Planarity : 0.004 0.057 5969 Dihedral : 16.664 143.190 5791 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.32 % Allowed : 15.13 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 3971 helix: 1.05 (0.12), residues: 1873 sheet: -0.10 (0.19), residues: 756 loop : -1.23 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 30 TYR 0.024 0.002 TYR N 134 PHE 0.034 0.002 PHE P 203 TRP 0.042 0.002 TRP P 245 HIS 0.018 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (36705) covalent geometry : angle 0.67320 / 0.36 (50248) hydrogen bonds : bond 0.04914 / 3.30 ( 1694) hydrogen bonds : angle 4.96856 / 3.55 ( 4842) metal coordination : bond 0.03557 / 2.44 ( 48) metal coordination : angle 9.20021 / 6.07 ( 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 915 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 833 time to evaluate : 1.224 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: A 38 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7155 (mt0) REVERT: A 72 ASP cc_start: 0.6981 (t70) cc_final: 0.6609 (t0) REVERT: A 98 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6660 (mm-30) REVERT: A 109 MET cc_start: 0.7235 (tpp) cc_final: 0.7027 (tpp) REVERT: A 121 PRO cc_start: 0.8336 (Cg_exo) cc_final: 0.8123 (Cg_endo) REVERT: A 165 GLU cc_start: 0.7471 (tp30) cc_final: 0.6993 (tp30) REVERT: A 199 ASP cc_start: 0.6643 (t0) cc_final: 0.6209 (t0) REVERT: A 223 PHE cc_start: 0.8342 (m-80) cc_final: 0.7578 (m-80) REVERT: A 254 LYS cc_start: 0.7556 (tppt) cc_final: 0.7251 (ttmt) REVERT: B 124 VAL cc_start: 0.8180 (p) cc_final: 0.7758 (m) REVERT: B 129 GLN cc_start: 0.7790 (mt0) cc_final: 0.7579 (mt0) REVERT: B 140 THR cc_start: 0.8008 (m) cc_final: 0.7753 (t) REVERT: B 206 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7216 (tp30) REVERT: B 208 GLN cc_start: 0.7681 (tt0) cc_final: 0.7378 (tt0) REVERT: C 24 LEU cc_start: 0.8154 (mm) cc_final: 0.7642 (mp) REVERT: C 203 PHE cc_start: 0.6717 (t80) cc_final: 0.6336 (t80) REVERT: C 222 ARG cc_start: 0.5985 (ptm160) cc_final: 0.5682 (ptm160) REVERT: C 267 LYS cc_start: 0.7860 (pttp) cc_final: 0.7620 (pttp) REVERT: D 103 THR cc_start: 0.5579 (t) cc_final: 0.5232 (p) REVERT: D 104 MET cc_start: 0.6217 (mmp) cc_final: 0.5460 (mmp) REVERT: D 132 MET cc_start: 0.8098 (ppp) cc_final: 0.7789 (ppp) REVERT: D 236 GLU cc_start: 0.7012 (mp0) cc_final: 0.6620 (mp0) REVERT: D 238 GLN cc_start: 0.8463 (mt0) cc_final: 0.8110 (mt0) REVERT: E 86 ILE cc_start: 0.7818 (mm) cc_final: 0.7615 (mp) REVERT: E 157 HIS cc_start: 0.7640 (m-70) cc_final: 0.6853 (m-70) REVERT: E 158 GLN cc_start: 0.7722 (pt0) cc_final: 0.7335 (pt0) REVERT: E 161 LYS cc_start: 0.8304 (mttt) cc_final: 0.7834 (mttt) REVERT: E 181 THR cc_start: 0.8157 (p) cc_final: 0.7762 (t) REVERT: E 208 GLN cc_start: 0.7365 (tp-100) cc_final: 0.7147 (tm-30) REVERT: E 212 GLN cc_start: 0.7230 (mp10) cc_final: 0.6791 (mp10) REVERT: F 230 LYS cc_start: 0.8331 (tppp) cc_final: 0.7931 (tppp) REVERT: H 201 PHE cc_start: 0.7229 (t80) cc_final: 0.7022 (t80) REVERT: H 205 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7346 (mmmm) REVERT: H 230 LYS cc_start: 0.4767 (pttm) cc_final: 0.4527 (pttm) REVERT: R 418 MET cc_start: 0.6828 (ppp) cc_final: 0.6396 (ppp) REVERT: Q 360 LYS cc_start: 0.6055 (ptpp) cc_final: 0.5787 (ptpp) REVERT: Q 418 MET cc_start: 0.6839 (ppp) cc_final: 0.6362 (ppp) REVERT: I 72 ASP cc_start: 0.7163 (t70) cc_final: 0.6821 (t0) REVERT: I 98 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6687 (mm-30) REVERT: I 109 MET cc_start: 0.6591 (ttt) cc_final: 0.6129 (ttm) REVERT: I 165 GLU cc_start: 0.7246 (tp30) cc_final: 0.6833 (tp30) REVERT: I 183 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6969 (mt) REVERT: I 238 GLN cc_start: 0.7673 (tm-30) cc_final: 0.6997 (tm-30) REVERT: J 94 GLU cc_start: 0.6475 (pp20) cc_final: 0.6116 (pp20) REVERT: J 105 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7726 (ttmt) REVERT: J 129 GLN cc_start: 0.7789 (tt0) cc_final: 0.7396 (mt0) REVERT: J 206 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7468 (tp30) REVERT: J 211 GLN cc_start: 0.7308 (tm-30) cc_final: 0.7083 (tm-30) REVERT: K 222 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.3727 (ttt90) REVERT: L 104 MET cc_start: 0.4859 (mmp) cc_final: 0.4587 (mmp) REVERT: L 220 LYS cc_start: 0.5860 (mmtm) cc_final: 0.5503 (mmtm) REVERT: L 248 ASP cc_start: 0.6839 (p0) cc_final: 0.6606 (p0) REVERT: L 268 ASP cc_start: 0.7348 (p0) cc_final: 0.6765 (p0) REVERT: M 7 LEU cc_start: 0.7998 (tt) cc_final: 0.7762 (tt) REVERT: M 35 ASP cc_start: 0.6852 (m-30) cc_final: 0.6512 (m-30) REVERT: M 38 GLN cc_start: 0.7436 (mm-40) cc_final: 0.7169 (tm-30) REVERT: M 61 ASP cc_start: 0.7417 (t70) cc_final: 0.7074 (t0) REVERT: M 99 PHE cc_start: 0.6953 (m-80) cc_final: 0.6617 (m-80) REVERT: M 155 ARG cc_start: 0.7296 (mtt180) cc_final: 0.7067 (mtt180) REVERT: M 195 THR cc_start: 0.8136 (m) cc_final: 0.7536 (t) REVERT: M 259 ASP cc_start: 0.6917 (t0) cc_final: 0.6716 (t0) REVERT: M 271 PHE cc_start: 0.6082 (m-80) cc_final: 0.5836 (m-80) REVERT: N 105 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8237 (mtmm) REVERT: N 113 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7461 (mmtm) REVERT: N 213 GLN cc_start: 0.7915 (pp30) cc_final: 0.7519 (pp30) REVERT: N 241 THR cc_start: 0.8400 (t) cc_final: 0.8012 (m) REVERT: N 252 VAL cc_start: 0.8338 (p) cc_final: 0.8071 (m) REVERT: N 260 ARG cc_start: 0.6725 (mtm-85) cc_final: 0.6330 (mtm-85) REVERT: O 132 MET cc_start: 0.7412 (mpp) cc_final: 0.7199 (mpp) REVERT: P 132 MET cc_start: 0.6451 (tpt) cc_final: 0.6241 (tpt) REVERT: P 201 PHE cc_start: 0.7523 (t80) cc_final: 0.7244 (t80) outliers start: 82 outliers final: 64 residues processed: 852 average time/residue: 0.2366 time to fit residues: 322.4019 Evaluate side-chains 884 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 817 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 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 77 VAL Chi-restraints excluded: chain F residue 101 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 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 233 HIS 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 153 VAL Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 157 HIS Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 406 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 chunk 174 optimal weight: 0.1980 chunk 164 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 242 GLN E 69 HIS E 139 HIS ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 211 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 212 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** ** 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 = 0.4964 r_free = 0.4964 target = 0.271065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.252596 restraints weight = 85042.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.250247 restraints weight = 106417.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.248639 restraints weight = 84196.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.248364 restraints weight = 84711.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.248402 restraints weight = 68313.592| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 36753 Z= 0.192 Angle : 0.710 18.495 50271 Z= 0.368 Chirality : 0.047 0.246 5432 Planarity : 0.004 0.053 5969 Dihedral : 16.765 143.895 5791 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.83 % Allowed : 16.82 % 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: -0.07 (0.13), residues: 3971 helix: 0.94 (0.12), residues: 1874 sheet: -0.16 (0.19), residues: 758 loop : -1.32 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 155 TYR 0.024 0.002 TYR I 134 PHE 0.032 0.002 PHE N 99 TRP 0.048 0.002 TRP M 1 HIS 0.032 0.002 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (36705) covalent geometry : angle 0.68475 / 0.37 (50248) hydrogen bonds : bond 0.04786 / 3.19 ( 1694) hydrogen bonds : angle 4.98344 / 3.58 ( 4842) metal coordination : bond 0.03760 / 2.62 ( 48) metal coordination : angle 8.80750 / 5.74 ( 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 943 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 843 time to evaluate : 1.322 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: 0.7541 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: A 72 ASP cc_start: 0.7118 (t70) cc_final: 0.6693 (t0) REVERT: A 80 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 98 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6694 (mm-30) REVERT: A 121 PRO cc_start: 0.8300 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: A 165 GLU cc_start: 0.7449 (tp30) cc_final: 0.6976 (tp30) REVERT: A 183 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 199 ASP cc_start: 0.6585 (t0) cc_final: 0.6123 (t0) REVERT: A 206 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6379 (tm-30) REVERT: A 223 PHE cc_start: 0.8358 (m-80) cc_final: 0.7481 (m-80) REVERT: A 255 ASP cc_start: 0.7165 (t0) cc_final: 0.6910 (m-30) REVERT: B 124 VAL cc_start: 0.8233 (p) cc_final: 0.7850 (m) REVERT: B 140 THR cc_start: 0.8019 (m) cc_final: 0.7774 (t) REVERT: B 206 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7261 (tp30) REVERT: B 208 GLN cc_start: 0.7806 (tt0) cc_final: 0.7458 (tt0) REVERT: C 9 GLU cc_start: 0.7583 (tp30) cc_final: 0.7296 (tp30) REVERT: C 24 LEU cc_start: 0.8088 (mm) cc_final: 0.7555 (mp) REVERT: C 104 MET cc_start: 0.4351 (ppp) cc_final: 0.4013 (ppp) REVERT: C 203 PHE cc_start: 0.6757 (t80) cc_final: 0.6329 (t80) REVERT: C 222 ARG cc_start: 0.6094 (ptm160) cc_final: 0.5763 (ptm160) REVERT: C 267 LYS cc_start: 0.7978 (pttp) cc_final: 0.7615 (pttp) REVERT: D 103 THR cc_start: 0.5584 (t) cc_final: 0.5274 (p) REVERT: D 104 MET cc_start: 0.6252 (mmp) cc_final: 0.5498 (mmp) REVERT: D 236 GLU cc_start: 0.7006 (mp0) cc_final: 0.6604 (mp0) REVERT: D 238 GLN cc_start: 0.8421 (mt0) cc_final: 0.8075 (mt0) REVERT: D 260 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.6388 (mmm-85) REVERT: E 155 ARG cc_start: 0.6780 (mtt180) cc_final: 0.6538 (mtt180) REVERT: E 157 HIS cc_start: 0.7700 (m-70) cc_final: 0.6935 (m-70) REVERT: E 158 GLN cc_start: 0.7731 (pt0) cc_final: 0.7307 (pt0) REVERT: E 161 LYS cc_start: 0.8406 (mttt) cc_final: 0.7907 (mttt) REVERT: E 181 THR cc_start: 0.8154 (p) cc_final: 0.7796 (t) REVERT: E 208 GLN cc_start: 0.7501 (tp-100) cc_final: 0.7295 (tm-30) REVERT: E 212 GLN cc_start: 0.7342 (mp10) cc_final: 0.6745 (mp10) REVERT: E 213 GLN cc_start: 0.6773 (pm20) cc_final: 0.6389 (pp30) REVERT: F 64 GLN cc_start: 0.5844 (tp40) cc_final: 0.5348 (tp-100) REVERT: F 213 GLN cc_start: 0.7949 (pp30) cc_final: 0.7732 (tm-30) REVERT: H 201 PHE cc_start: 0.7478 (t80) cc_final: 0.7278 (t80) REVERT: H 251 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5908 (mp) REVERT: R 418 MET cc_start: 0.6786 (ppp) cc_final: 0.6337 (ppp) REVERT: Q 360 LYS cc_start: 0.6107 (ptpp) cc_final: 0.5784 (ptpp) REVERT: Q 418 MET cc_start: 0.6847 (ppp) cc_final: 0.6349 (ppp) REVERT: I 72 ASP cc_start: 0.7143 (t70) cc_final: 0.6827 (t0) REVERT: I 89 GLU cc_start: 0.6879 (tp30) cc_final: 0.6669 (tp30) REVERT: I 109 MET cc_start: 0.6726 (ttt) cc_final: 0.5987 (ttm) REVERT: I 165 GLU cc_start: 0.7285 (tp30) cc_final: 0.6879 (tp30) REVERT: I 183 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7049 (mt) REVERT: I 199 ASP cc_start: 0.6194 (t0) cc_final: 0.5985 (t0) REVERT: I 238 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7084 (tm-30) REVERT: J 94 GLU cc_start: 0.6446 (pp20) cc_final: 0.6051 (pp20) REVERT: J 97 GLN cc_start: 0.7482 (tp40) cc_final: 0.7043 (tp40) REVERT: J 105 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7642 (ttpt) REVERT: J 129 GLN cc_start: 0.7773 (tt0) cc_final: 0.7311 (mt0) REVERT: J 206 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7454 (tp30) REVERT: K 222 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.4179 (ttt90) REVERT: L 80 GLU cc_start: 0.5391 (tm-30) cc_final: 0.5020 (tm-30) REVERT: L 104 MET cc_start: 0.4871 (mmp) cc_final: 0.4594 (mmp) REVERT: L 220 LYS cc_start: 0.5926 (mmtm) cc_final: 0.5548 (mmtm) REVERT: L 248 ASP cc_start: 0.6911 (p0) cc_final: 0.6634 (p0) REVERT: L 259 ASP cc_start: 0.7717 (p0) cc_final: 0.7352 (p0) REVERT: L 268 ASP cc_start: 0.7379 (p0) cc_final: 0.6737 (p0) REVERT: M 7 LEU cc_start: 0.8079 (tt) cc_final: 0.7843 (tt) REVERT: M 35 ASP cc_start: 0.6884 (m-30) cc_final: 0.6577 (m-30) REVERT: M 38 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7308 (tm-30) REVERT: M 44 GLN cc_start: 0.5539 (tp40) cc_final: 0.5320 (tp40) REVERT: M 61 ASP cc_start: 0.7367 (t70) cc_final: 0.7089 (t0) REVERT: M 99 PHE cc_start: 0.7000 (m-80) cc_final: 0.6614 (m-80) REVERT: M 155 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7043 (mtt180) REVERT: M 164 LEU cc_start: 0.7483 (mt) cc_final: 0.7082 (pp) REVERT: M 195 THR cc_start: 0.8155 (m) cc_final: 0.7571 (t) REVERT: M 199 ASP cc_start: 0.6558 (t0) cc_final: 0.5185 (t0) REVERT: M 271 PHE cc_start: 0.6158 (m-80) cc_final: 0.5931 (m-80) REVERT: N 113 LYS cc_start: 0.7739 (mmmt) cc_final: 0.7527 (mmtm) REVERT: N 213 GLN cc_start: 0.7956 (pp30) cc_final: 0.7526 (pp30) REVERT: N 241 THR cc_start: 0.8447 (t) cc_final: 0.8041 (p) REVERT: N 260 ARG cc_start: 0.6758 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: O 132 MET cc_start: 0.7459 (mpp) cc_final: 0.7220 (mpp) REVERT: P 130 LEU cc_start: 0.8072 (mt) cc_final: 0.7793 (mt) REVERT: P 132 MET cc_start: 0.6431 (tpt) cc_final: 0.6175 (tpt) REVERT: P 201 PHE cc_start: 0.7549 (t80) cc_final: 0.7299 (t80) outliers start: 100 outliers final: 72 residues processed: 873 average time/residue: 0.2336 time to fit residues: 327.4940 Evaluate side-chains 909 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 832 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 52 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL 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 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 203 PHE Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 414 GLU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 276 LYS Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 139 HIS Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 204 ASN Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 206 GLU 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: 0.9980 chunk 321 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 355 optimal weight: 0.2980 chunk 308 optimal weight: 0.5980 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 406 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS D 208 GLN D 242 GLN 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 146 ASN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS M 162 ASN ** M 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 GLN ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.270469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.251720 restraints weight = 84770.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.249564 restraints weight = 109514.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.248479 restraints weight = 95833.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.248386 restraints weight = 85970.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.247973 restraints weight = 81804.578| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 36753 Z= 0.185 Angle : 0.710 17.332 50271 Z= 0.367 Chirality : 0.047 0.258 5432 Planarity : 0.004 0.080 5969 Dihedral : 16.847 144.655 5791 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.11 % Allowed : 17.61 % Favored : 79.28 % 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: -0.14 (0.13), residues: 3971 helix: 0.85 (0.12), residues: 1888 sheet: -0.19 (0.19), residues: 736 loop : -1.31 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 155 TYR 0.025 0.002 TYR I 134 PHE 0.034 0.002 PHE N 99 TRP 0.044 0.002 TRP M 1 HIS 0.021 0.001 HIS N 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (36705) covalent geometry : angle 0.68761 / 0.37 (50248) hydrogen bonds : bond 0.04602 / 3.07 ( 1694) hydrogen bonds : angle 4.88470 / 3.49 ( 4842) metal coordination : bond 0.02877 / 2.01 ( 48) metal coordination : angle 8.22680 / 5.77 ( 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 945 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 835 time to evaluate : 1.281 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: A 38 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7211 (mt0) REVERT: A 72 ASP cc_start: 0.7209 (t70) cc_final: 0.6734 (t0) REVERT: A 121 PRO cc_start: 0.8219 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: A 138 GLU cc_start: 0.6991 (mp0) cc_final: 0.6524 (mp0) REVERT: A 165 GLU cc_start: 0.7462 (tp30) cc_final: 0.7019 (tp30) REVERT: A 183 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7214 (mt) REVERT: A 199 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6056 (t0) REVERT: A 206 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6360 (tm-30) REVERT: A 223 PHE cc_start: 0.8319 (m-80) cc_final: 0.7495 (m-80) REVERT: A 254 LYS cc_start: 0.7521 (tppt) cc_final: 0.7287 (ttmt) REVERT: A 255 ASP cc_start: 0.7140 (t0) cc_final: 0.6880 (m-30) REVERT: B 124 VAL cc_start: 0.8239 (p) cc_final: 0.7878 (m) REVERT: B 140 THR cc_start: 0.8051 (m) cc_final: 0.7807 (t) REVERT: B 206 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7222 (tp30) REVERT: B 208 GLN cc_start: 0.7846 (tt0) cc_final: 0.7551 (tt0) REVERT: C 9 GLU cc_start: 0.7523 (tp30) cc_final: 0.7261 (tp30) REVERT: C 24 LEU cc_start: 0.8124 (mm) cc_final: 0.7609 (mp) REVERT: C 203 PHE cc_start: 0.6580 (t80) cc_final: 0.6311 (t80) REVERT: C 267 LYS cc_start: 0.8001 (pttp) cc_final: 0.7629 (pttp) REVERT: D 103 THR cc_start: 0.5636 (t) cc_final: 0.5276 (p) REVERT: D 104 MET cc_start: 0.6024 (mmp) cc_final: 0.5353 (mmp) REVERT: D 220 LYS cc_start: 0.5699 (mmtm) cc_final: 0.5350 (mmtm) REVERT: D 236 GLU cc_start: 0.7072 (mp0) cc_final: 0.6657 (mp0) REVERT: D 238 GLN cc_start: 0.8456 (mt0) cc_final: 0.8114 (mt0) REVERT: D 260 ARG cc_start: 0.6772 (mmm-85) cc_final: 0.6406 (mmm-85) REVERT: E 25 GLU cc_start: 0.6136 (mm-30) cc_final: 0.5575 (mm-30) REVERT: E 35 ASP cc_start: 0.6670 (m-30) cc_final: 0.6212 (m-30) REVERT: E 155 ARG cc_start: 0.6769 (mtt180) cc_final: 0.6529 (mtt180) REVERT: E 157 HIS cc_start: 0.7734 (m-70) cc_final: 0.7029 (m-70) REVERT: E 158 GLN cc_start: 0.7721 (pt0) cc_final: 0.7350 (pt0) REVERT: E 161 LYS cc_start: 0.8413 (mttt) cc_final: 0.7901 (mttt) REVERT: E 195 THR cc_start: 0.8192 (m) cc_final: 0.7513 (t) REVERT: E 208 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7226 (tm-30) REVERT: E 212 GLN cc_start: 0.7358 (mp10) cc_final: 0.6484 (mp10) REVERT: E 270 LYS cc_start: 0.6452 (mtpt) cc_final: 0.5996 (pttt) REVERT: F 64 GLN cc_start: 0.5736 (tp40) cc_final: 0.5376 (tp-100) REVERT: F 110 PHE cc_start: 0.7602 (m-10) cc_final: 0.6938 (m-80) REVERT: F 254 LYS cc_start: 0.8101 (tptt) cc_final: 0.7845 (tptt) REVERT: H 201 PHE cc_start: 0.7439 (t80) cc_final: 0.7149 (t80) REVERT: H 230 LYS cc_start: 0.4837 (pttm) cc_final: 0.4520 (pttm) REVERT: R 418 MET cc_start: 0.6760 (ppp) cc_final: 0.6339 (ppp) REVERT: Q 360 LYS cc_start: 0.6477 (ptpp) cc_final: 0.6120 (ptpp) REVERT: Q 418 MET cc_start: 0.6881 (ppp) cc_final: 0.6399 (ppp) REVERT: I 35 ASP cc_start: 0.7141 (t70) cc_final: 0.6925 (t70) REVERT: I 72 ASP cc_start: 0.7206 (t70) cc_final: 0.6904 (t0) REVERT: I 109 MET cc_start: 0.6954 (ttt) cc_final: 0.6703 (ttm) REVERT: I 165 GLU cc_start: 0.7345 (tp30) cc_final: 0.6925 (tp30) REVERT: I 183 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7000 (mt) REVERT: I 238 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7146 (tm-30) REVERT: J 94 GLU cc_start: 0.6607 (pp20) cc_final: 0.6173 (pp20) REVERT: J 129 GLN cc_start: 0.7751 (tt0) cc_final: 0.7304 (mt0) REVERT: J 206 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7335 (tp30) REVERT: L 80 GLU cc_start: 0.5714 (tm-30) cc_final: 0.5426 (tm-30) REVERT: L 104 MET cc_start: 0.4901 (mmp) cc_final: 0.4616 (mmp) REVERT: L 220 LYS cc_start: 0.5982 (mmtm) cc_final: 0.5624 (mmtm) REVERT: L 248 ASP cc_start: 0.6889 (p0) cc_final: 0.6657 (p0) REVERT: L 256 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6752 (mtp85) REVERT: L 268 ASP cc_start: 0.7373 (p0) cc_final: 0.6725 (p0) REVERT: M 1 TRP cc_start: 0.5629 (t-100) cc_final: 0.5371 (t-100) REVERT: M 35 ASP cc_start: 0.6945 (m-30) cc_final: 0.6573 (m-30) REVERT: M 38 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7322 (tm-30) REVERT: M 61 ASP cc_start: 0.7424 (t70) cc_final: 0.7106 (t0) REVERT: M 99 PHE cc_start: 0.7047 (m-80) cc_final: 0.6597 (m-80) REVERT: M 155 ARG cc_start: 0.7276 (mtt180) cc_final: 0.7041 (mtt180) REVERT: M 158 GLN cc_start: 0.7685 (mm110) cc_final: 0.7282 (mm-40) REVERT: M 161 LYS cc_start: 0.8705 (mttt) cc_final: 0.8497 (mttt) REVERT: M 195 THR cc_start: 0.8036 (m) cc_final: 0.7506 (t) REVERT: M 259 ASP cc_start: 0.6990 (t0) cc_final: 0.6748 (t0) REVERT: M 271 PHE cc_start: 0.6279 (m-80) cc_final: 0.6059 (m-80) REVERT: N 107 TYR cc_start: 0.8323 (t80) cc_final: 0.7961 (t80) REVERT: N 213 GLN cc_start: 0.7867 (pp30) cc_final: 0.7410 (pp30) REVERT: N 241 THR cc_start: 0.8449 (t) cc_final: 0.8061 (p) REVERT: N 260 ARG cc_start: 0.6779 (mtm-85) cc_final: 0.6379 (mtm-85) REVERT: N 270 LYS cc_start: 0.7346 (mtmm) cc_final: 0.7129 (mtmt) REVERT: P 130 LEU cc_start: 0.8069 (mt) cc_final: 0.7799 (mt) REVERT: P 132 MET cc_start: 0.6548 (tpt) cc_final: 0.6265 (tpt) REVERT: P 201 PHE cc_start: 0.7584 (t80) cc_final: 0.7367 (t80) outliers start: 110 outliers final: 84 residues processed: 874 average time/residue: 0.2376 time to fit residues: 332.3366 Evaluate side-chains 912 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 823 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 52 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 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 208 GLN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 139 HIS 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 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 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 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 R residue 414 GLU Chi-restraints excluded: chain I residue 9 GLU Chi-restraints excluded: chain I residue 14 LYS Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain 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 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 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 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 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 156 THR Chi-restraints excluded: chain P residue 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 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: 0.9980 chunk 29 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 383 optimal weight: 1.9990 chunk 319 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 57 optimal weight: 30.0000 chunk 310 optimal weight: 0.0020 chunk 213 optimal weight: 0.3980 chunk 287 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS ** 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 69 HIS F 208 GLN F 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS M 162 ASN ** M 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 HIS ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.243063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186079 restraints weight = 67167.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.191500 restraints weight = 31474.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.193755 restraints weight = 19373.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.196106 restraints weight = 15352.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.196368 restraints weight = 12730.944| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36753 Z= 0.141 Angle : 0.705 16.625 50271 Z= 0.360 Chirality : 0.046 0.279 5432 Planarity : 0.004 0.059 5969 Dihedral : 16.857 144.871 5791 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.80 % Allowed : 18.69 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 3971 helix: 0.91 (0.12), residues: 1882 sheet: -0.13 (0.19), residues: 742 loop : -1.26 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 155 TYR 0.022 0.001 TYR P 134 PHE 0.039 0.001 PHE N 99 TRP 0.033 0.001 TRP P 106 HIS 0.030 0.001 HIS M 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (36705) covalent geometry : angle 0.68589 / 0.36 (50248) hydrogen bonds : bond 0.04108 / 2.73 ( 1694) hydrogen bonds : angle 4.78302 / 3.42 ( 4842) metal coordination : bond 0.02416 / 1.57 ( 48) metal coordination : angle 7.74470 / 5.28 ( 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 932 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 833 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7115 (t70) cc_final: 0.6655 (t0) REVERT: A 109 MET cc_start: 0.7256 (tpp) cc_final: 0.6859 (tpp) REVERT: A 138 GLU cc_start: 0.6864 (mp0) cc_final: 0.6467 (mp0) REVERT: A 148 GLN cc_start: 0.8774 (tt0) cc_final: 0.8566 (mt0) REVERT: A 165 GLU cc_start: 0.7501 (tp30) cc_final: 0.7155 (tp30) REVERT: A 183 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 199 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6121 (t0) REVERT: A 223 PHE cc_start: 0.8304 (m-80) cc_final: 0.7494 (m-80) REVERT: A 254 LYS cc_start: 0.7391 (tppt) cc_final: 0.7190 (ttmt) REVERT: A 255 ASP cc_start: 0.7088 (t0) cc_final: 0.6879 (m-30) REVERT: B 124 VAL cc_start: 0.8320 (p) cc_final: 0.7970 (m) REVERT: B 140 THR cc_start: 0.7958 (m) cc_final: 0.7670 (t) REVERT: B 208 GLN cc_start: 0.7767 (tt0) cc_final: 0.7441 (tt0) REVERT: C 9 GLU cc_start: 0.7547 (tp30) cc_final: 0.7265 (tp30) REVERT: C 24 LEU cc_start: 0.8118 (mm) cc_final: 0.7659 (mp) REVERT: C 203 PHE cc_start: 0.7031 (t80) cc_final: 0.6452 (t80) REVERT: C 207 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: C 222 ARG cc_start: 0.5558 (ptm160) cc_final: 0.4883 (ptm160) REVERT: C 267 LYS cc_start: 0.8258 (pttp) cc_final: 0.7859 (pttp) REVERT: D 103 THR cc_start: 0.6448 (t) cc_final: 0.5719 (p) REVERT: D 104 MET cc_start: 0.6839 (mmp) cc_final: 0.5871 (mmp) REVERT: D 109 MET cc_start: 0.6620 (tpt) cc_final: 0.6177 (tmm) REVERT: D 132 MET cc_start: 0.8529 (ppp) cc_final: 0.8160 (ppp) REVERT: D 220 LYS cc_start: 0.5692 (mmtm) cc_final: 0.5365 (mmtm) REVERT: D 236 GLU cc_start: 0.6874 (mp0) cc_final: 0.6554 (mp0) REVERT: D 238 GLN cc_start: 0.8213 (mt0) cc_final: 0.7957 (mt0) REVERT: D 260 ARG cc_start: 0.6582 (mmm-85) cc_final: 0.6357 (mmm-85) REVERT: E 24 LEU cc_start: 0.6942 (mp) cc_final: 0.6657 (tp) REVERT: E 25 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5882 (mm-30) REVERT: E 129 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6728 (mm-40) REVERT: E 157 HIS cc_start: 0.8069 (m-70) cc_final: 0.7483 (m-70) REVERT: E 158 GLN cc_start: 0.7913 (pt0) cc_final: 0.7528 (pt0) REVERT: E 161 LYS cc_start: 0.8418 (mttt) cc_final: 0.7831 (mttt) REVERT: E 195 THR cc_start: 0.8076 (m) cc_final: 0.7460 (t) REVERT: E 208 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7145 (tm-30) REVERT: E 212 GLN cc_start: 0.7502 (mp10) cc_final: 0.6432 (mp10) REVERT: E 270 LYS cc_start: 0.6592 (mtpt) cc_final: 0.6077 (pttt) REVERT: F 64 GLN cc_start: 0.5902 (tp40) cc_final: 0.5523 (tp-100) REVERT: F 110 PHE cc_start: 0.7569 (m-10) cc_final: 0.6819 (m-80) REVERT: F 213 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: F 254 LYS cc_start: 0.8094 (tptt) cc_final: 0.7852 (tptt) REVERT: G 175 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7405 (mm-30) REVERT: H 201 PHE cc_start: 0.8017 (t80) cc_final: 0.7484 (t80) REVERT: H 205 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7539 (mmmm) REVERT: H 262 LEU cc_start: 0.6748 (mm) cc_final: 0.6493 (mm) REVERT: R 418 MET cc_start: 0.7362 (ppp) cc_final: 0.6796 (ppp) REVERT: Q 360 LYS cc_start: 0.6125 (ptpp) cc_final: 0.5697 (ptpp) REVERT: Q 413 MET cc_start: 0.6353 (mtt) cc_final: 0.6122 (mmt) REVERT: Q 418 MET cc_start: 0.7523 (ppp) cc_final: 0.6931 (ppp) REVERT: I 52 LEU cc_start: 0.8250 (mm) cc_final: 0.8000 (mt) REVERT: I 72 ASP cc_start: 0.7050 (t70) cc_final: 0.6740 (t70) REVERT: I 165 GLU cc_start: 0.7281 (tp30) cc_final: 0.6931 (tp30) REVERT: I 183 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7282 (mt) REVERT: I 199 ASP cc_start: 0.6397 (t0) cc_final: 0.6169 (t0) REVERT: I 238 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7055 (tm-30) REVERT: J 10 GLU cc_start: 0.6918 (tp30) cc_final: 0.6664 (tp30) REVERT: J 94 GLU cc_start: 0.6580 (pp20) cc_final: 0.6166 (pp20) REVERT: J 129 GLN cc_start: 0.7694 (tt0) cc_final: 0.7267 (mt0) REVERT: J 206 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7247 (tp30) REVERT: L 104 MET cc_start: 0.5300 (mmp) cc_final: 0.4952 (mmp) REVERT: L 133 LYS cc_start: 0.7564 (mmmt) cc_final: 0.7356 (mmmt) REVERT: L 220 LYS cc_start: 0.5930 (mmtm) cc_final: 0.5559 (mmtm) REVERT: L 248 ASP cc_start: 0.6858 (p0) cc_final: 0.6548 (p0) REVERT: L 268 ASP cc_start: 0.7191 (p0) cc_final: 0.6589 (p0) REVERT: M 1 TRP cc_start: 0.5282 (t-100) cc_final: 0.5029 (t-100) REVERT: M 24 LEU cc_start: 0.7671 (tp) cc_final: 0.7454 (tp) REVERT: M 35 ASP cc_start: 0.6777 (m-30) cc_final: 0.6396 (m-30) REVERT: M 38 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7296 (tm-30) REVERT: M 61 ASP cc_start: 0.7550 (t70) cc_final: 0.7100 (t0) REVERT: M 80 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7421 (tm-30) REVERT: M 99 PHE cc_start: 0.7490 (m-80) cc_final: 0.6792 (m-80) REVERT: M 129 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7764 (mm-40) REVERT: M 155 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7192 (mtt180) REVERT: M 164 LEU cc_start: 0.7810 (mt) cc_final: 0.7138 (pp) REVERT: M 195 THR cc_start: 0.8000 (m) cc_final: 0.7324 (t) REVERT: M 259 ASP cc_start: 0.7571 (t0) cc_final: 0.7246 (t0) REVERT: M 267 LYS cc_start: 0.7694 (tptt) cc_final: 0.7371 (tppt) REVERT: N 107 TYR cc_start: 0.8400 (t80) cc_final: 0.7470 (t80) REVERT: N 213 GLN cc_start: 0.7892 (pp30) cc_final: 0.7446 (pp30) REVERT: N 241 THR cc_start: 0.8359 (t) cc_final: 0.7990 (p) REVERT: N 260 ARG cc_start: 0.6674 (mtm-85) cc_final: 0.6339 (mtm-85) REVERT: P 132 MET cc_start: 0.8013 (tpt) cc_final: 0.7097 (tpt) REVERT: P 201 PHE cc_start: 0.8307 (t80) cc_final: 0.7952 (t80) REVERT: P 206 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6061 (pp20) REVERT: P 207 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7227 (mm110) outliers start: 99 outliers final: 80 residues processed: 866 average time/residue: 0.2370 time to fit residues: 328.9658 Evaluate side-chains 905 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 819 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 52 LEU 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 172 ASN Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 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 208 GLN Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 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 I residue 269 VAL Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 168 ILE 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 68 THR 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 157 HIS 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 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 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: 9.9990 chunk 275 optimal weight: 0.5980 chunk 254 optimal weight: 0.7980 chunk 201 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 320 optimal weight: 0.5980 chunk 356 optimal weight: 2.9990 chunk 359 optimal weight: 0.7980 chunk 279 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN B 82 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 64 GLN E 69 HIS E 139 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN F 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 157 HIS N 102 GLN ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 HIS ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.241194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183671 restraints weight = 66477.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.188803 restraints weight = 30304.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.192023 restraints weight = 18801.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.193716 restraints weight = 14386.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.194453 restraints weight = 12569.157| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36753 Z= 0.161 Angle : 0.719 18.266 50271 Z= 0.368 Chirality : 0.046 0.246 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.895 145.130 5791 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 19.45 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 3971 helix: 0.89 (0.12), residues: 1884 sheet: -0.09 (0.19), residues: 718 loop : -1.19 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 155 TYR 0.019 0.001 TYR I 134 PHE 0.039 0.001 PHE N 99 TRP 0.037 0.002 TRP M 1 HIS 0.024 0.001 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (36705) covalent geometry : angle 0.70007 / 0.37 (50248) hydrogen bonds : bond 0.04202 / 2.80 ( 1694) hydrogen bonds : angle 4.78626 / 3.42 ( 4842) metal coordination : bond 0.02497 / 1.58 ( 48) metal coordination : angle 7.79054 / 5.24 ( 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 921 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 820 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7164 (t70) cc_final: 0.6716 (t0) REVERT: A 138 GLU cc_start: 0.6876 (mp0) cc_final: 0.6454 (mp0) REVERT: A 148 GLN cc_start: 0.8802 (tt0) cc_final: 0.8586 (mt0) REVERT: A 165 GLU cc_start: 0.7508 (tp30) cc_final: 0.7163 (tp30) REVERT: A 183 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7438 (mt) REVERT: A 223 PHE cc_start: 0.8299 (m-80) cc_final: 0.7473 (m-80) REVERT: A 254 LYS cc_start: 0.7432 (tppt) cc_final: 0.7209 (ttmt) REVERT: A 255 ASP cc_start: 0.7185 (t0) cc_final: 0.6946 (m-30) REVERT: B 124 VAL cc_start: 0.8327 (p) cc_final: 0.7984 (m) REVERT: B 140 THR cc_start: 0.8007 (m) cc_final: 0.7627 (t) REVERT: B 208 GLN cc_start: 0.7819 (tt0) cc_final: 0.7501 (tt0) REVERT: C 9 GLU cc_start: 0.7516 (tp30) cc_final: 0.7266 (tp30) REVERT: C 24 LEU cc_start: 0.8132 (mm) cc_final: 0.7664 (mp) REVERT: C 203 PHE cc_start: 0.7036 (t80) cc_final: 0.6461 (t80) REVERT: C 207 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6042 (pm20) REVERT: C 222 ARG cc_start: 0.5713 (ptm160) cc_final: 0.5022 (ptm160) REVERT: C 267 LYS cc_start: 0.8209 (pttp) cc_final: 0.7824 (pttp) REVERT: D 103 THR cc_start: 0.6450 (t) cc_final: 0.5739 (p) REVERT: D 104 MET cc_start: 0.6850 (mmp) cc_final: 0.5924 (mmp) REVERT: D 109 MET cc_start: 0.6595 (tpt) cc_final: 0.6166 (tmm) REVERT: D 132 MET cc_start: 0.8395 (ppp) cc_final: 0.8016 (ppp) REVERT: D 162 ASN cc_start: 0.6929 (m110) cc_final: 0.6659 (p0) REVERT: D 220 LYS cc_start: 0.5699 (mmtm) cc_final: 0.5409 (mmtm) REVERT: D 236 GLU cc_start: 0.6906 (mp0) cc_final: 0.6558 (mp0) REVERT: D 238 GLN cc_start: 0.8245 (mt0) cc_final: 0.7982 (mt0) REVERT: E 25 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6125 (mm-30) REVERT: E 129 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6792 (mm-40) REVERT: E 157 HIS cc_start: 0.8063 (m-70) cc_final: 0.7549 (m-70) REVERT: E 158 GLN cc_start: 0.7898 (pt0) cc_final: 0.7450 (pt0) REVERT: E 161 LYS cc_start: 0.8413 (mttt) cc_final: 0.7861 (mttt) REVERT: E 195 THR cc_start: 0.8105 (m) cc_final: 0.7492 (t) REVERT: E 208 GLN cc_start: 0.7544 (tp40) cc_final: 0.7221 (tm-30) REVERT: E 212 GLN cc_start: 0.7451 (mp10) cc_final: 0.6771 (mp10) REVERT: E 270 LYS cc_start: 0.6678 (mtpt) cc_final: 0.6259 (pttt) REVERT: F 110 PHE cc_start: 0.7643 (m-10) cc_final: 0.6864 (m-80) REVERT: F 213 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: F 254 LYS cc_start: 0.8098 (tptt) cc_final: 0.7844 (tptt) REVERT: H 62 HIS cc_start: 0.6453 (t-170) cc_final: 0.6237 (t-90) REVERT: H 110 PHE cc_start: 0.7276 (m-10) cc_final: 0.7016 (m-80) REVERT: H 201 PHE cc_start: 0.8036 (t80) cc_final: 0.7570 (t80) REVERT: H 205 LYS cc_start: 0.8073 (mmmm) cc_final: 0.7696 (mmmm) REVERT: H 262 LEU cc_start: 0.6790 (mm) cc_final: 0.6543 (mm) REVERT: R 368 LEU cc_start: 0.4722 (OUTLIER) cc_final: 0.4509 (mm) REVERT: R 418 MET cc_start: 0.7273 (ppp) cc_final: 0.6707 (ppp) REVERT: Q 360 LYS cc_start: 0.6269 (ptpp) cc_final: 0.5849 (ptpp) REVERT: Q 418 MET cc_start: 0.7431 (ppp) cc_final: 0.6816 (ppp) REVERT: I 52 LEU cc_start: 0.8291 (mm) cc_final: 0.8050 (mt) REVERT: I 72 ASP cc_start: 0.7105 (t70) cc_final: 0.6817 (t70) REVERT: I 165 GLU cc_start: 0.7328 (tp30) cc_final: 0.6954 (tp30) REVERT: I 183 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7307 (mt) REVERT: I 199 ASP cc_start: 0.6405 (t0) cc_final: 0.6181 (t0) REVERT: I 238 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7085 (tm-30) REVERT: J 10 GLU cc_start: 0.6949 (tp30) cc_final: 0.6700 (tp30) REVERT: J 94 GLU cc_start: 0.6650 (pp20) cc_final: 0.6244 (pp20) REVERT: J 129 GLN cc_start: 0.7701 (tt0) cc_final: 0.7313 (mt0) REVERT: J 206 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7245 (tp30) REVERT: L 80 GLU cc_start: 0.7261 (tp30) cc_final: 0.6887 (tp30) REVERT: L 104 MET cc_start: 0.5327 (mmp) cc_final: 0.4970 (mmp) REVERT: L 220 LYS cc_start: 0.6001 (mmtm) cc_final: 0.5679 (mmtm) REVERT: L 248 ASP cc_start: 0.6855 (p0) cc_final: 0.6555 (p0) REVERT: L 256 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6500 (mtp85) REVERT: L 268 ASP cc_start: 0.7185 (p0) cc_final: 0.6839 (p0) REVERT: M 24 LEU cc_start: 0.7827 (tp) cc_final: 0.7603 (tp) REVERT: M 35 ASP cc_start: 0.6814 (m-30) cc_final: 0.6474 (m-30) REVERT: M 38 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7303 (tm-30) REVERT: M 61 ASP cc_start: 0.7542 (t70) cc_final: 0.7121 (t0) REVERT: M 80 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7399 (tm-30) REVERT: M 87 TYR cc_start: 0.7401 (t80) cc_final: 0.7123 (t80) REVERT: M 99 PHE cc_start: 0.7473 (m-80) cc_final: 0.6787 (m-80) REVERT: M 164 LEU cc_start: 0.7871 (mt) cc_final: 0.7276 (pp) REVERT: M 195 THR cc_start: 0.7958 (m) cc_final: 0.7298 (t) REVERT: M 245 TRP cc_start: 0.7427 (t60) cc_final: 0.6800 (t-100) REVERT: M 259 ASP cc_start: 0.7597 (t0) cc_final: 0.7321 (t0) REVERT: M 267 LYS cc_start: 0.7692 (tptt) cc_final: 0.7368 (tppt) REVERT: N 107 TYR cc_start: 0.8505 (t80) cc_final: 0.7374 (t80) REVERT: N 213 GLN cc_start: 0.7864 (pp30) cc_final: 0.7429 (pp30) REVERT: N 241 THR cc_start: 0.8364 (t) cc_final: 0.8019 (p) REVERT: N 260 ARG cc_start: 0.6686 (mtm-85) cc_final: 0.6346 (mtm-85) REVERT: P 85 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.5034 (mm) REVERT: P 132 MET cc_start: 0.7913 (tpt) cc_final: 0.7070 (tpt) REVERT: P 201 PHE cc_start: 0.8295 (t80) cc_final: 0.8011 (t80) REVERT: P 206 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6100 (pp20) REVERT: P 207 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7232 (mm110) outliers start: 101 outliers final: 85 residues processed: 859 average time/residue: 0.2342 time to fit residues: 323.1075 Evaluate side-chains 907 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 814 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 52 LEU 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 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 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 101 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 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 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 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 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 198 MET 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 68 THR 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 N residue 102 GLN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 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: 1.9990 chunk 182 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 389 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 348 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 69 HIS ** E 139 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 ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 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 = 0.4764 r_free = 0.4764 target = 0.241732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.186628 restraints weight = 66858.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.188878 restraints weight = 37951.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190002 restraints weight = 27099.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.190989 restraints weight = 20827.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191208 restraints weight = 19771.239| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 36753 Z= 0.175 Angle : 0.735 18.388 50271 Z= 0.377 Chirality : 0.046 0.264 5432 Planarity : 0.004 0.051 5969 Dihedral : 16.945 145.294 5791 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.97 % Allowed : 19.71 % 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: -0.10 (0.13), residues: 3971 helix: 0.83 (0.12), residues: 1890 sheet: -0.09 (0.19), residues: 708 loop : -1.22 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 155 TYR 0.023 0.002 TYR I 134 PHE 0.051 0.002 PHE N 99 TRP 0.039 0.002 TRP M 1 HIS 0.019 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (36705) covalent geometry : angle 0.71721 / 0.38 (50248) hydrogen bonds : bond 0.04280 / 2.85 ( 1694) hydrogen bonds : angle 4.77279 / 3.41 ( 4842) metal coordination : bond 0.02408 / 1.51 ( 48) metal coordination : angle 7.62479 / 5.13 ( 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 928 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 823 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7184 (t70) cc_final: 0.6753 (t0) REVERT: A 109 MET cc_start: 0.7148 (tpp) cc_final: 0.6926 (tpp) REVERT: A 138 GLU cc_start: 0.6900 (mp0) cc_final: 0.6477 (mp0) REVERT: A 148 GLN cc_start: 0.8892 (tt0) cc_final: 0.8679 (mt0) REVERT: A 165 GLU cc_start: 0.7517 (tp30) cc_final: 0.7174 (tp30) REVERT: A 183 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7491 (mt) REVERT: A 223 PHE cc_start: 0.8375 (m-80) cc_final: 0.7568 (m-80) REVERT: A 255 ASP cc_start: 0.7303 (t0) cc_final: 0.7052 (m-30) REVERT: B 116 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6316 (tt0) REVERT: B 124 VAL cc_start: 0.8355 (p) cc_final: 0.7992 (m) REVERT: B 140 THR cc_start: 0.8020 (m) cc_final: 0.7819 (t) REVERT: B 208 GLN cc_start: 0.7803 (tt0) cc_final: 0.7498 (tt0) REVERT: C 9 GLU cc_start: 0.7553 (tp30) cc_final: 0.7323 (tp30) REVERT: C 24 LEU cc_start: 0.8153 (mm) cc_final: 0.7681 (mp) REVERT: C 203 PHE cc_start: 0.7103 (t80) cc_final: 0.6531 (t80) REVERT: C 207 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: C 222 ARG cc_start: 0.5530 (ptm160) cc_final: 0.4813 (ptm160) REVERT: C 267 LYS cc_start: 0.8211 (pttp) cc_final: 0.7861 (pttp) REVERT: D 103 THR cc_start: 0.6562 (t) cc_final: 0.5832 (p) REVERT: D 104 MET cc_start: 0.6767 (mmp) cc_final: 0.5865 (mmp) REVERT: D 109 MET cc_start: 0.6773 (tpt) cc_final: 0.6321 (tmm) REVERT: D 132 MET cc_start: 0.8449 (ppp) cc_final: 0.8102 (ppp) REVERT: D 220 LYS cc_start: 0.5660 (mmtm) cc_final: 0.5346 (mmtm) REVERT: D 236 GLU cc_start: 0.6959 (mp0) cc_final: 0.6549 (mp0) REVERT: E 15 TRP cc_start: 0.7078 (m-10) cc_final: 0.4857 (m-10) REVERT: E 129 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6845 (mm-40) REVERT: E 157 HIS cc_start: 0.8252 (m-70) cc_final: 0.7659 (m-70) REVERT: E 158 GLN cc_start: 0.7983 (pt0) cc_final: 0.7540 (pt0) REVERT: E 161 LYS cc_start: 0.8500 (mttt) cc_final: 0.7894 (mttt) REVERT: E 195 THR cc_start: 0.8075 (m) cc_final: 0.7521 (t) REVERT: E 208 GLN cc_start: 0.7639 (tp40) cc_final: 0.7271 (tm-30) REVERT: E 212 GLN cc_start: 0.7602 (mp10) cc_final: 0.6820 (mp10) REVERT: F 64 GLN cc_start: 0.5867 (tp40) cc_final: 0.5451 (tp40) REVERT: F 110 PHE cc_start: 0.7634 (m-10) cc_final: 0.6947 (m-80) REVERT: F 129 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7616 (mp10) REVERT: F 132 MET cc_start: 0.6793 (tpt) cc_final: 0.6545 (tpt) REVERT: F 213 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7794 (pp30) REVERT: F 241 THR cc_start: 0.8335 (t) cc_final: 0.8077 (m) REVERT: F 254 LYS cc_start: 0.8133 (tptt) cc_final: 0.7789 (tptt) REVERT: G 11 GLU cc_start: 0.7709 (tp30) cc_final: 0.7311 (tp30) REVERT: G 155 ARG cc_start: 0.7912 (pmt170) cc_final: 0.7564 (tpt170) REVERT: H 110 PHE cc_start: 0.7353 (m-10) cc_final: 0.6985 (m-80) REVERT: H 162 ASN cc_start: 0.8068 (p0) cc_final: 0.7796 (p0) REVERT: H 201 PHE cc_start: 0.8070 (t80) cc_final: 0.7590 (t80) REVERT: H 205 LYS cc_start: 0.8072 (mmmm) cc_final: 0.7665 (mmmm) REVERT: H 262 LEU cc_start: 0.6860 (mm) cc_final: 0.6563 (mm) REVERT: R 368 LEU cc_start: 0.4697 (OUTLIER) cc_final: 0.4403 (mm) REVERT: R 418 MET cc_start: 0.7395 (ppp) cc_final: 0.6835 (ppp) REVERT: Q 360 LYS cc_start: 0.6094 (ptpp) cc_final: 0.5666 (ptpp) REVERT: Q 413 MET cc_start: 0.6435 (mtt) cc_final: 0.6185 (mmt) REVERT: Q 418 MET cc_start: 0.7546 (ppp) cc_final: 0.6967 (ppp) REVERT: I 52 LEU cc_start: 0.8294 (mm) cc_final: 0.8045 (mt) REVERT: I 72 ASP cc_start: 0.7120 (t70) cc_final: 0.6836 (t70) REVERT: I 165 GLU cc_start: 0.7327 (tp30) cc_final: 0.6963 (tp30) REVERT: I 183 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7375 (mt) REVERT: I 238 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7170 (tm-30) REVERT: I 254 LYS cc_start: 0.7928 (tppt) cc_final: 0.7512 (tppt) REVERT: J 94 GLU cc_start: 0.6700 (pp20) cc_final: 0.6293 (pp20) REVERT: J 129 GLN cc_start: 0.7739 (tt0) cc_final: 0.7310 (mt0) REVERT: J 206 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7268 (tp30) REVERT: K 11 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6549 (mt-10) REVERT: L 80 GLU cc_start: 0.7596 (tp30) cc_final: 0.7061 (tp30) REVERT: L 104 MET cc_start: 0.5362 (mmp) cc_final: 0.5008 (mmp) REVERT: L 220 LYS cc_start: 0.6000 (mmtm) cc_final: 0.5652 (mmtm) REVERT: L 248 ASP cc_start: 0.6918 (p0) cc_final: 0.6604 (p0) REVERT: L 268 ASP cc_start: 0.7256 (p0) cc_final: 0.6499 (p0) REVERT: M 15 TRP cc_start: 0.7252 (m100) cc_final: 0.6888 (m-10) REVERT: M 24 LEU cc_start: 0.7987 (tp) cc_final: 0.7769 (tp) REVERT: M 35 ASP cc_start: 0.6901 (m-30) cc_final: 0.6547 (m-30) REVERT: M 44 GLN cc_start: 0.5238 (mm-40) cc_final: 0.4779 (mm110) REVERT: M 61 ASP cc_start: 0.7581 (t70) cc_final: 0.7120 (t0) REVERT: M 99 PHE cc_start: 0.7746 (m-80) cc_final: 0.6924 (m-80) REVERT: M 195 THR cc_start: 0.7890 (m) cc_final: 0.7308 (t) REVERT: M 245 TRP cc_start: 0.7594 (t60) cc_final: 0.7277 (t-100) REVERT: M 259 ASP cc_start: 0.7654 (t0) cc_final: 0.7355 (t0) REVERT: M 267 LYS cc_start: 0.7739 (tptt) cc_final: 0.7412 (tppt) REVERT: N 78 TRP cc_start: 0.7456 (m100) cc_final: 0.6614 (m100) REVERT: N 156 THR cc_start: 0.8013 (p) cc_final: 0.7800 (p) REVERT: N 213 GLN cc_start: 0.7799 (pp30) cc_final: 0.7353 (pp30) REVERT: N 230 LYS cc_start: 0.8402 (tppp) cc_final: 0.8199 (tppp) REVERT: N 241 THR cc_start: 0.8413 (t) cc_final: 0.8108 (p) REVERT: N 260 ARG cc_start: 0.6796 (mtm-85) cc_final: 0.6412 (mtm-85) REVERT: O 109 MET cc_start: 0.5190 (pmm) cc_final: 0.4967 (pmm) REVERT: P 85 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4986 (mm) REVERT: P 132 MET cc_start: 0.8019 (tpt) cc_final: 0.7170 (tpt) REVERT: P 201 PHE cc_start: 0.8362 (t80) cc_final: 0.8102 (t80) outliers start: 105 outliers final: 87 residues processed: 864 average time/residue: 0.2374 time to fit residues: 328.1908 Evaluate side-chains 903 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 810 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 52 LEU 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 251 ILE Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 172 ASN Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 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 16 HIS 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 206 GLU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU 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 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 7 LEU Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 198 MET 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 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 202 ILE Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 102 GLN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 186 ASN Chi-restraints excluded: chain N residue 221 ILE Chi-restraints excluded: chain O residue 34 GLU Chi-restraints excluded: chain O residue 85 LEU Chi-restraints excluded: chain P residue 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 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: 0.0870 chunk 307 optimal weight: 0.5980 chunk 342 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 285 optimal weight: 6.9990 chunk 400 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN ** M 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS N 102 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.242260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.187155 restraints weight = 67106.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189484 restraints weight = 36841.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.191236 restraints weight = 25515.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.191411 restraints weight = 20298.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192035 restraints weight = 20179.015| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36753 Z= 0.155 Angle : 0.745 17.434 50271 Z= 0.379 Chirality : 0.046 0.262 5432 Planarity : 0.005 0.093 5969 Dihedral : 16.963 145.281 5791 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.63 % Allowed : 20.44 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 3971 helix: 0.85 (0.12), residues: 1884 sheet: -0.05 (0.19), residues: 710 loop : -1.22 (0.15), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 231 TYR 0.021 0.001 TYR O 87 PHE 0.041 0.001 PHE N 99 TRP 0.044 0.002 TRP M 1 HIS 0.007 0.001 HIS J 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (36705) covalent geometry : angle 0.72798 / 0.38 (50248) hydrogen bonds : bond 0.04139 / 2.78 ( 1694) hydrogen bonds : angle 4.73543 / 3.39 ( 4842) metal coordination : bond 0.02294 / 1.42 ( 48) metal coordination : angle 7.38957 / 4.96 ( 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 919 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 826 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7239 (t70) cc_final: 0.6771 (t0) REVERT: A 109 MET cc_start: 0.7088 (tpp) cc_final: 0.6875 (tpp) REVERT: A 138 GLU cc_start: 0.6889 (mp0) cc_final: 0.6460 (mp0) REVERT: A 148 GLN cc_start: 0.8883 (tt0) cc_final: 0.8671 (mt0) REVERT: A 165 GLU cc_start: 0.7497 (tp30) cc_final: 0.7166 (tp30) REVERT: A 183 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 223 PHE cc_start: 0.8353 (m-80) cc_final: 0.7540 (m-80) REVERT: B 116 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6302 (tt0) REVERT: B 124 VAL cc_start: 0.8416 (p) cc_final: 0.8082 (m) REVERT: B 208 GLN cc_start: 0.7748 (tt0) cc_final: 0.7441 (tt0) REVERT: C 9 GLU cc_start: 0.7543 (tp30) cc_final: 0.7303 (tp30) REVERT: C 24 LEU cc_start: 0.8142 (mm) cc_final: 0.7659 (mp) REVERT: C 203 PHE cc_start: 0.7105 (t80) cc_final: 0.6542 (t80) REVERT: C 204 ASN cc_start: 0.8305 (m-40) cc_final: 0.7876 (p0) REVERT: C 205 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8107 (mmmt) REVERT: C 207 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: C 222 ARG cc_start: 0.5651 (ptm160) cc_final: 0.4985 (ptm160) REVERT: C 267 LYS cc_start: 0.8188 (pttp) cc_final: 0.7888 (pttp) REVERT: D 103 THR cc_start: 0.6558 (t) cc_final: 0.5811 (p) REVERT: D 104 MET cc_start: 0.6758 (mmp) cc_final: 0.5852 (mmp) REVERT: D 132 MET cc_start: 0.8442 (ppp) cc_final: 0.8106 (ppp) REVERT: D 162 ASN cc_start: 0.7199 (m110) cc_final: 0.6862 (p0) REVERT: D 220 LYS cc_start: 0.5659 (mmtm) cc_final: 0.5323 (mmtm) REVERT: D 236 GLU cc_start: 0.6958 (mp0) cc_final: 0.6543 (mp0) REVERT: E 129 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6986 (mm-40) REVERT: E 157 HIS cc_start: 0.8228 (m-70) cc_final: 0.7640 (m-70) REVERT: E 158 GLN cc_start: 0.8071 (pt0) cc_final: 0.7635 (pt0) REVERT: E 161 LYS cc_start: 0.8539 (mttt) cc_final: 0.7923 (mttt) REVERT: E 195 THR cc_start: 0.8054 (m) cc_final: 0.7493 (t) REVERT: E 208 GLN cc_start: 0.7589 (tp40) cc_final: 0.7223 (tm-30) REVERT: E 212 GLN cc_start: 0.7623 (mp10) cc_final: 0.6843 (mp10) REVERT: F 64 GLN cc_start: 0.5812 (tp40) cc_final: 0.5370 (tp40) REVERT: F 110 PHE cc_start: 0.7630 (m-10) cc_final: 0.6962 (m-80) REVERT: F 129 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7677 (mp10) REVERT: F 213 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7677 (pp30) REVERT: F 241 THR cc_start: 0.8301 (t) cc_final: 0.8078 (m) REVERT: F 254 LYS cc_start: 0.8130 (tptt) cc_final: 0.7782 (tptt) REVERT: G 11 GLU cc_start: 0.7704 (tp30) cc_final: 0.7288 (tp30) REVERT: G 155 ARG cc_start: 0.7878 (pmt170) cc_final: 0.7547 (tpt170) REVERT: H 110 PHE cc_start: 0.7570 (m-10) cc_final: 0.7117 (m-80) REVERT: H 162 ASN cc_start: 0.8203 (p0) cc_final: 0.7890 (p0) REVERT: H 201 PHE cc_start: 0.8209 (t80) cc_final: 0.7669 (t80) REVERT: H 205 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7653 (mmmm) REVERT: H 230 LYS cc_start: 0.5652 (pttm) cc_final: 0.5373 (pttm) REVERT: H 242 GLN cc_start: 0.7872 (tp-100) cc_final: 0.6888 (tp-100) REVERT: H 262 LEU cc_start: 0.6841 (mm) cc_final: 0.6546 (mm) REVERT: R 368 LEU cc_start: 0.4767 (OUTLIER) cc_final: 0.4515 (mm) REVERT: R 418 MET cc_start: 0.7386 (ppp) cc_final: 0.6828 (ppp) REVERT: Q 360 LYS cc_start: 0.6108 (ptpp) cc_final: 0.5675 (ptpp) REVERT: Q 413 MET cc_start: 0.6434 (mtt) cc_final: 0.6177 (mmt) REVERT: Q 418 MET cc_start: 0.7536 (ppp) cc_final: 0.6963 (ppp) REVERT: I 52 LEU cc_start: 0.8281 (mm) cc_final: 0.8059 (mt) REVERT: I 72 ASP cc_start: 0.7110 (t70) cc_final: 0.6827 (t70) REVERT: I 165 GLU cc_start: 0.7309 (tp30) cc_final: 0.6954 (tp30) REVERT: I 183 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7409 (mt) REVERT: I 199 ASP cc_start: 0.6433 (t0) cc_final: 0.6143 (t0) REVERT: I 238 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7122 (tm-30) REVERT: I 254 LYS cc_start: 0.7922 (tppt) cc_final: 0.7517 (tppt) REVERT: J 94 GLU cc_start: 0.6710 (pp20) cc_final: 0.6317 (pp20) REVERT: J 129 GLN cc_start: 0.7767 (tt0) cc_final: 0.7297 (mt0) REVERT: J 206 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7275 (tp30) REVERT: K 11 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6497 (mm-30) REVERT: L 80 GLU cc_start: 0.7585 (tp30) cc_final: 0.7135 (tp30) REVERT: L 104 MET cc_start: 0.5344 (mmp) cc_final: 0.4985 (mmp) REVERT: L 220 LYS cc_start: 0.6022 (mmtm) cc_final: 0.5634 (mmtm) REVERT: L 248 ASP cc_start: 0.6918 (p0) cc_final: 0.6575 (p0) REVERT: L 256 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6272 (mtp85) REVERT: L 268 ASP cc_start: 0.7276 (p0) cc_final: 0.6452 (p0) REVERT: M 15 TRP cc_start: 0.7247 (m100) cc_final: 0.7031 (m100) REVERT: M 35 ASP cc_start: 0.6902 (m-30) cc_final: 0.6480 (m-30) REVERT: M 61 ASP cc_start: 0.7594 (t70) cc_final: 0.7109 (t0) REVERT: M 99 PHE cc_start: 0.7668 (m-80) cc_final: 0.6842 (m-80) REVERT: M 164 LEU cc_start: 0.8112 (mt) cc_final: 0.7350 (pp) REVERT: M 178 LEU cc_start: 0.7859 (tp) cc_final: 0.7649 (tt) REVERT: M 195 THR cc_start: 0.7733 (m) cc_final: 0.7143 (t) REVERT: M 245 TRP cc_start: 0.7601 (t60) cc_final: 0.6925 (t-100) REVERT: M 259 ASP cc_start: 0.7923 (t0) cc_final: 0.7584 (t0) REVERT: M 267 LYS cc_start: 0.7723 (tptt) cc_final: 0.7401 (tppt) REVERT: N 78 TRP cc_start: 0.7424 (m100) cc_final: 0.6516 (m100) REVERT: N 213 GLN cc_start: 0.7779 (pp30) cc_final: 0.7346 (pp30) REVERT: N 230 LYS cc_start: 0.8406 (tppp) cc_final: 0.8195 (tppp) REVERT: N 241 THR cc_start: 0.8492 (t) cc_final: 0.8168 (p) REVERT: N 260 ARG cc_start: 0.6786 (mtm-85) cc_final: 0.6404 (mtm-85) REVERT: O 170 MET cc_start: 0.6581 (tpt) cc_final: 0.6355 (tmm) REVERT: P 85 LEU cc_start: 0.5317 (OUTLIER) cc_final: 0.5064 (mm) REVERT: P 106 TRP cc_start: 0.5453 (t60) cc_final: 0.5185 (t60) REVERT: P 132 MET cc_start: 0.8016 (tpt) cc_final: 0.7112 (tpt) REVERT: P 201 PHE cc_start: 0.8362 (t80) cc_final: 0.8143 (t80) REVERT: P 206 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6540 (pp20) outliers start: 93 outliers final: 79 residues processed: 865 average time/residue: 0.2335 time to fit residues: 324.3111 Evaluate side-chains 903 residues out of total 3537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 815 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 52 LEU 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 251 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 116 GLN 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 207 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 102 GLN Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 78 TRP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 206 GLU Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain R residue 368 LEU 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 114 SER Chi-restraints excluded: chain J residue 140 THR Chi-restraints excluded: chain J residue 172 ASN Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 23 HIS Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 233 HIS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 198 MET 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 30 ARG Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 131 LEU 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 63 TRP Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 168 ILE Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain P residue 199 ASP Chi-restraints excluded: chain P residue 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: 0.6980 chunk 27 optimal weight: 0.0170 chunk 379 optimal weight: 0.7980 chunk 310 optimal weight: 0.0170 chunk 169 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 299 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 195 optimal weight: 8.9990 chunk 167 optimal weight: 0.1980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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 213 GLN ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 GLN ** M 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 HIS ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.242642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.185694 restraints weight = 64131.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.190621 restraints weight = 29501.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.193585 restraints weight = 18202.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.195381 restraints weight = 13870.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.195970 restraints weight = 11916.365| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 36753 Z= 0.141 Angle : 0.744 16.997 50271 Z= 0.379 Chirality : 0.046 0.307 5432 Planarity : 0.004 0.066 5969 Dihedral : 16.953 145.091 5791 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 20.95 % Favored : 76.45 % Cbeta Deviations : 0.03 % 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: 0.87 (0.12), residues: 1886 sheet: 0.02 (0.19), residues: 710 loop : -1.24 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 155 TYR 0.023 0.001 TYR O 87 PHE 0.050 0.001 PHE J 110 TRP 0.036 0.002 TRP P 106 HIS 0.006 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (36705) covalent geometry : angle 0.72807 / 0.38 (50248) hydrogen bonds : bond 0.03962 / 2.63 ( 1694) hydrogen bonds : angle 4.71044 / 3.38 ( 4842) metal coordination : bond 0.02185 / 1.36 ( 48) metal coordination : angle 7.23467 / 4.95 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8610.78 seconds wall clock time: 148 minutes 45.80 seconds (8925.80 seconds total)