Starting phenix.real_space_refine on Mon Jul 6 06:21:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnw_38517/07_2026/8xnw_38517.map" } resolution = 3.6 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= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 9 5.49 5 S 246 5.16 5 C 21663 2.51 5 N 5755 2.21 5 O 6146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33848 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1636 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2532 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 951 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain breaks: 2 Chain: "r" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 354 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 6, 'TRANS': 37} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-4': 1, 'UQ9:plan-5': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1178 SG CYS B 99 80.773 63.378 105.627 1.00 29.52 S ATOM 1681 SG CYS B 164 78.050 59.601 110.426 1.00 28.96 S ATOM 1911 SG CYS B 194 83.219 59.707 109.786 1.00 29.28 S ATOM 1184 SG CYS B 100 79.664 59.394 104.644 1.00 30.11 S ATOM 7686 SG CYS E 134 139.631 55.437 153.329 1.00 56.01 S ATOM 7720 SG CYS E 139 142.382 57.351 152.522 1.00 56.50 S ATOM 8004 SG CYS E 175 137.171 58.873 155.921 1.00 54.42 S ATOM 8027 SG CYS E 179 140.324 60.903 155.785 1.00 57.95 S ATOM 11557 SG CYS F 425 120.637 63.891 155.917 1.00 45.60 S ATOM 11235 SG CYS F 385 120.903 61.633 150.042 1.00 39.95 S ATOM 11215 SG CYS F 382 116.542 62.536 152.248 1.00 40.29 S ATOM 11196 SG CYS F 379 118.608 58.452 155.010 1.00 43.09 S ATOM 12605 SG CYS G 131 101.225 51.191 137.897 1.00 31.31 S ATOM 12584 SG CYS G 128 103.182 55.271 133.487 1.00 30.26 S ATOM 12645 SG CYS G 137 100.611 57.023 139.515 1.00 33.13 S ATOM 13330 SG CYS G 226 102.552 50.958 146.519 1.00 34.31 S ATOM 13001 SG CYS G 182 105.547 49.504 151.771 1.00 36.31 S ATOM 12977 SG CYS G 179 104.835 54.845 149.924 1.00 35.62 S ATOM 12954 SG CYS G 176 108.510 50.814 147.397 1.00 34.05 S ATOM 12091 SG CYS G 64 105.940 60.863 152.180 1.00 35.53 S ATOM 12177 SG CYS G 75 106.621 62.991 150.605 1.00 36.47 S ATOM 12202 SG CYS G 78 105.254 67.427 152.874 1.00 36.76 S ATOM 12303 SG CYS G 92 102.838 65.190 154.681 1.00 39.04 S ATOM 20533 SG CYS I 152 87.294 53.354 113.619 1.00 27.39 S ATOM 20307 SG CYS I 123 86.768 54.304 119.000 1.00 27.30 S ATOM 20559 SG CYS I 155 89.516 58.212 115.415 1.00 27.04 S ATOM 20580 SG CYS I 158 92.787 53.078 116.222 1.00 26.60 S ATOM 20279 SG CYS I 119 92.987 50.212 122.618 1.00 28.85 S ATOM 20609 SG CYS I 162 99.297 50.240 120.631 1.00 28.07 S ATOM 20237 SG CYS I 113 95.981 45.178 122.750 1.00 28.61 S ATOM 20256 SG CYS I 116 98.218 49.517 126.573 1.00 29.24 S ATOM 25091 SG CYS R 79 112.531 43.832 125.669 1.00 32.60 S ATOM 25267 SG CYS R 104 110.106 42.332 127.020 1.00 32.49 S ATOM 25289 SG CYS R 107 109.496 43.080 123.603 1.00 30.78 S Time building chain proxies: 7.19, per 1000 atoms: 0.21 Number of scatterers: 33848 At special positions: 0 Unit cell: (167.2, 130.9, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 246 16.00 P 9 15.00 O 6146 8.00 N 5755 7.00 C 21663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 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: 3.43 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 35 sheets defined 49.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.314A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.583A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.249A pdb=" N PHE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 118' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 4.067A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.034A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.588A pdb=" N HIS D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.455A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.843A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.707A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.668A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.608A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.612A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.557A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.296A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.184A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.032A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.261A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.587A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.015A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.860A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.733A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.722A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.712A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.821A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 361 Processing helix chain 'G' and resid 377 through 386 removed outlier: 4.302A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 382 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.588A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.009A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.677A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.575A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 85 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.687A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.853A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 242 removed outlier: 4.207A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU H 227 " --> pdb=" O PHE H 223 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 277 Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 61 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.910A pdb=" N ILE I 67 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.285A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.589A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 114 through 122 removed outlier: 4.504A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 Processing helix chain 'P' and resid 178 through 195 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 removed outlier: 3.773A pdb=" N LEU P 231 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.118A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.936A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.445A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.520A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'R' and resid 42 through 49 removed outlier: 4.168A pdb=" N ARG R 47 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.311A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.709A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.681A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.991A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.947A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.544A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.680A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.056A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.893A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.900A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.544A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.659A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.717A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.740A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.580A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.534A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.740A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 27 Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.201A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.984A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 16 Processing helix chain 's' and resid 78 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.541A pdb=" N ILE B 132 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.858A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.400A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 84 removed outlier: 4.107A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.500A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.566A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.598A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.776A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AB7, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.349A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB9, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.096A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N CYS G 367 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA G 340 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.323A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.573A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC6, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.863A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.849A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.369A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD5, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 55 through 57 Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 38 through 41 1355 hydrogen bonds defined for protein. 3849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 11464 1.37 - 1.58: 22739 1.58 - 1.80: 218 1.80 - 2.01: 167 2.01 - 2.23: 80 Bond restraints: 34668 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ARG Q 106 " pdb=" O ARG Q 106 " ideal model delta sigma weight residual 1.236 1.339 -0.103 1.14e-02 7.69e+03 8.14e+01 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.181 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" CA TYR Z 143 " pdb=" C TYR Z 143 " ideal model delta sigma weight residual 1.524 1.419 0.104 1.23e-02 6.61e+03 7.21e+01 ... (remaining 34663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 46267 6.45 - 12.90: 570 12.90 - 19.35: 165 19.35 - 25.80: 3 25.80 - 32.25: 2 Bond angle restraints: 47007 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.00 25.64 1.52e+00 4.33e-01 2.85e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.47 19.70 1.26e+00 6.30e-01 2.44e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.80 16.53 1.14e+00 7.69e-01 2.10e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.59 16.74 1.20e+00 6.94e-01 1.95e+02 angle pdb=" N MET G 77 " pdb=" CA MET G 77 " pdb=" C MET G 77 " ideal model delta sigma weight residual 113.38 97.32 16.06 1.23e+00 6.61e-01 1.70e+02 ... (remaining 47002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 20574 35.19 - 70.38: 298 70.38 - 105.57: 34 105.57 - 140.77: 2 140.77 - 175.96: 1 Dihedral angle restraints: 20909 sinusoidal: 8746 harmonic: 12163 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 171.69 -78.69 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" CB CYS X 78 " pdb=" SG CYS X 78 " pdb=" SG CYS X 110 " pdb=" CB CYS X 110 " ideal model delta sinusoidal sigma weight residual 93.00 154.31 -61.31 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" N THR Z 144 " pdb=" C THR Z 144 " pdb=" CA THR Z 144 " pdb=" CB THR Z 144 " ideal model delta harmonic sigma weight residual 123.40 107.48 15.92 0 2.50e+00 1.60e-01 4.06e+01 ... (remaining 20906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4710 0.191 - 0.382: 391 0.382 - 0.573: 22 0.573 - 0.764: 3 0.764 - 0.955: 24 Chirality restraints: 5150 Sorted by residual: chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.60 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb="FE1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S3 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 5147 not shown) Planarity restraints: 5975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.013 2.00e-02 2.50e+03 2.72e-01 2.22e+03 pdb=" C1M UQ9 H 400 " 0.133 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.157 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " 0.128 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " 0.012 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " -0.117 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " 0.069 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.345 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.542 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " 0.498 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " 0.005 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " -0.386 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 B 302 " -0.058 2.00e-02 2.50e+03 2.23e-01 1.49e+03 pdb=" C1M UQ9 B 302 " -0.209 2.00e-02 2.50e+03 pdb=" C2 UQ9 B 302 " -0.050 2.00e-02 2.50e+03 pdb=" C3 UQ9 B 302 " 0.109 2.00e-02 2.50e+03 pdb=" C4 UQ9 B 302 " -0.017 2.00e-02 2.50e+03 pdb=" C5 UQ9 B 302 " -0.107 2.00e-02 2.50e+03 pdb=" C6 UQ9 B 302 " 0.086 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " 0.499 2.00e-02 2.50e+03 pdb=" O2 UQ9 B 302 " -0.190 2.00e-02 2.50e+03 pdb=" O3 UQ9 B 302 " 0.338 2.00e-02 2.50e+03 pdb=" O4 UQ9 B 302 " -0.068 2.00e-02 2.50e+03 pdb=" O5 UQ9 B 302 " -0.333 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 400 " -0.015 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C11 UQ9 H 400 " 0.104 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " 0.133 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 400 " -0.176 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 400 " -0.046 2.00e-02 2.50e+03 ... (remaining 5972 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 445 2.53 - 3.13: 31061 3.13 - 3.72: 54064 3.72 - 4.31: 81647 4.31 - 4.90: 128518 Nonbonded interactions: 295735 Sorted by model distance: nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.983 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 2.000 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.007 3.400 nonbonded pdb=" O ASN Z 24 " pdb=" OD1 ASN Z 24 " model vdw 2.045 3.040 ... (remaining 295730 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.020 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.610 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.021 1.241 34709 Z= 1.005 Angle : 2.163 43.608 47099 Z= 1.430 Chirality : 0.122 0.955 5150 Planarity : 0.009 0.272 5975 Dihedral : 12.678 175.958 13055 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 47.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.47 % Favored : 92.46 % Rotamer: Outliers : 0.44 % Allowed : 7.51 % Favored : 92.05 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % 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: -3.21 (0.12), residues: 4136 helix: -1.79 (0.11), residues: 1773 sheet: -2.17 (0.27), residues: 327 loop : -2.40 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 68 TYR 0.046 0.003 TYR B 112 PHE 0.031 0.002 PHE I 175 TRP 0.033 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.01455 / 0.92 (34668) covalent geometry : angle 2.05503 / 1.43 (47007) SS BOND : bond 0.00917 / 0.46 ( 4) SS BOND : angle 1.31875 / 0.64 ( 8) hydrogen bonds : bond 0.24974 / 16.39 ( 1355) hydrogen bonds : angle 9.63595 / 6.90 ( 3849) metal coordination : bond 0.47155 / 30.83 ( 37) metal coordination : angle 16.08247 / 12.04 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1709 time to evaluate : 1.331 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: A 48 ARG cc_start: 0.7180 (tpp80) cc_final: 0.6855 (ptt180) REVERT: B 88 SER cc_start: 0.7950 (p) cc_final: 0.7691 (p) REVERT: B 196 PRO cc_start: 0.7629 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: B 201 LEU cc_start: 0.9231 (tp) cc_final: 0.8516 (tp) REVERT: C 133 SER cc_start: 0.7504 (t) cc_final: 0.7292 (p) REVERT: C 178 PHE cc_start: 0.7004 (m-10) cc_final: 0.6598 (m-10) REVERT: D 144 MET cc_start: 0.7311 (mpp) cc_final: 0.6880 (mpp) REVERT: F 349 LEU cc_start: 0.6150 (tp) cc_final: 0.4818 (tp) REVERT: F 361 THR cc_start: 0.7066 (p) cc_final: 0.6262 (p) REVERT: G 144 MET cc_start: 0.8021 (tpt) cc_final: 0.7680 (tpt) REVERT: G 496 MET cc_start: 0.6363 (ttp) cc_final: 0.6130 (ttp) REVERT: H 277 TYR cc_start: 0.6865 (m-10) cc_final: 0.6540 (m-80) REVERT: H 285 LEU cc_start: 0.8568 (tt) cc_final: 0.8303 (tp) REVERT: P 328 MET cc_start: 0.7951 (tpt) cc_final: 0.7731 (tpt) REVERT: Q 160 TYR cc_start: 0.8117 (t80) cc_final: 0.7902 (t80) REVERT: Q 164 PHE cc_start: 0.5859 (m-80) cc_final: 0.5149 (m-80) REVERT: T 86 VAL cc_start: 0.7520 (t) cc_final: 0.7235 (t) REVERT: T 103 HIS cc_start: 0.6689 (m-70) cc_final: 0.6476 (m90) REVERT: T 105 MET cc_start: 0.7606 (mmt) cc_final: 0.7170 (mmt) REVERT: W 61 GLN cc_start: 0.6612 (tt0) cc_final: 0.6342 (tt0) REVERT: W 118 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7908 (Cg_endo) REVERT: X 47 ARG cc_start: 0.6786 (tpt170) cc_final: 0.6406 (tmt170) REVERT: X 69 ASN cc_start: 0.7552 (t0) cc_final: 0.7098 (t0) REVERT: b 11 ASN cc_start: 0.5713 (p0) cc_final: 0.5422 (p0) REVERT: q 89 TRP cc_start: 0.7249 (t60) cc_final: 0.6921 (t60) outliers start: 16 outliers final: 1 residues processed: 1713 average time/residue: 0.2422 time to fit residues: 652.9590 Evaluate side-chains 1008 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1007 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN B 166 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 102 HIS C 104 ASN C 195 HIS D 117 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 346 GLN D 381 HIS E 68 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 181 ASN E 190 ASN E 245 GLN F 220 GLN F 344 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN F 451 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN G 331 GLN G 388 ASN ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 604 GLN G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS P 43 HIS P 71 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN P 251 ASN P 341 GLN Q 71 HIS ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN S 92 GLN V 41 HIS W 61 GLN W 105 HIS Z 8 GLN Z 54 ASN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN b 71 GLN r 13 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.100846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083344 restraints weight = 103025.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.086104 restraints weight = 47182.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087948 restraints weight = 27811.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089147 restraints weight = 19285.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089922 restraints weight = 15064.670| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 34709 Z= 0.200 Angle : 1.078 70.450 47099 Z= 0.446 Chirality : 0.049 0.287 5150 Planarity : 0.007 0.125 5975 Dihedral : 8.856 135.696 4812 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 3.88 % Allowed : 18.07 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.87 (0.12), residues: 4136 helix: -0.50 (0.11), residues: 1834 sheet: -1.82 (0.27), residues: 336 loop : -1.82 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 87 TYR 0.044 0.003 TYR B 170 PHE 0.035 0.003 PHE H 19 TRP 0.027 0.002 TRP A 106 HIS 0.012 0.002 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (34668) covalent geometry : angle 0.85851 / 0.44 (47007) SS BOND : bond 0.00268 / 0.14 ( 4) SS BOND : angle 1.35184 / 0.75 ( 8) hydrogen bonds : bond 0.05931 / 3.87 ( 1355) hydrogen bonds : angle 5.98389 / 4.24 ( 3849) metal coordination : bond 0.01834 / 1.15 ( 37) metal coordination : angle 15.46161 / 11.39 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1161 time to evaluate : 1.350 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: A 27 MET cc_start: 0.7673 (mtm) cc_final: 0.7081 (mtm) REVERT: A 48 ARG cc_start: 0.8112 (tpp80) cc_final: 0.7079 (ptt180) REVERT: A 94 LEU cc_start: 0.9061 (tp) cc_final: 0.8847 (tp) REVERT: B 79 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8048 (t0) REVERT: B 80 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8297 (t0) REVERT: B 83 ASN cc_start: 0.8489 (m110) cc_final: 0.7383 (m-40) REVERT: B 126 ARG cc_start: 0.8903 (tpp-160) cc_final: 0.8583 (tpp-160) REVERT: B 129 ASP cc_start: 0.7742 (m-30) cc_final: 0.6784 (m-30) REVERT: B 140 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7731 (mtmt) REVERT: B 150 ASP cc_start: 0.8959 (m-30) cc_final: 0.8757 (m-30) REVERT: B 151 GLN cc_start: 0.8991 (mt0) cc_final: 0.8519 (mt0) REVERT: C 106 GLN cc_start: 0.8228 (mp10) cc_final: 0.7708 (mp10) REVERT: C 178 PHE cc_start: 0.7637 (m-10) cc_final: 0.7429 (m-10) REVERT: C 221 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 79 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6788 (t0) REVERT: D 101 LEU cc_start: 0.9158 (mt) cc_final: 0.8712 (mt) REVERT: D 197 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7885 (ptp) REVERT: D 443 MET cc_start: 0.7168 (mmt) cc_final: 0.6155 (mmt) REVERT: E 83 ASP cc_start: 0.9142 (t0) cc_final: 0.8863 (t0) REVERT: E 112 TYR cc_start: 0.9077 (m-80) cc_final: 0.8766 (m-80) REVERT: E 120 MET cc_start: 0.8448 (tpp) cc_final: 0.8224 (tpp) REVERT: E 122 ASN cc_start: 0.7260 (t0) cc_final: 0.7046 (t0) REVERT: E 184 MET cc_start: 0.7699 (ttp) cc_final: 0.7254 (ptt) REVERT: E 191 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: F 112 TYR cc_start: 0.8503 (m-80) cc_final: 0.7979 (m-80) REVERT: F 131 MET cc_start: 0.9082 (mmm) cc_final: 0.8158 (tpp) REVERT: F 157 TYR cc_start: 0.8363 (t80) cc_final: 0.7908 (t80) REVERT: F 164 ASN cc_start: 0.8172 (p0) cc_final: 0.7971 (p0) REVERT: F 206 CYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8290 (t) REVERT: F 262 PHE cc_start: 0.8609 (m-80) cc_final: 0.8207 (t80) REVERT: G 66 HIS cc_start: 0.8738 (t-90) cc_final: 0.8498 (t-90) REVERT: G 67 GLU cc_start: 0.8395 (tt0) cc_final: 0.7986 (tm-30) REVERT: G 150 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8104 (mtt-85) REVERT: G 329 MET cc_start: 0.8190 (mmm) cc_final: 0.7692 (mmm) REVERT: G 471 LYS cc_start: 0.8895 (mttp) cc_final: 0.8674 (mtmm) REVERT: G 513 MET cc_start: 0.9061 (tpp) cc_final: 0.8829 (tpp) REVERT: G 548 LEU cc_start: 0.8529 (tp) cc_final: 0.8241 (tp) REVERT: H 68 MET cc_start: 0.6687 (pmm) cc_final: 0.6312 (ttp) REVERT: H 114 TYR cc_start: 0.7619 (m-80) cc_final: 0.7325 (m-80) REVERT: H 156 MET cc_start: 0.8227 (mtm) cc_final: 0.7993 (mtm) REVERT: H 183 MET cc_start: 0.8532 (mtt) cc_final: 0.8145 (mtt) REVERT: H 184 MET cc_start: 0.8863 (mmm) cc_final: 0.8205 (mmm) REVERT: H 199 ASP cc_start: 0.7545 (t0) cc_final: 0.7276 (t0) REVERT: H 284 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8764 (mt0) REVERT: I 204 ASN cc_start: 0.8837 (m110) cc_final: 0.8481 (t0) REVERT: I 206 GLN cc_start: 0.8141 (tp40) cc_final: 0.7823 (tp40) REVERT: I 209 TYR cc_start: 0.9053 (p90) cc_final: 0.8784 (p90) REVERT: P 133 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7671 (mt-10) REVERT: P 217 PHE cc_start: 0.8319 (m-80) cc_final: 0.8036 (m-80) REVERT: P 298 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8222 (t80) REVERT: P 319 VAL cc_start: 0.9490 (t) cc_final: 0.9213 (t) REVERT: P 346 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7329 (mm-30) REVERT: P 351 GLU cc_start: 0.8443 (mm-30) cc_final: 0.6941 (mm-30) REVERT: P 367 GLU cc_start: 0.7902 (mp0) cc_final: 0.7310 (pm20) REVERT: Q 58 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8433 (mmtt) REVERT: Q 85 ASN cc_start: 0.8600 (t0) cc_final: 0.8203 (t0) REVERT: Q 100 GLU cc_start: 0.8101 (tp30) cc_final: 0.7863 (tt0) REVERT: R 74 HIS cc_start: 0.9140 (OUTLIER) cc_final: 0.8915 (m-70) REVERT: S 44 LEU cc_start: 0.9355 (tp) cc_final: 0.9080 (tt) REVERT: T 103 HIS cc_start: 0.8188 (m-70) cc_final: 0.7977 (m90) REVERT: T 139 MET cc_start: 0.6763 (mtt) cc_final: 0.6324 (ttm) REVERT: T 143 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7764 (mt-10) REVERT: V 53 ASN cc_start: 0.9005 (m-40) cc_final: 0.8758 (m-40) REVERT: W 58 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7296 (m) REVERT: W 99 VAL cc_start: 0.8832 (t) cc_final: 0.8448 (t) REVERT: W 118 PRO cc_start: 0.8294 (Cg_exo) cc_final: 0.7953 (Cg_endo) REVERT: X 47 ARG cc_start: 0.8249 (tpt170) cc_final: 0.6893 (tmt170) REVERT: X 69 ASN cc_start: 0.9022 (t0) cc_final: 0.8651 (t0) REVERT: Z 10 MET cc_start: 0.8813 (tpp) cc_final: 0.8554 (mmm) REVERT: Z 80 ASP cc_start: 0.7995 (m-30) cc_final: 0.7557 (m-30) REVERT: Z 86 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8576 (tp) REVERT: Z 93 GLU cc_start: 0.8213 (tp30) cc_final: 0.8004 (tp30) REVERT: Z 114 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8191 (p) REVERT: a 5 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9114 (mm) REVERT: a 61 TYR cc_start: 0.7541 (t80) cc_final: 0.7260 (t80) REVERT: b 11 ASN cc_start: 0.8105 (p0) cc_final: 0.7749 (p0) REVERT: b 43 SER cc_start: 0.9033 (p) cc_final: 0.8701 (m) REVERT: b 47 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8454 (ttpp) outliers start: 141 outliers final: 62 residues processed: 1221 average time/residue: 0.2104 time to fit residues: 420.6779 Evaluate side-chains 990 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 916 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 TYR Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 462 PHE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 68 optimal weight: 0.8980 chunk 353 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 246 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 384 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 74 GLN C 76 GLN D 131 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 303 HIS ** F 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN I 159 GLN P 71 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN W 94 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081163 restraints weight = 103101.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083878 restraints weight = 47442.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085692 restraints weight = 28195.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086859 restraints weight = 19669.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.087640 restraints weight = 15438.640| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34709 Z= 0.174 Angle : 0.983 72.883 47099 Z= 0.390 Chirality : 0.046 0.237 5150 Planarity : 0.006 0.156 5975 Dihedral : 8.512 147.434 4808 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 4.35 % Allowed : 20.35 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -1.35 (0.13), residues: 4136 helix: -0.05 (0.12), residues: 1836 sheet: -1.56 (0.28), residues: 342 loop : -1.57 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 218 TYR 0.032 0.002 TYR D 135 PHE 0.027 0.002 PHE A 62 TRP 0.028 0.002 TRP A 106 HIS 0.008 0.001 HIS R 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (34668) covalent geometry : angle 0.76203 / 0.39 (47007) SS BOND : bond 0.00212 / 0.11 ( 4) SS BOND : angle 0.95517 / 0.52 ( 8) hydrogen bonds : bond 0.04863 / 3.23 ( 1355) hydrogen bonds : angle 5.46380 / 3.87 ( 3849) metal coordination : bond 0.01916 / 1.23 ( 37) metal coordination : angle 14.70572 / 10.85 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 991 time to evaluate : 1.390 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: A 27 MET cc_start: 0.7780 (mtm) cc_final: 0.7386 (mtm) REVERT: A 35 ASN cc_start: 0.8552 (m-40) cc_final: 0.8339 (m-40) REVERT: A 48 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7101 (ptt180) REVERT: A 55 PHE cc_start: 0.9041 (p90) cc_final: 0.8325 (p90) REVERT: A 68 GLU cc_start: 0.8312 (tt0) cc_final: 0.7772 (tt0) REVERT: A 94 LEU cc_start: 0.9027 (tp) cc_final: 0.8585 (tp) REVERT: B 83 ASN cc_start: 0.8486 (m110) cc_final: 0.7914 (m110) REVERT: B 103 GLU cc_start: 0.8203 (tp30) cc_final: 0.7587 (tp30) REVERT: B 140 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7953 (mttt) REVERT: B 150 ASP cc_start: 0.9092 (m-30) cc_final: 0.8830 (m-30) REVERT: B 151 GLN cc_start: 0.8958 (mt0) cc_final: 0.8568 (mt0) REVERT: B 212 ILE cc_start: 0.9367 (mm) cc_final: 0.9119 (mm) REVERT: C 106 GLN cc_start: 0.8230 (mp10) cc_final: 0.7597 (mp10) REVERT: C 199 LYS cc_start: 0.9428 (tppt) cc_final: 0.9221 (tppt) REVERT: D 79 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.6921 (t0) REVERT: D 87 GLN cc_start: 0.8054 (tp40) cc_final: 0.7556 (tp-100) REVERT: D 101 LEU cc_start: 0.9091 (mt) cc_final: 0.8731 (mt) REVERT: E 83 ASP cc_start: 0.9184 (t0) cc_final: 0.8844 (t0) REVERT: E 122 ASN cc_start: 0.7171 (t0) cc_final: 0.6638 (t0) REVERT: E 184 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7082 (ptt) REVERT: E 191 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: F 75 TRP cc_start: 0.7517 (t60) cc_final: 0.6998 (t60) REVERT: F 131 MET cc_start: 0.9043 (mmm) cc_final: 0.8549 (tmm) REVERT: F 164 ASN cc_start: 0.8033 (p0) cc_final: 0.7790 (p0) REVERT: F 169 LEU cc_start: 0.9505 (tp) cc_final: 0.9272 (tp) REVERT: F 337 MET cc_start: 0.8341 (tpp) cc_final: 0.8139 (tpp) REVERT: F 457 HIS cc_start: 0.5447 (m-70) cc_final: 0.4653 (p-80) REVERT: G 117 MET cc_start: 0.8771 (mmm) cc_final: 0.8363 (mmm) REVERT: G 144 MET cc_start: 0.9219 (tpt) cc_final: 0.8946 (tpp) REVERT: G 160 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8801 (t) REVERT: G 329 MET cc_start: 0.8105 (mmm) cc_final: 0.7470 (mmm) REVERT: G 379 THR cc_start: 0.8508 (p) cc_final: 0.8289 (t) REVERT: H 59 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: H 68 MET cc_start: 0.6683 (pmm) cc_final: 0.6450 (ttp) REVERT: H 77 LEU cc_start: 0.8933 (tp) cc_final: 0.8724 (tt) REVERT: H 92 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8527 (Cg_endo) REVERT: H 104 PHE cc_start: 0.8959 (t80) cc_final: 0.8619 (t80) REVERT: H 114 TYR cc_start: 0.7411 (m-80) cc_final: 0.7179 (m-80) REVERT: H 142 TYR cc_start: 0.7116 (m-80) cc_final: 0.6859 (m-80) REVERT: H 143 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7701 (mt-10) REVERT: H 172 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7056 (ppp) REVERT: H 183 MET cc_start: 0.8554 (mtt) cc_final: 0.8280 (mtt) REVERT: H 184 MET cc_start: 0.8954 (mmm) cc_final: 0.8621 (mmm) REVERT: H 206 GLU cc_start: 0.8062 (mp0) cc_final: 0.7844 (mp0) REVERT: H 258 ASN cc_start: 0.7484 (m110) cc_final: 0.6819 (m110) REVERT: H 270 PHE cc_start: 0.8192 (m-10) cc_final: 0.7948 (m-10) REVERT: H 293 PHE cc_start: 0.8571 (m-10) cc_final: 0.8348 (m-80) REVERT: I 86 TYR cc_start: 0.8635 (t80) cc_final: 0.8380 (t80) REVERT: I 94 SER cc_start: 0.9367 (t) cc_final: 0.8916 (p) REVERT: I 149 MET cc_start: 0.9116 (mmm) cc_final: 0.8519 (mtt) REVERT: I 204 ASN cc_start: 0.8816 (m110) cc_final: 0.8413 (t0) REVERT: I 206 GLN cc_start: 0.8202 (tp40) cc_final: 0.7868 (tp40) REVERT: I 209 TYR cc_start: 0.9058 (p90) cc_final: 0.8789 (p90) REVERT: P 133 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7758 (tt0) REVERT: P 134 TRP cc_start: 0.8662 (p90) cc_final: 0.8223 (p90) REVERT: P 217 PHE cc_start: 0.8387 (m-80) cc_final: 0.7977 (m-80) REVERT: P 220 TYR cc_start: 0.8097 (m-80) cc_final: 0.7891 (m-80) REVERT: P 298 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8068 (t80) REVERT: P 367 GLU cc_start: 0.7722 (mp0) cc_final: 0.7110 (pm20) REVERT: P 368 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: Q 160 TYR cc_start: 0.7884 (t80) cc_final: 0.7653 (t80) REVERT: R 110 GLN cc_start: 0.7878 (mp10) cc_final: 0.7497 (mp10) REVERT: T 113 LEU cc_start: 0.8981 (mp) cc_final: 0.8727 (pt) REVERT: T 115 GLN cc_start: 0.8943 (tt0) cc_final: 0.8444 (tm-30) REVERT: T 117 GLU cc_start: 0.8243 (tm-30) cc_final: 0.6935 (tm-30) REVERT: T 139 MET cc_start: 0.6957 (mtt) cc_final: 0.6597 (ttm) REVERT: T 142 GLN cc_start: 0.8972 (tt0) cc_final: 0.8768 (tt0) REVERT: T 143 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7499 (mp0) REVERT: V 83 GLN cc_start: 0.8627 (tp40) cc_final: 0.8423 (tm-30) REVERT: W 57 ILE cc_start: 0.8443 (pp) cc_final: 0.8079 (pp) REVERT: W 58 THR cc_start: 0.7722 (t) cc_final: 0.7473 (m) REVERT: W 61 GLN cc_start: 0.7961 (tt0) cc_final: 0.7691 (tt0) REVERT: W 99 VAL cc_start: 0.8398 (t) cc_final: 0.8194 (t) REVERT: W 111 HIS cc_start: 0.7076 (m-70) cc_final: 0.6798 (m-70) REVERT: W 118 PRO cc_start: 0.8315 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: W 126 TYR cc_start: 0.8698 (m-80) cc_final: 0.8269 (m-80) REVERT: X 32 TYR cc_start: 0.9159 (t80) cc_final: 0.8949 (t80) REVERT: X 47 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7050 (tmt170) REVERT: X 69 ASN cc_start: 0.8972 (t0) cc_final: 0.8565 (t0) REVERT: Z 10 MET cc_start: 0.8909 (tpp) cc_final: 0.8496 (mmt) REVERT: Z 51 MET cc_start: 0.8095 (tmm) cc_final: 0.7805 (tmm) REVERT: Z 86 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8513 (tp) REVERT: Z 114 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (p) REVERT: Z 137 ASN cc_start: 0.7796 (p0) cc_final: 0.7487 (p0) REVERT: Z 142 TRP cc_start: 0.8233 (m100) cc_final: 0.7498 (m100) REVERT: a 5 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9055 (mm) REVERT: a 61 TYR cc_start: 0.7623 (t80) cc_final: 0.7273 (t80) REVERT: a 64 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7888 (mtpp) REVERT: b 11 ASN cc_start: 0.8111 (p0) cc_final: 0.7781 (p0) REVERT: b 43 SER cc_start: 0.9058 (p) cc_final: 0.8705 (m) REVERT: b 47 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8564 (ttpp) REVERT: q 86 TRP cc_start: 0.8491 (m100) cc_final: 0.7946 (m-10) outliers start: 158 outliers final: 84 residues processed: 1078 average time/residue: 0.2116 time to fit residues: 378.7346 Evaluate side-chains 983 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 887 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 437 ASP Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 368 GLU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 145 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 390 optimal weight: 0.0970 chunk 305 optimal weight: 20.0000 chunk 258 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 74 GLN D 87 GLN D 92 HIS D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS G 51 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 292 ASN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN X 30 HIS X 64 ASN X 69 ASN Z 76 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.095131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.077408 restraints weight = 103301.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080011 restraints weight = 48025.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081768 restraints weight = 28816.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082926 restraints weight = 20279.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083683 restraints weight = 15951.276| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34709 Z= 0.205 Angle : 0.989 76.512 47099 Z= 0.379 Chirality : 0.046 0.244 5150 Planarity : 0.006 0.141 5975 Dihedral : 8.439 156.337 4808 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.79 % Favored : 95.19 % Rotamer: Outliers : 5.17 % Allowed : 21.12 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -1.08 (0.13), residues: 4136 helix: 0.23 (0.12), residues: 1837 sheet: -1.30 (0.28), residues: 342 loop : -1.52 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG W 80 TYR 0.039 0.002 TYR D 135 PHE 0.027 0.002 PHE A 62 TRP 0.025 0.002 TRP A 106 HIS 0.011 0.001 HIS E 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (34668) covalent geometry : angle 0.74359 / 0.37 (47007) SS BOND : bond 0.00246 / 0.13 ( 4) SS BOND : angle 0.66465 / 0.33 ( 8) hydrogen bonds : bond 0.04426 / 2.96 ( 1355) hydrogen bonds : angle 5.29560 / 3.76 ( 3849) metal coordination : bond 0.02148 / 1.33 ( 37) metal coordination : angle 15.44623 / 11.32 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 936 time to evaluate : 1.459 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: A 35 ASN cc_start: 0.8729 (m-40) cc_final: 0.8467 (m-40) REVERT: A 48 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7150 (ptt180) REVERT: A 68 GLU cc_start: 0.8487 (tt0) cc_final: 0.7685 (tt0) REVERT: A 94 LEU cc_start: 0.9117 (tp) cc_final: 0.8449 (tp) REVERT: A 98 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 103 GLU cc_start: 0.8286 (tp30) cc_final: 0.7555 (tp30) REVERT: B 150 ASP cc_start: 0.9202 (m-30) cc_final: 0.8879 (m-30) REVERT: B 151 GLN cc_start: 0.8894 (mt0) cc_final: 0.8470 (mt0) REVERT: C 106 GLN cc_start: 0.8218 (mp10) cc_final: 0.7719 (mp10) REVERT: C 199 LYS cc_start: 0.9420 (tppt) cc_final: 0.9199 (tppt) REVERT: D 79 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.7184 (t0) REVERT: D 101 LEU cc_start: 0.9176 (mt) cc_final: 0.8881 (mt) REVERT: D 215 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8545 (tm-30) REVERT: D 300 TRP cc_start: 0.8986 (t-100) cc_final: 0.8735 (t-100) REVERT: D 443 MET cc_start: 0.7866 (mmt) cc_final: 0.7407 (mmt) REVERT: E 38 PHE cc_start: 0.6337 (m-80) cc_final: 0.6133 (m-10) REVERT: E 184 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7251 (ptp) REVERT: E 191 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: F 75 TRP cc_start: 0.7610 (t60) cc_final: 0.7023 (t60) REVERT: F 131 MET cc_start: 0.9110 (mmm) cc_final: 0.8430 (tmm) REVERT: F 164 ASN cc_start: 0.8006 (p0) cc_final: 0.7751 (p0) REVERT: F 169 LEU cc_start: 0.9501 (tp) cc_final: 0.9252 (tp) REVERT: F 357 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: G 42 MET cc_start: 0.7064 (tpp) cc_final: 0.6710 (tpp) REVERT: G 117 MET cc_start: 0.8933 (mmm) cc_final: 0.8707 (mmm) REVERT: G 144 MET cc_start: 0.9205 (tpt) cc_final: 0.8915 (tpp) REVERT: G 160 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8883 (t) REVERT: G 257 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.9071 (p) REVERT: G 329 MET cc_start: 0.8317 (mmm) cc_final: 0.7736 (mmm) REVERT: G 408 ARG cc_start: 0.8419 (ttt180) cc_final: 0.8204 (ttt180) REVERT: G 513 MET cc_start: 0.9045 (tpp) cc_final: 0.8637 (tpt) REVERT: G 707 MET cc_start: 0.9194 (mmt) cc_final: 0.8927 (mmp) REVERT: H 47 GLN cc_start: 0.9061 (tp40) cc_final: 0.8515 (tp40) REVERT: H 51 ASP cc_start: 0.9090 (p0) cc_final: 0.8825 (p0) REVERT: H 56 PHE cc_start: 0.8896 (m-80) cc_final: 0.8690 (m-80) REVERT: H 61 MET cc_start: 0.8827 (ppp) cc_final: 0.8545 (ppp) REVERT: H 92 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8539 (Cg_endo) REVERT: H 202 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8091 (tm-30) REVERT: H 206 GLU cc_start: 0.8149 (mp0) cc_final: 0.7547 (mp0) REVERT: H 222 LEU cc_start: 0.9470 (mp) cc_final: 0.8988 (mp) REVERT: H 258 ASN cc_start: 0.7383 (m-40) cc_final: 0.6856 (m-40) REVERT: H 262 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7863 (mm-30) REVERT: I 94 SER cc_start: 0.9417 (t) cc_final: 0.8656 (p) REVERT: I 146 ASP cc_start: 0.7946 (m-30) cc_final: 0.7687 (m-30) REVERT: I 204 ASN cc_start: 0.8811 (m110) cc_final: 0.8381 (t0) REVERT: I 206 GLN cc_start: 0.8201 (tp40) cc_final: 0.7915 (tp40) REVERT: P 97 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7735 (pmm) REVERT: P 133 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7819 (tt0) REVERT: P 134 TRP cc_start: 0.8789 (p90) cc_final: 0.8277 (p90) REVERT: P 298 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8176 (t80) REVERT: P 351 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7266 (mm-30) REVERT: P 367 GLU cc_start: 0.7550 (mp0) cc_final: 0.7090 (pm20) REVERT: P 368 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8264 (mt-10) REVERT: Q 139 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8562 (mm-30) REVERT: R 110 GLN cc_start: 0.7932 (mp10) cc_final: 0.7511 (mp10) REVERT: S 82 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8739 (mt) REVERT: T 100 VAL cc_start: 0.7040 (t) cc_final: 0.6249 (t) REVERT: T 108 LEU cc_start: 0.5864 (mp) cc_final: 0.5191 (tt) REVERT: T 142 GLN cc_start: 0.8958 (tt0) cc_final: 0.8593 (mt0) REVERT: T 143 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7556 (mp0) REVERT: V 83 GLN cc_start: 0.8688 (tp40) cc_final: 0.8485 (tm-30) REVERT: W 45 GLU cc_start: 0.8781 (tp30) cc_final: 0.8362 (tp30) REVERT: W 57 ILE cc_start: 0.8489 (pp) cc_final: 0.8196 (pp) REVERT: W 58 THR cc_start: 0.7707 (t) cc_final: 0.7483 (m) REVERT: W 118 PRO cc_start: 0.8293 (Cg_exo) cc_final: 0.7959 (Cg_endo) REVERT: W 126 TYR cc_start: 0.8985 (m-80) cc_final: 0.8559 (m-80) REVERT: X 47 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7053 (tmt170) REVERT: Z 10 MET cc_start: 0.8931 (tpp) cc_final: 0.8565 (mmt) REVERT: Z 51 MET cc_start: 0.8300 (tmm) cc_final: 0.8095 (tmm) REVERT: Z 80 ASP cc_start: 0.7926 (m-30) cc_final: 0.7368 (m-30) REVERT: Z 114 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8424 (p) REVERT: a 5 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9088 (mm) REVERT: a 61 TYR cc_start: 0.7699 (t80) cc_final: 0.7307 (t80) REVERT: b 11 ASN cc_start: 0.8183 (p0) cc_final: 0.7887 (p0) REVERT: b 43 SER cc_start: 0.9122 (p) cc_final: 0.8857 (m) REVERT: b 47 LYS cc_start: 0.8822 (ttpp) cc_final: 0.8613 (ttpp) REVERT: q 86 TRP cc_start: 0.8557 (m100) cc_final: 0.7983 (m-10) REVERT: s 90 PHE cc_start: 0.6603 (m-10) cc_final: 0.6389 (m-10) outliers start: 188 outliers final: 116 residues processed: 1041 average time/residue: 0.2108 time to fit residues: 365.7706 Evaluate side-chains 961 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 833 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 548 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 237 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 64 ASN Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 135 ASN Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 322 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 351 optimal weight: 0.6980 chunk 368 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 356 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 248 optimal weight: 0.5980 chunk 189 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN B 209 GLN C 235 ASN D 92 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN I 204 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078859 restraints weight = 103054.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081525 restraints weight = 47752.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083276 restraints weight = 28528.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084435 restraints weight = 20086.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085109 restraints weight = 15862.785| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 34709 Z= 0.148 Angle : 0.948 75.155 47099 Z= 0.359 Chirality : 0.045 0.247 5150 Planarity : 0.006 0.137 5975 Dihedral : 8.293 158.405 4808 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.35 % Favored : 95.62 % Rotamer: Outliers : 3.99 % Allowed : 22.72 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.94 (0.13), residues: 4136 helix: 0.36 (0.12), residues: 1841 sheet: -1.32 (0.28), residues: 346 loop : -1.43 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 82 TYR 0.048 0.002 TYR E 112 PHE 0.026 0.002 PHE A 62 TRP 0.016 0.001 TRP A 106 HIS 0.010 0.001 HIS E 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (34668) covalent geometry : angle 0.70831 / 0.36 (47007) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.72209 / 0.36 ( 8) hydrogen bonds : bond 0.04209 / 2.83 ( 1355) hydrogen bonds : angle 5.16037 / 3.66 ( 3849) metal coordination : bond 0.01622 / 1.16 ( 37) metal coordination : angle 14.94935 / 11.02 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 943 time to evaluate : 1.399 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: A 35 ASN cc_start: 0.8729 (m-40) cc_final: 0.8474 (m-40) REVERT: A 48 ARG cc_start: 0.8256 (tpp80) cc_final: 0.6973 (ptt180) REVERT: A 68 GLU cc_start: 0.8426 (tt0) cc_final: 0.7778 (tt0) REVERT: A 94 LEU cc_start: 0.9080 (tp) cc_final: 0.8293 (tp) REVERT: A 98 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 103 GLU cc_start: 0.8179 (tp30) cc_final: 0.7525 (tp30) REVERT: B 150 ASP cc_start: 0.9213 (m-30) cc_final: 0.8842 (m-30) REVERT: B 151 GLN cc_start: 0.8776 (mt0) cc_final: 0.8525 (mt0) REVERT: C 47 ARG cc_start: 0.7829 (mmm160) cc_final: 0.7478 (tpt170) REVERT: C 106 GLN cc_start: 0.8268 (mp10) cc_final: 0.7809 (mp10) REVERT: D 101 LEU cc_start: 0.9151 (mt) cc_final: 0.8891 (mt) REVERT: D 121 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7844 (mp0) REVERT: D 203 MET cc_start: 0.8632 (mmm) cc_final: 0.8069 (mmm) REVERT: D 215 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8467 (tm-30) REVERT: D 443 MET cc_start: 0.7712 (mmt) cc_final: 0.7385 (mmt) REVERT: E 184 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7255 (ptt) REVERT: E 191 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: E 205 ASP cc_start: 0.9124 (m-30) cc_final: 0.8891 (p0) REVERT: E 242 PHE cc_start: 0.6542 (t80) cc_final: 0.5913 (t80) REVERT: F 75 TRP cc_start: 0.7573 (t60) cc_final: 0.6926 (t60) REVERT: F 131 MET cc_start: 0.9025 (mmm) cc_final: 0.8688 (mmm) REVERT: F 164 ASN cc_start: 0.8013 (p0) cc_final: 0.7794 (p0) REVERT: F 169 LEU cc_start: 0.9490 (tp) cc_final: 0.9186 (tp) REVERT: F 450 MET cc_start: 0.8459 (mtt) cc_final: 0.8200 (mtt) REVERT: G 42 MET cc_start: 0.7154 (tpp) cc_final: 0.6745 (tpp) REVERT: G 67 GLU cc_start: 0.8443 (tt0) cc_final: 0.7628 (tm-30) REVERT: G 117 MET cc_start: 0.8899 (mmm) cc_final: 0.8273 (mmm) REVERT: G 144 MET cc_start: 0.9130 (tpt) cc_final: 0.8891 (tpp) REVERT: G 150 ARG cc_start: 0.8306 (mtt-85) cc_final: 0.8054 (mtt-85) REVERT: G 160 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8971 (t) REVERT: G 239 THR cc_start: 0.9000 (p) cc_final: 0.8764 (t) REVERT: G 257 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9044 (p) REVERT: G 272 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7627 (ttp-110) REVERT: G 277 MET cc_start: 0.8677 (ttp) cc_final: 0.8389 (ttt) REVERT: G 438 LEU cc_start: 0.9190 (mt) cc_final: 0.8821 (tp) REVERT: G 513 MET cc_start: 0.8998 (tpp) cc_final: 0.8607 (tpt) REVERT: G 605 GLN cc_start: 0.8462 (tt0) cc_final: 0.8035 (tt0) REVERT: G 712 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8729 (tppt) REVERT: H 51 ASP cc_start: 0.8929 (p0) cc_final: 0.8694 (p0) REVERT: H 92 PRO cc_start: 0.8771 (Cg_exo) cc_final: 0.8535 (Cg_endo) REVERT: H 172 MET cc_start: 0.7735 (tmm) cc_final: 0.7367 (tmm) REVERT: H 202 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8157 (tm-30) REVERT: H 206 GLU cc_start: 0.8150 (mp0) cc_final: 0.7780 (mp0) REVERT: H 222 LEU cc_start: 0.9475 (mp) cc_final: 0.9019 (mp) REVERT: H 251 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8068 (pt) REVERT: H 254 LEU cc_start: 0.8874 (mt) cc_final: 0.8647 (pp) REVERT: H 258 ASN cc_start: 0.7548 (m-40) cc_final: 0.6855 (m-40) REVERT: H 260 MET cc_start: 0.8739 (tmm) cc_final: 0.8502 (tmm) REVERT: H 262 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7917 (mm-30) REVERT: I 94 SER cc_start: 0.9360 (t) cc_final: 0.8663 (p) REVERT: I 204 ASN cc_start: 0.8800 (m-40) cc_final: 0.8381 (t0) REVERT: P 97 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7627 (pmm) REVERT: P 133 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7860 (tt0) REVERT: P 134 TRP cc_start: 0.8710 (p90) cc_final: 0.8200 (p90) REVERT: P 298 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8298 (t80) REVERT: P 351 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: P 367 GLU cc_start: 0.7529 (mp0) cc_final: 0.7114 (pm20) REVERT: P 368 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8217 (mt-10) REVERT: Q 58 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7932 (pptt) REVERT: R 110 GLN cc_start: 0.7899 (mp10) cc_final: 0.7445 (mp10) REVERT: T 108 LEU cc_start: 0.5651 (mp) cc_final: 0.5043 (tt) REVERT: T 115 GLN cc_start: 0.8851 (tt0) cc_final: 0.8268 (tm-30) REVERT: T 142 GLN cc_start: 0.8943 (tt0) cc_final: 0.8467 (tp40) REVERT: T 143 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7571 (mp0) REVERT: W 45 GLU cc_start: 0.8767 (tp30) cc_final: 0.8099 (tp30) REVERT: W 53 MET cc_start: 0.8744 (tpp) cc_final: 0.8514 (tpp) REVERT: W 56 ASP cc_start: 0.7293 (m-30) cc_final: 0.6873 (m-30) REVERT: W 58 THR cc_start: 0.7562 (t) cc_final: 0.7355 (m) REVERT: W 118 PRO cc_start: 0.8260 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: W 126 TYR cc_start: 0.9021 (m-80) cc_final: 0.8620 (m-80) REVERT: X 47 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7111 (tpt90) REVERT: Z 10 MET cc_start: 0.8905 (tpp) cc_final: 0.8535 (mmt) REVERT: Z 45 PHE cc_start: 0.8920 (t80) cc_final: 0.8602 (t80) REVERT: Z 80 ASP cc_start: 0.7864 (m-30) cc_final: 0.7322 (m-30) REVERT: Z 98 MET cc_start: 0.2175 (tpt) cc_final: 0.1614 (tpt) REVERT: Z 114 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8474 (p) REVERT: Z 137 ASN cc_start: 0.7881 (p0) cc_final: 0.7533 (p0) REVERT: a 5 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9006 (mm) REVERT: a 61 TYR cc_start: 0.7755 (t80) cc_final: 0.7290 (t80) REVERT: b 11 ASN cc_start: 0.8095 (p0) cc_final: 0.7814 (p0) REVERT: b 43 SER cc_start: 0.9098 (p) cc_final: 0.8859 (m) REVERT: b 47 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8549 (ttpp) REVERT: q 86 TRP cc_start: 0.8529 (m100) cc_final: 0.7913 (m100) REVERT: s 84 ASN cc_start: 0.8374 (m110) cc_final: 0.7174 (t0) REVERT: s 90 PHE cc_start: 0.6586 (m-10) cc_final: 0.6381 (m-10) outliers start: 145 outliers final: 88 residues processed: 1018 average time/residue: 0.2109 time to fit residues: 358.1610 Evaluate side-chains 954 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 854 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 548 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 132 ASP Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain r residue 92 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 95 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 74 GLN D 79 ASN D 92 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 270 ASN ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.095262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077400 restraints weight = 102743.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.079963 restraints weight = 48038.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081698 restraints weight = 29124.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082842 restraints weight = 20661.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083593 restraints weight = 16396.667| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 34709 Z= 0.167 Angle : 0.958 76.563 47099 Z= 0.362 Chirality : 0.045 0.245 5150 Planarity : 0.006 0.137 5975 Dihedral : 8.276 161.659 4808 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 4.26 % Allowed : 23.40 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.82 (0.13), residues: 4136 helix: 0.47 (0.12), residues: 1838 sheet: -1.33 (0.27), residues: 367 loop : -1.36 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 89 TYR 0.051 0.002 TYR E 112 PHE 0.022 0.002 PHE P 213 TRP 0.016 0.001 TRP A 106 HIS 0.012 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (34668) covalent geometry : angle 0.71207 / 0.36 (47007) SS BOND : bond 0.00231 / 0.12 ( 4) SS BOND : angle 0.66363 / 0.31 ( 8) hydrogen bonds : bond 0.04087 / 2.76 ( 1355) hydrogen bonds : angle 5.14859 / 3.64 ( 3849) metal coordination : bond 0.01809 / 1.20 ( 37) metal coordination : angle 15.18444 / 11.18 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 900 time to evaluate : 1.557 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: A 35 ASN cc_start: 0.8798 (m-40) cc_final: 0.8531 (m-40) REVERT: A 48 ARG cc_start: 0.8379 (tpp80) cc_final: 0.6873 (ptt180) REVERT: A 68 GLU cc_start: 0.8501 (tt0) cc_final: 0.8084 (tt0) REVERT: A 94 LEU cc_start: 0.9187 (tp) cc_final: 0.8480 (tp) REVERT: A 98 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 103 GLU cc_start: 0.8249 (tp30) cc_final: 0.7606 (tp30) REVERT: B 150 ASP cc_start: 0.9246 (m-30) cc_final: 0.8826 (m-30) REVERT: B 151 GLN cc_start: 0.8855 (mt0) cc_final: 0.8583 (mt0) REVERT: C 47 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7532 (tpt170) REVERT: C 106 GLN cc_start: 0.8415 (mp10) cc_final: 0.7861 (mp10) REVERT: C 206 TYR cc_start: 0.9163 (m-80) cc_final: 0.8752 (m-80) REVERT: D 215 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8448 (tm-30) REVERT: D 371 MET cc_start: 0.8990 (ppp) cc_final: 0.8766 (ppp) REVERT: D 414 ASP cc_start: 0.8222 (m-30) cc_final: 0.7896 (m-30) REVERT: D 437 LYS cc_start: 0.9090 (mttm) cc_final: 0.8789 (mtmt) REVERT: D 443 MET cc_start: 0.7660 (mmt) cc_final: 0.7377 (mmt) REVERT: E 40 HIS cc_start: 0.7961 (t-90) cc_final: 0.7727 (t-90) REVERT: E 184 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7254 (ptp) REVERT: E 191 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: E 242 PHE cc_start: 0.6534 (t80) cc_final: 0.6298 (t80) REVERT: F 75 TRP cc_start: 0.7670 (t60) cc_final: 0.7158 (t60) REVERT: F 131 MET cc_start: 0.9033 (mmm) cc_final: 0.8172 (tmm) REVERT: F 164 ASN cc_start: 0.7999 (p0) cc_final: 0.7771 (p0) REVERT: F 357 MET cc_start: 0.8119 (ttm) cc_final: 0.7463 (tmm) REVERT: F 408 GLU cc_start: 0.7295 (mp0) cc_final: 0.7055 (mp0) REVERT: G 67 GLU cc_start: 0.8284 (tt0) cc_final: 0.7628 (tm-30) REVERT: G 94 MET cc_start: 0.9056 (mmm) cc_final: 0.8812 (tpt) REVERT: G 117 MET cc_start: 0.9019 (mmm) cc_final: 0.8355 (mmm) REVERT: G 150 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.8047 (mtt-85) REVERT: G 160 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8988 (t) REVERT: G 257 VAL cc_start: 0.9406 (OUTLIER) cc_final: 0.9029 (p) REVERT: G 277 MET cc_start: 0.8691 (ttp) cc_final: 0.8437 (ttt) REVERT: G 438 LEU cc_start: 0.9121 (mt) cc_final: 0.8732 (tp) REVERT: G 513 MET cc_start: 0.9026 (tpp) cc_final: 0.8575 (tpt) REVERT: G 605 GLN cc_start: 0.8477 (tt0) cc_final: 0.8127 (tt0) REVERT: G 707 MET cc_start: 0.9121 (mmt) cc_final: 0.8838 (mmp) REVERT: G 712 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8731 (tppt) REVERT: H 17 MET cc_start: 0.9090 (tmm) cc_final: 0.8880 (tmm) REVERT: H 92 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8543 (Cg_endo) REVERT: H 202 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8257 (tm-30) REVERT: H 206 GLU cc_start: 0.8144 (mp0) cc_final: 0.7524 (mp0) REVERT: H 251 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8209 (pt) REVERT: H 262 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8119 (mm-30) REVERT: H 279 ARG cc_start: 0.7307 (ptm160) cc_final: 0.7004 (ptm160) REVERT: I 94 SER cc_start: 0.9359 (t) cc_final: 0.8666 (p) REVERT: I 204 ASN cc_start: 0.8824 (m-40) cc_final: 0.8501 (t0) REVERT: P 97 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7749 (pmm) REVERT: P 133 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7897 (tt0) REVERT: P 134 TRP cc_start: 0.8806 (p90) cc_final: 0.8311 (p90) REVERT: P 165 ILE cc_start: 0.9479 (mp) cc_final: 0.9271 (mt) REVERT: P 181 LEU cc_start: 0.9396 (mt) cc_final: 0.9182 (mp) REVERT: P 298 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8438 (t80) REVERT: P 351 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6999 (mm-30) REVERT: P 367 GLU cc_start: 0.7579 (mp0) cc_final: 0.7276 (pm20) REVERT: P 368 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8344 (mt-10) REVERT: Q 67 VAL cc_start: 0.8942 (t) cc_final: 0.8664 (m) REVERT: Q 88 GLN cc_start: 0.7217 (mt0) cc_final: 0.6908 (mm-40) REVERT: Q 99 MET cc_start: 0.8778 (ttp) cc_final: 0.8474 (ttp) REVERT: Q 132 GLU cc_start: 0.8797 (mp0) cc_final: 0.8582 (pm20) REVERT: Q 145 TYR cc_start: 0.8855 (p90) cc_final: 0.8556 (p90) REVERT: Q 148 GLU cc_start: 0.8216 (tp30) cc_final: 0.7767 (mt-10) REVERT: R 110 GLN cc_start: 0.7847 (mp10) cc_final: 0.7411 (mp10) REVERT: T 108 LEU cc_start: 0.5639 (mp) cc_final: 0.4968 (tt) REVERT: T 115 GLN cc_start: 0.8825 (tt0) cc_final: 0.8311 (tm-30) REVERT: T 142 GLN cc_start: 0.8897 (tt0) cc_final: 0.8689 (mm110) REVERT: T 143 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7635 (mp0) REVERT: V 58 MET cc_start: 0.7953 (mtp) cc_final: 0.7721 (ptm) REVERT: V 85 GLU cc_start: 0.8654 (pp20) cc_final: 0.8087 (pt0) REVERT: W 30 GLU cc_start: 0.8769 (pt0) cc_final: 0.8524 (pt0) REVERT: W 45 GLU cc_start: 0.8875 (tp30) cc_final: 0.8044 (tp30) REVERT: W 52 LEU cc_start: 0.9319 (tp) cc_final: 0.9100 (tt) REVERT: W 57 ILE cc_start: 0.8544 (pp) cc_final: 0.8259 (pp) REVERT: W 60 LYS cc_start: 0.8908 (ptmt) cc_final: 0.8675 (ptmm) REVERT: W 118 PRO cc_start: 0.8274 (Cg_exo) cc_final: 0.7943 (Cg_endo) REVERT: W 126 TYR cc_start: 0.9179 (m-80) cc_final: 0.8820 (m-80) REVERT: X 32 TYR cc_start: 0.9078 (t80) cc_final: 0.8826 (t80) REVERT: X 47 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7111 (tpt90) REVERT: Z 10 MET cc_start: 0.8963 (tpp) cc_final: 0.8631 (mmt) REVERT: Z 98 MET cc_start: 0.1996 (tpt) cc_final: 0.1621 (tpt) REVERT: Z 114 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (p) REVERT: a 5 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.9024 (mm) REVERT: a 61 TYR cc_start: 0.7820 (t80) cc_final: 0.7318 (t80) REVERT: b 11 ASN cc_start: 0.8006 (p0) cc_final: 0.7746 (p0) REVERT: b 43 SER cc_start: 0.9112 (p) cc_final: 0.8904 (m) REVERT: b 47 LYS cc_start: 0.8772 (ttpp) cc_final: 0.8534 (ttpp) REVERT: q 86 TRP cc_start: 0.8571 (m100) cc_final: 0.7923 (m100) REVERT: r 8 ILE cc_start: 0.8239 (mm) cc_final: 0.8024 (mt) REVERT: s 84 ASN cc_start: 0.8372 (m110) cc_final: 0.7195 (t0) REVERT: s 90 PHE cc_start: 0.6778 (m-10) cc_final: 0.6554 (m-10) outliers start: 155 outliers final: 109 residues processed: 976 average time/residue: 0.2121 time to fit residues: 345.8303 Evaluate side-chains 947 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 826 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 73 GLN Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 398 optimal weight: 0.0770 chunk 87 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 312 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 360 optimal weight: 20.0000 chunk 100 optimal weight: 0.4980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 270 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.096134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.078549 restraints weight = 103572.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.081098 restraints weight = 50085.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082787 restraints weight = 30687.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083938 restraints weight = 21949.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084683 restraints weight = 17450.084| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 34709 Z= 0.149 Angle : 0.948 75.643 47099 Z= 0.360 Chirality : 0.045 0.276 5150 Planarity : 0.005 0.136 5975 Dihedral : 8.203 163.474 4808 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.62 % Favored : 95.36 % Rotamer: Outliers : 4.15 % Allowed : 24.37 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.78 (0.13), residues: 4136 helix: 0.47 (0.12), residues: 1847 sheet: -1.27 (0.28), residues: 355 loop : -1.32 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 82 TYR 0.051 0.002 TYR E 112 PHE 0.025 0.002 PHE A 62 TRP 0.020 0.001 TRP F 413 HIS 0.009 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (34668) covalent geometry : angle 0.71356 / 0.36 (47007) SS BOND : bond 0.00168 / 0.08 ( 4) SS BOND : angle 0.59971 / 0.27 ( 8) hydrogen bonds : bond 0.03987 / 2.70 ( 1355) hydrogen bonds : angle 5.12424 / 3.62 ( 3849) metal coordination : bond 0.01550 / 1.09 ( 37) metal coordination : angle 14.79702 / 11.02 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 904 time to evaluate : 1.347 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: A 35 ASN cc_start: 0.8800 (m-40) cc_final: 0.8559 (m-40) REVERT: A 48 ARG cc_start: 0.8406 (tpp80) cc_final: 0.6827 (ptt180) REVERT: A 68 GLU cc_start: 0.8474 (tt0) cc_final: 0.8184 (tt0) REVERT: A 94 LEU cc_start: 0.9210 (tp) cc_final: 0.8545 (tp) REVERT: A 98 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8367 (mm) REVERT: B 103 GLU cc_start: 0.8252 (tp30) cc_final: 0.7574 (tp30) REVERT: B 150 ASP cc_start: 0.9268 (m-30) cc_final: 0.8826 (m-30) REVERT: B 151 GLN cc_start: 0.8824 (mt0) cc_final: 0.8600 (mt0) REVERT: C 106 GLN cc_start: 0.8378 (mp10) cc_final: 0.7813 (mp10) REVERT: C 172 MET cc_start: 0.9372 (mmp) cc_final: 0.8868 (mmm) REVERT: C 206 TYR cc_start: 0.9151 (m-80) cc_final: 0.8718 (m-80) REVERT: D 185 MET cc_start: 0.9239 (tpp) cc_final: 0.8552 (tpp) REVERT: D 210 MET cc_start: 0.8684 (mtm) cc_final: 0.8177 (mpp) REVERT: D 215 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 356 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8783 (pp) REVERT: D 371 MET cc_start: 0.9006 (ppp) cc_final: 0.8780 (ppp) REVERT: D 414 ASP cc_start: 0.8231 (m-30) cc_final: 0.7972 (m-30) REVERT: D 443 MET cc_start: 0.7462 (mmt) cc_final: 0.7230 (mmt) REVERT: E 40 HIS cc_start: 0.8093 (t-90) cc_final: 0.7866 (t-90) REVERT: E 52 PHE cc_start: 0.7944 (t80) cc_final: 0.7447 (t80) REVERT: E 122 ASN cc_start: 0.7293 (t0) cc_final: 0.7072 (m-40) REVERT: E 184 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7204 (ptt) REVERT: E 191 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: E 205 ASP cc_start: 0.9162 (m-30) cc_final: 0.8863 (p0) REVERT: F 75 TRP cc_start: 0.7754 (t60) cc_final: 0.7235 (t60) REVERT: F 164 ASN cc_start: 0.7916 (p0) cc_final: 0.7643 (p0) REVERT: F 357 MET cc_start: 0.8144 (ttm) cc_final: 0.7463 (tmm) REVERT: F 408 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: G 67 GLU cc_start: 0.8271 (tt0) cc_final: 0.7639 (tm-30) REVERT: G 117 MET cc_start: 0.9013 (mmm) cc_final: 0.8395 (mmm) REVERT: G 160 VAL cc_start: 0.9202 (OUTLIER) cc_final: 0.8987 (t) REVERT: G 257 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9001 (p) REVERT: G 277 MET cc_start: 0.8663 (ttp) cc_final: 0.8405 (ttt) REVERT: G 329 MET cc_start: 0.8327 (mmm) cc_final: 0.7684 (mmm) REVERT: G 438 LEU cc_start: 0.9166 (mt) cc_final: 0.8794 (tp) REVERT: G 513 MET cc_start: 0.9004 (tpp) cc_final: 0.8615 (tpt) REVERT: G 605 GLN cc_start: 0.8453 (tt0) cc_final: 0.8104 (tt0) REVERT: G 707 MET cc_start: 0.9112 (mmt) cc_final: 0.8837 (mmp) REVERT: G 712 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8893 (tppt) REVERT: H 17 MET cc_start: 0.9076 (tmm) cc_final: 0.8838 (tmm) REVERT: H 35 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8388 (tptt) REVERT: H 92 PRO cc_start: 0.8784 (Cg_exo) cc_final: 0.8547 (Cg_endo) REVERT: H 173 TRP cc_start: 0.7636 (m-10) cc_final: 0.7347 (m-90) REVERT: H 202 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8073 (tm-30) REVERT: H 206 GLU cc_start: 0.8177 (mp0) cc_final: 0.7832 (mp0) REVERT: H 228 TYR cc_start: 0.8830 (m-80) cc_final: 0.8553 (m-10) REVERT: H 258 ASN cc_start: 0.7629 (m-40) cc_final: 0.6907 (m-40) REVERT: H 260 MET cc_start: 0.8805 (tmm) cc_final: 0.8488 (tmm) REVERT: H 261 MET cc_start: 0.8480 (mmm) cc_final: 0.8120 (mmt) REVERT: H 262 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8157 (mm-30) REVERT: H 287 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.8100 (t70) REVERT: I 94 SER cc_start: 0.9382 (t) cc_final: 0.8671 (p) REVERT: I 204 ASN cc_start: 0.8894 (m-40) cc_final: 0.8464 (t0) REVERT: P 97 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7735 (pmm) REVERT: P 133 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7877 (tt0) REVERT: P 134 TRP cc_start: 0.8760 (p90) cc_final: 0.8285 (p90) REVERT: P 165 ILE cc_start: 0.9427 (mp) cc_final: 0.9215 (mt) REVERT: P 298 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8463 (t80) REVERT: P 360 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8338 (tmt-80) REVERT: P 368 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8293 (mt-10) REVERT: Q 67 VAL cc_start: 0.8908 (t) cc_final: 0.8628 (m) REVERT: Q 99 MET cc_start: 0.8787 (ttp) cc_final: 0.8567 (ttp) REVERT: R 110 GLN cc_start: 0.7868 (mp10) cc_final: 0.7466 (mp10) REVERT: T 108 LEU cc_start: 0.5584 (mp) cc_final: 0.4867 (tt) REVERT: T 115 GLN cc_start: 0.8785 (tt0) cc_final: 0.8213 (tm-30) REVERT: T 143 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7620 (mp0) REVERT: V 85 GLU cc_start: 0.8686 (pp20) cc_final: 0.8192 (pt0) REVERT: W 45 GLU cc_start: 0.8895 (tp30) cc_final: 0.7977 (tp30) REVERT: W 53 MET cc_start: 0.8715 (tpp) cc_final: 0.8481 (tpp) REVERT: W 118 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7967 (Cg_endo) REVERT: W 126 TYR cc_start: 0.9203 (m-80) cc_final: 0.8828 (m-80) REVERT: X 32 TYR cc_start: 0.9054 (t80) cc_final: 0.8786 (t80) REVERT: X 37 ASP cc_start: 0.6864 (p0) cc_final: 0.5922 (p0) REVERT: X 47 ARG cc_start: 0.8147 (tpt170) cc_final: 0.7121 (tpt90) REVERT: Z 10 MET cc_start: 0.8992 (tpp) cc_final: 0.8654 (mmt) REVERT: Z 98 MET cc_start: 0.1929 (tpt) cc_final: 0.1642 (tpt) REVERT: Z 137 ASN cc_start: 0.7803 (p0) cc_final: 0.7586 (p0) REVERT: a 5 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9015 (mm) REVERT: a 61 TYR cc_start: 0.7851 (t80) cc_final: 0.7333 (t80) REVERT: b 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7736 (ptp) REVERT: b 47 LYS cc_start: 0.8761 (ttpp) cc_final: 0.8515 (ttpp) REVERT: q 86 TRP cc_start: 0.8610 (m100) cc_final: 0.7930 (m100) REVERT: q 132 LYS cc_start: 0.8378 (tttp) cc_final: 0.8085 (ptmm) REVERT: r 8 ILE cc_start: 0.8271 (mm) cc_final: 0.8067 (mt) REVERT: s 90 PHE cc_start: 0.6855 (m-10) cc_final: 0.6650 (m-10) outliers start: 151 outliers final: 100 residues processed: 986 average time/residue: 0.2130 time to fit residues: 348.3133 Evaluate side-chains 944 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 830 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 6 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 92 LYS Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 245 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.0370 chunk 236 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 390 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 270 optimal weight: 0.8980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN F 436 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS T 115 GLN V 50 GLN Z 76 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.079363 restraints weight = 102601.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081964 restraints weight = 49553.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083671 restraints weight = 30099.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084814 restraints weight = 21398.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085547 restraints weight = 16971.273| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34709 Z= 0.142 Angle : 0.950 75.700 47099 Z= 0.362 Chirality : 0.045 0.266 5150 Planarity : 0.005 0.136 5975 Dihedral : 8.118 163.676 4808 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.45 % Rotamer: Outliers : 3.66 % Allowed : 25.47 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4136 helix: 0.45 (0.12), residues: 1855 sheet: -1.20 (0.28), residues: 353 loop : -1.28 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG T 82 TYR 0.053 0.002 TYR E 112 PHE 0.033 0.002 PHE A 55 TRP 0.018 0.001 TRP a 2 HIS 0.007 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (34668) covalent geometry : angle 0.72481 / 0.36 (47007) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.60302 / 0.29 ( 8) hydrogen bonds : bond 0.03885 / 2.62 ( 1355) hydrogen bonds : angle 5.07941 / 3.59 ( 3849) metal coordination : bond 0.01417 / 1.02 ( 37) metal coordination : angle 14.55547 / 10.78 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 872 time to evaluate : 1.522 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: A 1 MET cc_start: 0.8156 (tpp) cc_final: 0.7914 (tpp) REVERT: A 35 ASN cc_start: 0.8799 (m-40) cc_final: 0.8562 (m-40) REVERT: A 48 ARG cc_start: 0.8482 (tpp80) cc_final: 0.6832 (ptt180) REVERT: A 87 MET cc_start: 0.8534 (tmm) cc_final: 0.8325 (tmm) REVERT: A 94 LEU cc_start: 0.9219 (tp) cc_final: 0.8774 (tp) REVERT: A 98 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8389 (mm) REVERT: B 103 GLU cc_start: 0.8286 (tp30) cc_final: 0.7735 (tp30) REVERT: B 150 ASP cc_start: 0.9284 (m-30) cc_final: 0.8856 (m-30) REVERT: B 151 GLN cc_start: 0.8839 (mt0) cc_final: 0.8587 (mt0) REVERT: B 209 GLN cc_start: 0.8640 (mt0) cc_final: 0.8345 (mt0) REVERT: C 47 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7498 (tpt170) REVERT: C 106 GLN cc_start: 0.8479 (mp10) cc_final: 0.7849 (mp10) REVERT: C 108 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8621 (mmmt) REVERT: C 172 MET cc_start: 0.9369 (mmp) cc_final: 0.8876 (mmm) REVERT: D 105 MET cc_start: 0.8035 (mmm) cc_final: 0.7650 (mmm) REVERT: D 203 MET cc_start: 0.8571 (mmm) cc_final: 0.8164 (mmm) REVERT: D 204 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8374 (m-10) REVERT: D 215 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 443 MET cc_start: 0.7315 (mmt) cc_final: 0.7114 (mmt) REVERT: E 52 PHE cc_start: 0.7927 (t80) cc_final: 0.7494 (t80) REVERT: E 54 PHE cc_start: 0.8422 (m-80) cc_final: 0.7119 (m-80) REVERT: E 59 TYR cc_start: 0.8260 (m-80) cc_final: 0.7973 (m-80) REVERT: E 184 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7282 (ptt) REVERT: E 191 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: E 205 ASP cc_start: 0.9196 (m-30) cc_final: 0.8953 (p0) REVERT: F 75 TRP cc_start: 0.7801 (t60) cc_final: 0.7293 (t60) REVERT: F 164 ASN cc_start: 0.7794 (p0) cc_final: 0.7284 (t0) REVERT: F 357 MET cc_start: 0.7702 (ttm) cc_final: 0.6974 (tmm) REVERT: F 408 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: G 67 GLU cc_start: 0.8224 (tt0) cc_final: 0.7607 (tm-30) REVERT: G 117 MET cc_start: 0.9012 (mmm) cc_final: 0.8389 (mmm) REVERT: G 160 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (t) REVERT: G 257 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.8924 (p) REVERT: G 277 MET cc_start: 0.8666 (ttp) cc_final: 0.8446 (ttt) REVERT: G 329 MET cc_start: 0.8430 (mmm) cc_final: 0.7588 (mmm) REVERT: G 438 LEU cc_start: 0.9166 (mt) cc_final: 0.8801 (tp) REVERT: G 513 MET cc_start: 0.9032 (tpp) cc_final: 0.8588 (tpt) REVERT: G 605 GLN cc_start: 0.8487 (tt0) cc_final: 0.8108 (tt0) REVERT: G 712 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8910 (tppt) REVERT: H 47 GLN cc_start: 0.8944 (tp40) cc_final: 0.8227 (tp-100) REVERT: H 51 ASP cc_start: 0.9017 (p0) cc_final: 0.8709 (p0) REVERT: H 57 MET cc_start: 0.8056 (mmm) cc_final: 0.7784 (mmt) REVERT: H 92 PRO cc_start: 0.8792 (Cg_exo) cc_final: 0.8550 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8102 (mt-10) REVERT: H 172 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7345 (tmm) REVERT: H 173 TRP cc_start: 0.7691 (m-10) cc_final: 0.6889 (m-90) REVERT: H 202 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8220 (tm-30) REVERT: H 206 GLU cc_start: 0.8174 (mp0) cc_final: 0.7736 (mp0) REVERT: H 228 TYR cc_start: 0.8825 (m-80) cc_final: 0.8613 (m-80) REVERT: H 258 ASN cc_start: 0.7606 (m-40) cc_final: 0.6862 (m-40) REVERT: H 261 MET cc_start: 0.8506 (mmm) cc_final: 0.8281 (mmt) REVERT: H 262 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8170 (mm-30) REVERT: H 287 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.8171 (t70) REVERT: I 94 SER cc_start: 0.9465 (t) cc_final: 0.8773 (p) REVERT: I 204 ASN cc_start: 0.8919 (m-40) cc_final: 0.8569 (t0) REVERT: P 79 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8185 (mm-40) REVERT: P 97 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7749 (pmm) REVERT: P 133 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7872 (tt0) REVERT: P 134 TRP cc_start: 0.8739 (p90) cc_final: 0.8311 (p90) REVERT: P 165 ILE cc_start: 0.9423 (mp) cc_final: 0.9200 (mt) REVERT: P 181 LEU cc_start: 0.9352 (mt) cc_final: 0.9086 (mp) REVERT: P 298 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8510 (t80) REVERT: P 360 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8372 (tmt-80) REVERT: Q 87 MET cc_start: 0.7672 (mtt) cc_final: 0.7469 (mtp) REVERT: Q 99 MET cc_start: 0.8730 (ttp) cc_final: 0.8488 (ttp) REVERT: Q 148 GLU cc_start: 0.8308 (tp30) cc_final: 0.7685 (mt-10) REVERT: R 110 GLN cc_start: 0.7703 (mp10) cc_final: 0.7366 (mp10) REVERT: T 108 LEU cc_start: 0.5402 (mp) cc_final: 0.4739 (tt) REVERT: T 115 GLN cc_start: 0.8775 (tt0) cc_final: 0.8237 (tm-30) REVERT: T 143 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7609 (mp0) REVERT: V 85 GLU cc_start: 0.8666 (pp20) cc_final: 0.8246 (pt0) REVERT: W 45 GLU cc_start: 0.8924 (tp30) cc_final: 0.7984 (tp30) REVERT: W 53 MET cc_start: 0.8702 (tpp) cc_final: 0.8394 (tpp) REVERT: W 68 GLU cc_start: 0.8767 (pt0) cc_final: 0.8477 (pp20) REVERT: W 118 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: W 124 LYS cc_start: 0.8700 (tptt) cc_final: 0.7916 (tptt) REVERT: W 126 TYR cc_start: 0.9200 (m-80) cc_final: 0.8820 (m-80) REVERT: X 26 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8832 (ttpt) REVERT: X 32 TYR cc_start: 0.9048 (t80) cc_final: 0.8834 (t80) REVERT: X 37 ASP cc_start: 0.6783 (p0) cc_final: 0.5888 (p0) REVERT: X 47 ARG cc_start: 0.8174 (tpt170) cc_final: 0.7169 (tpt90) REVERT: Z 10 MET cc_start: 0.8988 (tpp) cc_final: 0.8658 (mmt) REVERT: Z 98 MET cc_start: 0.1777 (tpt) cc_final: 0.1573 (tpt) REVERT: a 5 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9002 (mm) REVERT: a 61 TYR cc_start: 0.7884 (t80) cc_final: 0.7371 (t80) REVERT: b 44 MET cc_start: 0.8117 (ptp) cc_final: 0.7690 (ptp) REVERT: b 47 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8529 (ttpp) REVERT: q 86 TRP cc_start: 0.8643 (m100) cc_final: 0.7970 (m100) REVERT: r 8 ILE cc_start: 0.8297 (mm) cc_final: 0.8074 (mt) outliers start: 133 outliers final: 96 residues processed: 943 average time/residue: 0.2103 time to fit residues: 330.9509 Evaluate side-chains 939 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 829 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 43 HIS Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 328 MET Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 339 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 336 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 406 optimal weight: 0.0070 chunk 33 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077170 restraints weight = 102946.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.079687 restraints weight = 48617.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081362 restraints weight = 29422.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082473 restraints weight = 20874.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083202 restraints weight = 16583.083| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34709 Z= 0.177 Angle : 0.989 78.037 47099 Z= 0.377 Chirality : 0.046 0.273 5150 Planarity : 0.006 0.136 5975 Dihedral : 8.139 166.269 4808 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 3.74 % Allowed : 25.63 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.73 (0.13), residues: 4136 helix: 0.48 (0.12), residues: 1856 sheet: -1.27 (0.28), residues: 345 loop : -1.26 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 82 TYR 0.053 0.002 TYR E 112 PHE 0.028 0.002 PHE A 62 TRP 0.020 0.001 TRP a 2 HIS 0.009 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (34668) covalent geometry : angle 0.75578 / 0.37 (47007) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 0.60179 / 0.28 ( 8) hydrogen bonds : bond 0.03904 / 2.66 ( 1355) hydrogen bonds : angle 5.11724 / 3.62 ( 3849) metal coordination : bond 0.01843 / 1.20 ( 37) metal coordination : angle 15.11028 / 11.11 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 833 time to evaluate : 1.378 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: A 1 MET cc_start: 0.8176 (tpp) cc_final: 0.7831 (tpp) REVERT: A 35 ASN cc_start: 0.8800 (m-40) cc_final: 0.8588 (m-40) REVERT: A 48 ARG cc_start: 0.8491 (tpp80) cc_final: 0.6679 (ptt180) REVERT: A 68 GLU cc_start: 0.8427 (tt0) cc_final: 0.7712 (tt0) REVERT: A 73 LEU cc_start: 0.9109 (mt) cc_final: 0.8798 (mt) REVERT: A 94 LEU cc_start: 0.9189 (tp) cc_final: 0.8764 (tp) REVERT: A 98 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8327 (mm) REVERT: B 103 GLU cc_start: 0.8301 (tp30) cc_final: 0.7783 (tp30) REVERT: B 150 ASP cc_start: 0.9270 (m-30) cc_final: 0.8855 (m-30) REVERT: B 151 GLN cc_start: 0.8851 (mt0) cc_final: 0.8621 (mt0) REVERT: C 47 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7532 (tpt170) REVERT: C 106 GLN cc_start: 0.8472 (mp10) cc_final: 0.8037 (mp10) REVERT: D 80 MET cc_start: 0.9004 (tpp) cc_final: 0.8676 (tpp) REVERT: D 105 MET cc_start: 0.8166 (mmm) cc_final: 0.7784 (mmm) REVERT: D 185 MET cc_start: 0.9109 (tpp) cc_final: 0.8308 (tpp) REVERT: D 204 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: D 210 MET cc_start: 0.8531 (mtm) cc_final: 0.7832 (mpp) REVERT: D 215 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8297 (tm-30) REVERT: D 257 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7658 (mt-10) REVERT: D 356 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8854 (pp) REVERT: E 59 TYR cc_start: 0.8377 (m-80) cc_final: 0.7963 (m-80) REVERT: E 123 ARG cc_start: 0.8113 (mtm180) cc_final: 0.7692 (mtm-85) REVERT: E 184 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7331 (ptt) REVERT: E 191 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: E 202 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8334 (tm-30) REVERT: E 205 ASP cc_start: 0.9167 (m-30) cc_final: 0.8947 (p0) REVERT: E 235 GLU cc_start: 0.7430 (mp0) cc_final: 0.6449 (pp20) REVERT: F 75 TRP cc_start: 0.7855 (t60) cc_final: 0.7356 (t60) REVERT: F 164 ASN cc_start: 0.7796 (p0) cc_final: 0.7318 (t0) REVERT: F 405 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8321 (mmm160) REVERT: F 408 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: G 67 GLU cc_start: 0.8212 (tt0) cc_final: 0.7670 (tm-30) REVERT: G 117 MET cc_start: 0.9045 (mmm) cc_final: 0.8486 (mmm) REVERT: G 160 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8980 (t) REVERT: G 257 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.8928 (p) REVERT: G 277 MET cc_start: 0.8616 (ttp) cc_final: 0.8405 (ttt) REVERT: G 513 MET cc_start: 0.9037 (tpp) cc_final: 0.8672 (tpt) REVERT: G 605 GLN cc_start: 0.8481 (tt0) cc_final: 0.8137 (tt0) REVERT: G 707 MET cc_start: 0.9059 (mmt) cc_final: 0.8814 (mmp) REVERT: G 712 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8864 (tppt) REVERT: H 56 PHE cc_start: 0.8936 (m-80) cc_final: 0.8723 (m-80) REVERT: H 57 MET cc_start: 0.7960 (mmm) cc_final: 0.7678 (mmt) REVERT: H 92 PRO cc_start: 0.8834 (Cg_exo) cc_final: 0.8596 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8256 (mt-10) REVERT: H 172 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: H 202 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8008 (tm-30) REVERT: H 206 GLU cc_start: 0.8217 (mp0) cc_final: 0.7757 (mp0) REVERT: H 228 TYR cc_start: 0.8796 (m-80) cc_final: 0.8559 (m-80) REVERT: H 258 ASN cc_start: 0.7577 (m-40) cc_final: 0.6907 (m-40) REVERT: H 287 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.8107 (t70) REVERT: I 94 SER cc_start: 0.9479 (t) cc_final: 0.8804 (p) REVERT: I 204 ASN cc_start: 0.8879 (m-40) cc_final: 0.8457 (t0) REVERT: P 97 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7871 (pmm) REVERT: P 102 GLN cc_start: 0.8327 (tp-100) cc_final: 0.8084 (tp-100) REVERT: P 133 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7827 (tt0) REVERT: P 134 TRP cc_start: 0.8808 (p90) cc_final: 0.8395 (p90) REVERT: P 165 ILE cc_start: 0.9435 (mp) cc_final: 0.9202 (mt) REVERT: P 174 MET cc_start: 0.8468 (mmm) cc_final: 0.8119 (mmp) REVERT: P 296 PHE cc_start: 0.8701 (p90) cc_final: 0.8483 (p90) REVERT: P 360 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8360 (tmt-80) REVERT: Q 99 MET cc_start: 0.8835 (ttp) cc_final: 0.8544 (ttp) REVERT: Q 112 MET cc_start: 0.8603 (mmm) cc_final: 0.7904 (mmm) REVERT: R 110 GLN cc_start: 0.7690 (mp10) cc_final: 0.7345 (mp10) REVERT: T 108 LEU cc_start: 0.5403 (mp) cc_final: 0.4735 (tt) REVERT: T 115 GLN cc_start: 0.8892 (tt0) cc_final: 0.8387 (tm-30) REVERT: T 143 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7567 (mp0) REVERT: V 85 GLU cc_start: 0.8609 (pp20) cc_final: 0.8243 (pt0) REVERT: W 45 GLU cc_start: 0.8941 (tp30) cc_final: 0.8054 (tp30) REVERT: W 53 MET cc_start: 0.8782 (tpp) cc_final: 0.8448 (tpp) REVERT: W 68 GLU cc_start: 0.8634 (pt0) cc_final: 0.8383 (pp20) REVERT: W 124 LYS cc_start: 0.8731 (tptt) cc_final: 0.7944 (tptt) REVERT: W 126 TYR cc_start: 0.9235 (m-80) cc_final: 0.8857 (m-80) REVERT: X 32 TYR cc_start: 0.9054 (t80) cc_final: 0.8781 (t80) REVERT: X 37 ASP cc_start: 0.6741 (p0) cc_final: 0.5903 (p0) REVERT: X 47 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7107 (tpt90) REVERT: Z 10 MET cc_start: 0.8988 (tpp) cc_final: 0.8689 (mmt) REVERT: Z 86 ILE cc_start: 0.8988 (mm) cc_final: 0.8762 (tt) REVERT: Z 133 MET cc_start: 0.8132 (tpt) cc_final: 0.7800 (tpt) REVERT: a 5 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9028 (mm) REVERT: a 61 TYR cc_start: 0.7881 (t80) cc_final: 0.7370 (t80) REVERT: b 44 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7904 (ptp) REVERT: q 86 TRP cc_start: 0.8716 (m100) cc_final: 0.8069 (m100) REVERT: r 8 ILE cc_start: 0.8267 (mm) cc_final: 0.8061 (mt) REVERT: s 90 PHE cc_start: 0.6828 (m-10) cc_final: 0.6518 (m-80) outliers start: 136 outliers final: 98 residues processed: 913 average time/residue: 0.2101 time to fit residues: 319.3827 Evaluate side-chains 922 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 808 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 386 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 373 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS V 50 GLN ** X 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077227 restraints weight = 103722.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079762 restraints weight = 48701.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.081421 restraints weight = 29295.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082551 restraints weight = 20812.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083280 restraints weight = 16455.717| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.433 34709 Z= 0.238 Angle : 1.071 78.049 47099 Z= 0.450 Chirality : 0.048 0.601 5150 Planarity : 0.006 0.136 5975 Dihedral : 8.139 166.327 4808 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 3.55 % Allowed : 25.99 % Favored : 70.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.71 (0.13), residues: 4136 helix: 0.48 (0.12), residues: 1856 sheet: -1.20 (0.29), residues: 341 loop : -1.25 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 100 TYR 0.051 0.002 TYR E 112 PHE 0.049 0.002 PHE E 52 TRP 0.017 0.001 TRP a 2 HIS 0.040 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.24 (34668) covalent geometry : angle 0.86115 / 0.45 (47007) SS BOND : bond 0.00203 / 0.10 ( 4) SS BOND : angle 0.62443 / 0.30 ( 8) hydrogen bonds : bond 0.03928 / 2.67 ( 1355) hydrogen bonds : angle 5.13454 / 3.63 ( 3849) metal coordination : bond 0.01784 / 1.17 ( 37) metal coordination : angle 15.11740 / 11.12 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8272 Ramachandran restraints generated. 4136 Oldfield, 0 Emsley, 4136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 812 time to evaluate : 1.389 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: A 1 MET cc_start: 0.8165 (tpp) cc_final: 0.7844 (tpp) REVERT: A 35 ASN cc_start: 0.8796 (m-40) cc_final: 0.8584 (m-40) REVERT: A 48 ARG cc_start: 0.8486 (tpp80) cc_final: 0.6679 (ptt180) REVERT: A 68 GLU cc_start: 0.8444 (tt0) cc_final: 0.7712 (tt0) REVERT: A 73 LEU cc_start: 0.9104 (mt) cc_final: 0.8810 (mt) REVERT: A 94 LEU cc_start: 0.9186 (tp) cc_final: 0.8762 (tp) REVERT: A 98 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8311 (mm) REVERT: B 103 GLU cc_start: 0.8307 (tp30) cc_final: 0.7781 (tp30) REVERT: B 150 ASP cc_start: 0.9262 (m-30) cc_final: 0.8852 (m-30) REVERT: B 151 GLN cc_start: 0.8843 (mt0) cc_final: 0.8618 (mt0) REVERT: C 47 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7534 (tpt170) REVERT: C 106 GLN cc_start: 0.8449 (mp10) cc_final: 0.8037 (mp10) REVERT: D 80 MET cc_start: 0.9006 (tpp) cc_final: 0.8667 (tpp) REVERT: D 105 MET cc_start: 0.8188 (mmm) cc_final: 0.7771 (mmm) REVERT: D 185 MET cc_start: 0.9113 (tpp) cc_final: 0.8292 (tpp) REVERT: D 204 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: D 210 MET cc_start: 0.8534 (mtm) cc_final: 0.7829 (mpp) REVERT: D 215 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 257 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7697 (mt-10) REVERT: D 356 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8851 (pp) REVERT: E 59 TYR cc_start: 0.8378 (m-80) cc_final: 0.7957 (m-80) REVERT: E 123 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7687 (mtm-85) REVERT: E 184 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7332 (ptt) REVERT: E 191 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: E 202 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: E 205 ASP cc_start: 0.9168 (m-30) cc_final: 0.8958 (p0) REVERT: E 235 GLU cc_start: 0.7429 (mp0) cc_final: 0.6448 (pp20) REVERT: F 75 TRP cc_start: 0.7853 (t60) cc_final: 0.7357 (t60) REVERT: F 164 ASN cc_start: 0.7783 (p0) cc_final: 0.7312 (t0) REVERT: F 405 ARG cc_start: 0.8602 (mmm160) cc_final: 0.8318 (mmm160) REVERT: F 408 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: G 67 GLU cc_start: 0.8216 (tt0) cc_final: 0.7667 (tm-30) REVERT: G 117 MET cc_start: 0.9043 (mmm) cc_final: 0.8482 (mmm) REVERT: G 160 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8982 (t) REVERT: G 257 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.8929 (p) REVERT: G 277 MET cc_start: 0.8622 (ttp) cc_final: 0.8413 (ttt) REVERT: G 513 MET cc_start: 0.9039 (tpp) cc_final: 0.8667 (tpt) REVERT: G 605 GLN cc_start: 0.8488 (tt0) cc_final: 0.8133 (tt0) REVERT: G 707 MET cc_start: 0.9053 (mmt) cc_final: 0.8806 (mmp) REVERT: G 712 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8881 (tppt) REVERT: H 92 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8593 (Cg_endo) REVERT: H 143 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8259 (mt-10) REVERT: H 172 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7317 (tmm) REVERT: H 202 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7999 (tm-30) REVERT: H 206 GLU cc_start: 0.8160 (mp0) cc_final: 0.7838 (mp0) REVERT: H 258 ASN cc_start: 0.7216 (m-40) cc_final: 0.6906 (m-40) REVERT: H 287 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.8114 (t70) REVERT: I 94 SER cc_start: 0.9480 (t) cc_final: 0.8800 (p) REVERT: I 204 ASN cc_start: 0.8884 (m-40) cc_final: 0.8458 (t0) REVERT: P 97 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7872 (pmm) REVERT: P 102 GLN cc_start: 0.8363 (tp-100) cc_final: 0.7612 (tp-100) REVERT: P 133 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7828 (tt0) REVERT: P 134 TRP cc_start: 0.8808 (p90) cc_final: 0.8396 (p90) REVERT: P 162 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7253 (tm-30) REVERT: P 165 ILE cc_start: 0.9436 (mp) cc_final: 0.9203 (mt) REVERT: P 174 MET cc_start: 0.8475 (mmm) cc_final: 0.8148 (mmp) REVERT: P 296 PHE cc_start: 0.8698 (p90) cc_final: 0.8482 (p90) REVERT: P 360 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8365 (tmt-80) REVERT: Q 99 MET cc_start: 0.8792 (ttp) cc_final: 0.8541 (ttp) REVERT: Q 112 MET cc_start: 0.8611 (mmm) cc_final: 0.7950 (mmm) REVERT: R 110 GLN cc_start: 0.7688 (mp10) cc_final: 0.7343 (mp10) REVERT: T 108 LEU cc_start: 0.5409 (mp) cc_final: 0.4740 (tt) REVERT: T 115 GLN cc_start: 0.8898 (tt0) cc_final: 0.8440 (tm-30) REVERT: T 143 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7564 (mp0) REVERT: V 85 GLU cc_start: 0.8609 (pp20) cc_final: 0.8242 (pt0) REVERT: W 45 GLU cc_start: 0.8938 (tp30) cc_final: 0.8060 (tp30) REVERT: W 53 MET cc_start: 0.8782 (tpp) cc_final: 0.8440 (tpp) REVERT: W 68 GLU cc_start: 0.8642 (pt0) cc_final: 0.8385 (pp20) REVERT: W 124 LYS cc_start: 0.8736 (tptt) cc_final: 0.7949 (tptt) REVERT: W 126 TYR cc_start: 0.9243 (m-80) cc_final: 0.8865 (m-80) REVERT: X 32 TYR cc_start: 0.9052 (t80) cc_final: 0.8774 (t80) REVERT: X 37 ASP cc_start: 0.6754 (p0) cc_final: 0.5899 (p0) REVERT: X 47 ARG cc_start: 0.8141 (tpt170) cc_final: 0.7104 (tpt90) REVERT: Z 10 MET cc_start: 0.8978 (tpp) cc_final: 0.8680 (mmt) REVERT: Z 86 ILE cc_start: 0.8986 (mm) cc_final: 0.8761 (tt) REVERT: Z 133 MET cc_start: 0.8141 (tpt) cc_final: 0.7817 (tpt) REVERT: a 5 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9026 (mm) REVERT: a 61 TYR cc_start: 0.7875 (t80) cc_final: 0.7365 (t80) REVERT: b 44 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7798 (ptp) REVERT: b 47 LYS cc_start: 0.9313 (tptt) cc_final: 0.8602 (ttpp) REVERT: q 86 TRP cc_start: 0.8717 (m100) cc_final: 0.8069 (m100) REVERT: r 8 ILE cc_start: 0.8269 (mm) cc_final: 0.8059 (mt) REVERT: s 90 PHE cc_start: 0.6831 (m-10) cc_final: 0.6530 (m-80) outliers start: 129 outliers final: 111 residues processed: 886 average time/residue: 0.2112 time to fit residues: 311.6995 Evaluate side-chains 932 residues out of total 3636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 805 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 92 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 52 ARG Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 213 MET Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 223 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 130 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 308 SER Chi-restraints excluded: chain P residue 318 LYS Chi-restraints excluded: chain P residue 352 VAL Chi-restraints excluded: chain P residue 360 ARG Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain R residue 74 HIS Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 93 LEU Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 78 LEU Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain s residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 402 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 361 optimal weight: 1.9990 chunk 179 optimal weight: 0.0030 chunk 379 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 344 GLN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 115 GLN V 50 GLN W 102 GLN Z 76 GLN a 31 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078899 restraints weight = 102404.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.081467 restraints weight = 48170.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083149 restraints weight = 28992.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.084287 restraints weight = 20543.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.084942 restraints weight = 16260.198| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34709 Z= 0.143 Angle : 0.990 76.636 47099 Z= 0.386 Chirality : 0.046 0.279 5150 Planarity : 0.006 0.136 5975 Dihedral : 8.066 166.425 4808 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 3.19 % Allowed : 26.51 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.40 % 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: -0.74 (0.13), residues: 4136 helix: 0.44 (0.12), residues: 1866 sheet: -1.19 (0.28), residues: 351 loop : -1.26 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T 82 TYR 0.057 0.002 TYR E 112 PHE 0.034 0.002 PHE A 55 TRP 0.022 0.001 TRP V 114 HIS 0.010 0.001 HIS E 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (34668) covalent geometry : angle 0.78169 / 0.38 (47007) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.60534 / 0.30 ( 8) hydrogen bonds : bond 0.03916 / 2.65 ( 1355) hydrogen bonds : angle 5.12125 / 3.62 ( 3849) metal coordination : bond 0.01429 / 1.04 ( 37) metal coordination : angle 14.40245 / 10.65 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8422.29 seconds wall clock time: 145 minutes 58.45 seconds (8758.45 seconds total)