Starting phenix.real_space_refine on Tue May 5 22:36:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnp_38510/05_2026/8xnp_38510.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.083 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 12 5.49 5 S 246 5.16 5 C 21793 2.51 5 N 5784 2.21 5 O 6184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34048 Number of models: 1 Model: "" Number of chains: 34 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: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} 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: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2538 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 22, 'TRANS': 295} Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} 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: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} 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: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain breaks: 1 Chain: "r" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 28 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "a" 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 79.789 61.295 106.441 1.00 29.52 S ATOM 1681 SG CYS B 164 77.053 57.521 111.236 1.00 28.96 S ATOM 1911 SG CYS B 194 82.224 57.615 110.600 1.00 29.28 S ATOM 1184 SG CYS B 100 78.671 57.315 105.454 1.00 30.11 S ATOM 7691 SG CYS E 134 138.753 53.297 154.069 1.00 56.01 S ATOM 7725 SG CYS E 139 141.182 55.048 153.453 1.00 56.50 S ATOM 8009 SG CYS E 175 136.173 56.569 156.775 1.00 54.42 S ATOM 8032 SG CYS E 179 139.398 58.370 157.023 1.00 57.95 S ATOM 11562 SG CYS F 425 119.682 61.649 156.734 1.00 45.60 S ATOM 11240 SG CYS F 385 119.948 59.384 150.861 1.00 39.95 S ATOM 11220 SG CYS F 382 115.587 60.294 153.068 1.00 40.29 S ATOM 11201 SG CYS F 379 117.649 56.210 155.832 1.00 43.09 S ATOM 12610 SG CYS G 131 100.159 49.008 138.774 1.00 31.31 S ATOM 12589 SG CYS G 128 102.116 53.093 134.369 1.00 30.26 S ATOM 12650 SG CYS G 137 99.558 54.837 140.403 1.00 33.13 S ATOM 13335 SG CYS G 226 101.496 48.752 147.389 1.00 34.31 S ATOM 13006 SG CYS G 182 104.577 46.986 153.151 1.00 36.31 S ATOM 12982 SG CYS G 179 103.790 52.628 150.801 1.00 35.62 S ATOM 12959 SG CYS G 176 107.457 48.597 148.260 1.00 34.05 S ATOM 12096 SG CYS G 64 104.913 58.639 153.069 1.00 35.53 S ATOM 12182 SG CYS G 75 105.594 60.771 151.498 1.00 36.47 S ATOM 12207 SG CYS G 78 104.260 65.092 153.744 1.00 36.76 S ATOM 12308 SG CYS G 92 104.046 63.059 156.849 1.00 39.04 S ATOM 20336 SG CYS I 123 86.144 52.262 119.588 1.00 27.30 S ATOM 20562 SG CYS I 152 86.084 51.284 114.431 1.00 27.39 S ATOM 20609 SG CYS I 158 91.674 51.592 116.701 1.00 26.60 S ATOM 20588 SG CYS I 155 88.397 55.892 116.458 1.00 27.04 S ATOM 20285 SG CYS I 116 95.946 48.335 127.092 1.00 29.24 S ATOM 20308 SG CYS I 119 91.689 47.963 123.605 1.00 28.85 S ATOM 20266 SG CYS I 113 95.102 43.285 123.605 1.00 28.61 S ATOM 20638 SG CYS I 162 97.856 48.078 121.760 1.00 28.07 S ATOM 25147 SG CYS R 79 111.500 41.741 126.513 1.00 32.60 S ATOM 25323 SG CYS R 104 109.069 40.161 127.835 1.00 32.49 S ATOM 25345 SG CYS R 107 108.462 40.914 124.419 1.00 30.78 S Time building chain proxies: 7.27, per 1000 atoms: 0.21 Number of scatterers: 34048 At special positions: 0 Unit cell: (166.1, 129.8, 204.6, 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 12 15.00 O 6184 8.00 N 5784 7.00 C 21793 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=2.00 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.10 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 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: 3.48 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " 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="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " 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="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="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 303 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 303 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 304 " pdb="FE3 SF4 I 304 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 304 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 304 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 304 " - pdb=" SG CYS I 119 " 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 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7860 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 36 sheets defined 49.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 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: 3.584A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.250A pdb=" N PHE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.505A 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 168 through 172 removed outlier: 3.590A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) 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: 3.603A 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 161 through 174 removed outlier: 4.114A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.705A 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: 3.856A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A 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: 3.847A 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: 4.094A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.507A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.706A 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: 3.660A 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: 4.207A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.743A 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: 3.669A 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: 3.531A 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: 4.470A 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 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.638A pdb=" N ALA E 76 " --> pdb=" O HIS E 73 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.525A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.684A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.559A 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: 4.294A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.564A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.922A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.515A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) 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: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 removed outlier: 3.930A pdb=" N GLY F 237 " --> pdb=" O GLY F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.600A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.532A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.862A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.039A 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: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.808A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.775A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A 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 146 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A 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 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.670A 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: 4.026A 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: 4.008A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.635A 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 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.521A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A 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: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.680A 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: 4.551A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.097A 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: 4.002A 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 211 through 215 removed outlier: 4.349A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 242 removed outlier: 4.074A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.538A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) 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 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.864A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.144A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.803A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.873A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.597A 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 removed outlier: 3.594A pdb=" N LYS P 189 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.081A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.621A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.034A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 45 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.650A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 3.513A pdb=" N TYR S 41 " --> pdb=" O ILE S 37 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.810A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.676A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.857A pdb=" N ARG W 33 " --> pdb=" O ASN W 29 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.517A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 98 through 100 No H-bonds generated for 'chain 'W' and resid 98 through 100' Processing helix chain 'W' and resid 102 through 107 Processing helix chain 'W' and resid 120 through 127 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.528A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 35 removed outlier: 4.624A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 27 removed outlier: 4.498A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 6 through 15 removed outlier: 4.399A pdb=" N ALA b 12 " --> pdb=" O PHE b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.759A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.602A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.537A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.127A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 78 through 88 removed outlier: 3.657A pdb=" N ASP s 86 " --> pdb=" O ASP s 82 " (cutoff:3.500A) 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: 5.839A 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: 7.931A 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 72 through 73 removed outlier: 3.568A pdb=" N CYS C 86 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.831A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.981A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.149A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.533A pdb=" N PHE D 84 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 97 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.510A 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: 5.541A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA9, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.356A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.501A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 170 through 171 removed outlier: 3.515A pdb=" N TYR E 192 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.442A 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: 6.228A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.720A 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: 6.979A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB4, 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: 7.486A 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=AB5, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.807A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.867A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.314A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.456A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.359A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC9, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.359A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 263 through 264 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 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 52 through 53 removed outlier: 7.650A pdb=" N GLN R 52 " --> pdb=" O VAL q 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.508A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.672A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.240A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1417 hydrogen bonds defined for protein. 4128 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: 6.78 Time building geometry restraints manager: 4.40 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: 11529 1.37 - 1.59: 22858 1.59 - 1.80: 263 1.80 - 2.02: 134 2.02 - 2.23: 80 Bond restraints: 34864 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 1.33e+03 bond pdb=" N PRO H 60 " pdb=" CD PRO H 60 " ideal model delta sigma weight residual 1.473 1.666 -0.193 1.40e-02 5.10e+03 1.91e+02 bond pdb=" CB7 CDL a 101 " pdb=" OB8 CDL a 101 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" CA7 CDL a 101 " pdb=" OA8 CDL a 101 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.10e-02 8.26e+03 1.08e+02 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 ... (remaining 34859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 46472 6.66 - 13.31: 606 13.31 - 19.97: 163 19.97 - 26.63: 1 26.63 - 33.28: 2 Bond angle restraints: 47244 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 89.10 25.54 1.52e+00 4.33e-01 2.82e+02 angle pdb=" N VAL H 208 " pdb=" CA VAL H 208 " pdb=" C VAL H 208 " ideal model delta sigma weight residual 111.62 100.83 10.79 7.90e-01 1.60e+00 1.87e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.81 -18.64 1.40e+00 5.10e-01 1.77e+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 97.28 16.10 1.23e+00 6.61e-01 1.71e+02 angle pdb=" N VAL I 164 " pdb=" CA VAL I 164 " pdb=" C VAL I 164 " ideal model delta sigma weight residual 112.83 100.09 12.74 9.90e-01 1.02e+00 1.66e+02 ... (remaining 47239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 20618 34.47 - 68.94: 396 68.94 - 103.42: 35 103.42 - 137.89: 6 137.89 - 172.36: 1 Dihedral angle restraints: 21056 sinusoidal: 8861 harmonic: 12195 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 93.00 161.55 -68.55 1 1.00e+01 1.00e-02 6.09e+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 31.39 61.61 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.65 -16.95 0 2.50e+00 1.60e-01 4.59e+01 ... (remaining 21053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4537 0.183 - 0.366: 550 0.366 - 0.549: 48 0.549 - 0.731: 4 0.731 - 0.914: 24 Chirality restraints: 5163 Sorted by residual: chirality pdb="FE3 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S4 SF4 I 304 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb="FE2 SF4 I 303 " pdb=" S1 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 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb="FE4 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S3 SF4 I 304 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5160 not shown) Planarity restraints: 5997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 B 302 " 0.034 2.00e-02 2.50e+03 2.02e-01 1.22e+03 pdb=" C1M UQ9 B 302 " 0.208 2.00e-02 2.50e+03 pdb=" C2 UQ9 B 302 " -0.132 2.00e-02 2.50e+03 pdb=" C3 UQ9 B 302 " 0.100 2.00e-02 2.50e+03 pdb=" C4 UQ9 B 302 " -0.007 2.00e-02 2.50e+03 pdb=" C5 UQ9 B 302 " -0.038 2.00e-02 2.50e+03 pdb=" C6 UQ9 B 302 " 0.026 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " 0.079 2.00e-02 2.50e+03 pdb=" O2 UQ9 B 302 " -0.463 2.00e-02 2.50e+03 pdb=" O3 UQ9 B 302 " 0.412 2.00e-02 2.50e+03 pdb=" O4 UQ9 B 302 " -0.105 2.00e-02 2.50e+03 pdb=" O5 UQ9 B 302 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 B 302 " 0.235 2.00e-02 2.50e+03 1.98e-01 4.90e+02 pdb=" C13 UQ9 B 302 " -0.329 2.00e-02 2.50e+03 pdb=" C14 UQ9 B 302 " -0.072 2.00e-02 2.50e+03 pdb=" C15 UQ9 B 302 " 0.000 2.00e-02 2.50e+03 pdb=" C16 UQ9 B 302 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 B 302 " 0.106 2.00e-02 2.50e+03 8.81e-02 9.71e+01 pdb=" C18 UQ9 B 302 " -0.140 2.00e-02 2.50e+03 pdb=" C19 UQ9 B 302 " -0.033 2.00e-02 2.50e+03 pdb=" C20 UQ9 B 302 " 0.082 2.00e-02 2.50e+03 pdb=" C21 UQ9 B 302 " -0.015 2.00e-02 2.50e+03 ... (remaining 5994 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 88 2.38 - 3.01: 22861 3.01 - 3.64: 53325 3.64 - 4.27: 83459 4.27 - 4.90: 135533 Nonbonded interactions: 295266 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.903 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.979 3.120 ... (remaining 295261 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.520 Find NCS groups from input model: 0.240 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: 45.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.023 1.141 34905 Z= 1.054 Angle : 2.271 52.546 47336 Z= 1.519 Chirality : 0.133 0.914 5163 Planarity : 0.008 0.202 5997 Dihedral : 13.586 172.359 13184 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 47.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 0.41 % Allowed : 7.83 % Favored : 91.76 % Cbeta Deviations : 1.70 % 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: -2.15 (0.12), residues: 4153 helix: -0.79 (0.11), residues: 1800 sheet: -1.23 (0.27), residues: 364 loop : -2.05 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.046 0.003 TYR B 112 PHE 0.029 0.002 PHE D 200 TRP 0.034 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01468 (34864) covalent geometry : angle 2.14587 (47244) SS BOND : bond 0.03605 ( 4) SS BOND : angle 5.78172 ( 8) hydrogen bonds : bond 0.24566 ( 1417) hydrogen bonds : angle 8.94763 ( 4128) metal coordination : bond 0.52811 ( 37) metal coordination : angle 17.72747 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1776 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1761 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: A 68 GLU cc_start: 0.7236 (pt0) cc_final: 0.7029 (pt0) REVERT: B 82 ILE cc_start: 0.8605 (mt) cc_final: 0.8339 (mt) REVERT: B 206 LEU cc_start: 0.8492 (mt) cc_final: 0.8238 (mp) REVERT: C 150 THR cc_start: 0.8444 (m) cc_final: 0.8194 (t) REVERT: D 143 SER cc_start: 0.7905 (m) cc_final: 0.7548 (p) REVERT: D 463 ARG cc_start: 0.6171 (ptt90) cc_final: 0.5728 (ptt90) REVERT: E 53 ASP cc_start: 0.7162 (t70) cc_final: 0.6940 (t0) REVERT: E 207 LEU cc_start: 0.6859 (mt) cc_final: 0.6174 (mt) REVERT: H 285 LEU cc_start: 0.8104 (tt) cc_final: 0.7828 (tt) REVERT: I 177 THR cc_start: 0.6608 (p) cc_final: 0.6143 (p) REVERT: P 217 PHE cc_start: 0.7947 (m-10) cc_final: 0.7594 (m-80) REVERT: P 277 VAL cc_start: 0.8971 (t) cc_final: 0.8535 (t) REVERT: Q 94 THR cc_start: 0.8588 (m) cc_final: 0.8356 (t) REVERT: Q 164 PHE cc_start: 0.6960 (m-80) cc_final: 0.5785 (m-80) REVERT: R 103 THR cc_start: 0.7262 (p) cc_final: 0.6999 (p) REVERT: S 68 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5960 (mtm110) REVERT: T 86 VAL cc_start: 0.7201 (t) cc_final: 0.6909 (m) REVERT: T 124 ASP cc_start: 0.7268 (m-30) cc_final: 0.6283 (m-30) REVERT: V 64 ASP cc_start: 0.6072 (t0) cc_final: 0.5669 (t70) REVERT: W 57 ILE cc_start: 0.6764 (pt) cc_final: 0.6454 (pt) REVERT: W 101 LYS cc_start: 0.8753 (mtpm) cc_final: 0.8522 (mtmt) REVERT: X 68 LEU cc_start: 0.7839 (mt) cc_final: 0.7082 (mt) REVERT: a 38 VAL cc_start: 0.8664 (t) cc_final: 0.8343 (p) REVERT: b 22 SER cc_start: 0.8750 (t) cc_final: 0.8455 (p) outliers start: 15 outliers final: 1 residues processed: 1768 average time/residue: 0.2396 time to fit residues: 666.6129 Evaluate side-chains 1034 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1031 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain S residue 68 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 166 ASN B 207 GLN C 88 HIS ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS C 195 HIS D 83 ASN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 233 HIS D 265 ASN D 346 GLN D 454 GLN E 105 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN F 220 GLN F 277 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 346 GLN F 451 GLN G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN G 205 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS G 495 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS G 604 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN I 126 GLN P 72 HIS P 171 ASN P 238 GLN P 251 ASN Q 71 HIS V 21 HIS V 50 GLN V 110 ASN W 54 GLN W 61 GLN W 94 GLN W 105 HIS X 40 ASN Z 76 GLN a 42 GLN a 58 ASN b 83 ASN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 54 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN r 21 GLN r 25 GLN s 76 ASN s 84 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087032 restraints weight = 89233.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.089844 restraints weight = 41692.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091687 restraints weight = 25207.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092890 restraints weight = 18072.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093636 restraints weight = 14508.485| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34905 Z= 0.239 Angle : 1.083 73.022 47336 Z= 0.452 Chirality : 0.051 0.261 5163 Planarity : 0.007 0.119 5997 Dihedral : 10.390 164.823 4925 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 4.75 % Allowed : 17.22 % Favored : 78.03 % Cbeta Deviations : 0.00 % 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: -1.04 (0.13), residues: 4153 helix: 0.18 (0.12), residues: 1886 sheet: -1.20 (0.26), residues: 372 loop : -1.43 (0.14), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 135 TYR 0.047 0.003 TYR E 112 PHE 0.034 0.003 PHE P 64 TRP 0.032 0.002 TRP F 51 HIS 0.013 0.002 HIS P 356 Details of bonding type rmsd covalent geometry : bond 0.00542 (34864) covalent geometry : angle 0.86960 (47244) SS BOND : bond 0.01336 ( 4) SS BOND : angle 3.25035 ( 8) hydrogen bonds : bond 0.05921 ( 1417) hydrogen bonds : angle 5.73166 ( 4128) metal coordination : bond 0.03059 ( 37) metal coordination : angle 15.33042 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1081 time to evaluate : 1.425 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 12 LEU cc_start: 0.9265 (mt) cc_final: 0.8854 (tt) REVERT: A 27 MET cc_start: 0.7737 (ptt) cc_final: 0.7386 (mtm) REVERT: A 53 MET cc_start: 0.7884 (ppp) cc_final: 0.7456 (ppp) REVERT: A 62 PHE cc_start: 0.8867 (t80) cc_final: 0.8647 (t80) REVERT: A 83 LYS cc_start: 0.8372 (mmtm) cc_final: 0.7584 (mtmt) REVERT: A 87 MET cc_start: 0.8624 (ttp) cc_final: 0.8159 (tmm) REVERT: A 88 MET cc_start: 0.8511 (ptm) cc_final: 0.8291 (ttp) REVERT: B 76 THR cc_start: 0.8972 (p) cc_final: 0.8734 (t) REVERT: B 79 ASP cc_start: 0.8574 (m-30) cc_final: 0.8124 (t0) REVERT: B 133 VAL cc_start: 0.9169 (t) cc_final: 0.8948 (p) REVERT: B 141 MET cc_start: 0.8977 (tpt) cc_final: 0.8706 (tpt) REVERT: B 147 LYS cc_start: 0.8788 (tptm) cc_final: 0.8452 (tptp) REVERT: B 161 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7684 (ttt) REVERT: B 170 TYR cc_start: 0.9113 (t80) cc_final: 0.8774 (t80) REVERT: B 173 TYR cc_start: 0.8680 (m-80) cc_final: 0.8444 (m-80) REVERT: B 201 LEU cc_start: 0.9430 (tp) cc_final: 0.8852 (tp) REVERT: B 211 LYS cc_start: 0.8932 (tttp) cc_final: 0.8676 (tttm) REVERT: B 215 GLU cc_start: 0.8623 (pt0) cc_final: 0.8334 (pt0) REVERT: C 166 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 216 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8406 (mmtt) REVERT: C 221 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8198 (mt-10) REVERT: C 224 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6722 (tt0) REVERT: D 84 PHE cc_start: 0.9214 (t80) cc_final: 0.8918 (t80) REVERT: D 124 ILE cc_start: 0.9455 (mt) cc_final: 0.9244 (mp) REVERT: D 144 MET cc_start: 0.8007 (mpp) cc_final: 0.7691 (mpp) REVERT: D 210 MET cc_start: 0.8865 (mtm) cc_final: 0.8626 (mtm) REVERT: D 265 ASN cc_start: 0.8441 (t0) cc_final: 0.8048 (t0) REVERT: D 282 ASP cc_start: 0.8912 (m-30) cc_final: 0.8708 (m-30) REVERT: D 311 TYR cc_start: 0.8716 (m-80) cc_final: 0.8244 (m-80) REVERT: D 398 THR cc_start: 0.9215 (t) cc_final: 0.8890 (p) REVERT: E 54 PHE cc_start: 0.8283 (m-80) cc_final: 0.7781 (m-80) REVERT: E 67 LYS cc_start: 0.8902 (ptmt) cc_final: 0.8645 (mmtt) REVERT: E 69 TYR cc_start: 0.7284 (m-80) cc_final: 0.6839 (m-80) REVERT: E 120 MET cc_start: 0.8442 (tpp) cc_final: 0.7871 (mmm) REVERT: E 125 PRO cc_start: 0.8708 (Cg_endo) cc_final: 0.7708 (Cg_exo) REVERT: E 168 PHE cc_start: 0.7530 (m-80) cc_final: 0.6537 (m-10) REVERT: E 174 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: E 184 MET cc_start: 0.7234 (ttp) cc_final: 0.6845 (ptm) REVERT: E 189 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6062 (t0) REVERT: F 61 ASP cc_start: 0.6351 (p0) cc_final: 0.6097 (p0) REVERT: F 170 GLN cc_start: 0.7755 (mt0) cc_final: 0.7248 (mt0) REVERT: F 208 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8115 (tm-30) REVERT: F 396 MET cc_start: 0.8816 (mmm) cc_final: 0.8593 (mmm) REVERT: F 429 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7626 (t70) REVERT: G 62 ARG cc_start: 0.8362 (ptt-90) cc_final: 0.7770 (ptt-90) REVERT: G 114 GLU cc_start: 0.8079 (tt0) cc_final: 0.7385 (tt0) REVERT: G 172 ILE cc_start: 0.9385 (mt) cc_final: 0.9059 (tp) REVERT: G 215 MET cc_start: 0.7539 (ptp) cc_final: 0.7334 (ptp) REVERT: G 391 ILE cc_start: 0.8372 (mm) cc_final: 0.8058 (mm) REVERT: G 434 SER cc_start: 0.9280 (p) cc_final: 0.8910 (t) REVERT: G 471 LYS cc_start: 0.8502 (mttp) cc_final: 0.8059 (mmmm) REVERT: G 640 ASP cc_start: 0.7917 (p0) cc_final: 0.7707 (p0) REVERT: G 657 ASP cc_start: 0.7557 (t0) cc_final: 0.7112 (t0) REVERT: H 24 GLU cc_start: 0.8726 (tt0) cc_final: 0.8416 (tt0) REVERT: H 31 MET cc_start: 0.9271 (mtp) cc_final: 0.8591 (mtp) REVERT: H 32 GLN cc_start: 0.9359 (mt0) cc_final: 0.9139 (mt0) REVERT: H 124 ASN cc_start: 0.8243 (t0) cc_final: 0.8020 (t0) REVERT: H 170 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7795 (mt-10) REVERT: H 199 ASP cc_start: 0.7796 (t0) cc_final: 0.7338 (t0) REVERT: I 59 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7027 (ttp-110) REVERT: I 128 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8993 (mp) REVERT: I 139 SER cc_start: 0.8588 (t) cc_final: 0.8220 (p) REVERT: I 182 GLU cc_start: 0.8242 (tt0) cc_final: 0.7883 (tt0) REVERT: I 195 ASP cc_start: 0.8977 (t0) cc_final: 0.8694 (m-30) REVERT: I 208 ASP cc_start: 0.8243 (t70) cc_final: 0.7024 (t70) REVERT: P 97 MET cc_start: 0.8364 (ptp) cc_final: 0.7979 (ptp) REVERT: P 332 LEU cc_start: 0.8071 (tp) cc_final: 0.7670 (tt) REVERT: Q 69 GLU cc_start: 0.7462 (tp30) cc_final: 0.7094 (tp30) REVERT: Q 107 TRP cc_start: 0.8802 (p90) cc_final: 0.8509 (p90) REVERT: Q 128 PHE cc_start: 0.8375 (m-80) cc_final: 0.8115 (m-80) REVERT: Q 139 GLU cc_start: 0.8903 (tp30) cc_final: 0.8331 (mm-30) REVERT: Q 145 TYR cc_start: 0.8954 (p90) cc_final: 0.8599 (p90) REVERT: Q 159 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8581 (p) REVERT: Q 160 TYR cc_start: 0.8495 (t80) cc_final: 0.7692 (t80) REVERT: Q 164 PHE cc_start: 0.7797 (m-80) cc_final: 0.5996 (m-80) REVERT: R 48 PHE cc_start: 0.6768 (m-80) cc_final: 0.6517 (m-80) REVERT: R 96 ASP cc_start: 0.7550 (t0) cc_final: 0.7167 (t0) REVERT: S 31 GLN cc_start: 0.9105 (tp40) cc_final: 0.8579 (pm20) REVERT: S 40 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8365 (ttm-80) REVERT: S 68 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7763 (tmm-80) REVERT: T 99 SER cc_start: 0.8035 (m) cc_final: 0.7476 (p) REVERT: T 146 ASP cc_start: 0.9022 (m-30) cc_final: 0.8681 (m-30) REVERT: V 64 ASP cc_start: 0.7727 (t0) cc_final: 0.7362 (t0) REVERT: V 73 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8015 (mp10) REVERT: W 53 MET cc_start: 0.9182 (mtt) cc_final: 0.8890 (mtt) REVERT: W 55 LEU cc_start: 0.8406 (mp) cc_final: 0.8192 (mp) REVERT: X 32 TYR cc_start: 0.8748 (t80) cc_final: 0.8535 (t80) REVERT: X 44 MET cc_start: 0.9063 (tpp) cc_final: 0.8594 (tpp) REVERT: X 46 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4873 (m) REVERT: X 117 TRP cc_start: 0.8103 (m-10) cc_final: 0.7841 (m-10) REVERT: Z 24 ASN cc_start: 0.8316 (t0) cc_final: 0.7892 (t0) REVERT: Z 125 TYR cc_start: 0.8630 (m-80) cc_final: 0.8423 (m-80) REVERT: a 1 MET cc_start: 0.7444 (mmt) cc_final: 0.7177 (mmp) REVERT: a 2 TRP cc_start: 0.8489 (p-90) cc_final: 0.8065 (p-90) REVERT: a 34 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (ptpt) REVERT: a 38 VAL cc_start: 0.9156 (t) cc_final: 0.8752 (p) REVERT: a 54 ILE cc_start: 0.8812 (mm) cc_final: 0.8562 (mm) REVERT: b 32 MET cc_start: 0.9193 (mmt) cc_final: 0.8928 (mmt) REVERT: b 44 MET cc_start: 0.8476 (mtp) cc_final: 0.7476 (ptp) REVERT: b 78 LEU cc_start: 0.8890 (mp) cc_final: 0.8664 (mp) REVERT: q 93 MET cc_start: 0.7143 (tmm) cc_final: 0.6757 (tmm) REVERT: r 93 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8417 (mmmm) outliers start: 173 outliers final: 83 residues processed: 1178 average time/residue: 0.2153 time to fit residues: 418.1201 Evaluate side-chains 972 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 879 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain S residue 71 PHE Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 ASP Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 34 LYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain r residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 115 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 377 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 362 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN F 436 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 460 HIS G 663 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS P 93 HIS ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 285 HIS ** Q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** 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 = 0.3672 r_free = 0.3672 target = 0.106018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087543 restraints weight = 89791.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090477 restraints weight = 39589.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092391 restraints weight = 23239.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093634 restraints weight = 16287.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094432 restraints weight = 12920.339| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34905 Z= 0.157 Angle : 0.929 71.831 47336 Z= 0.374 Chirality : 0.046 0.246 5163 Planarity : 0.005 0.121 5997 Dihedral : 9.922 162.467 4921 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 4.26 % Allowed : 19.71 % Favored : 76.03 % Cbeta Deviations : 0.00 % 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: -0.60 (0.13), residues: 4153 helix: 0.59 (0.12), residues: 1878 sheet: -1.10 (0.26), residues: 372 loop : -1.22 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG r 12 TYR 0.035 0.002 TYR E 112 PHE 0.035 0.002 PHE H 270 TRP 0.028 0.002 TRP Z 116 HIS 0.008 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00347 (34864) covalent geometry : angle 0.73543 (47244) SS BOND : bond 0.00248 ( 4) SS BOND : angle 2.16092 ( 8) hydrogen bonds : bond 0.04901 ( 1417) hydrogen bonds : angle 5.23650 ( 4128) metal coordination : bond 0.01712 ( 37) metal coordination : angle 13.49247 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1014 time to evaluate : 1.317 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: A 12 LEU cc_start: 0.9331 (mt) cc_final: 0.9013 (tt) REVERT: A 19 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 27 MET cc_start: 0.7311 (ptt) cc_final: 0.7063 (mtm) REVERT: A 53 MET cc_start: 0.7787 (ppp) cc_final: 0.7359 (ppp) REVERT: A 83 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7637 (mtmt) REVERT: A 87 MET cc_start: 0.8428 (ttp) cc_final: 0.8028 (tmm) REVERT: A 99 SER cc_start: 0.8998 (t) cc_final: 0.8739 (p) REVERT: B 147 LYS cc_start: 0.8720 (tptm) cc_final: 0.8514 (tptp) REVERT: B 161 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7427 (ttt) REVERT: B 188 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8216 (t0) REVERT: B 201 LEU cc_start: 0.9309 (tp) cc_final: 0.8538 (tp) REVERT: B 211 LYS cc_start: 0.8912 (tttp) cc_final: 0.8542 (tttt) REVERT: C 84 GLU cc_start: 0.7422 (pt0) cc_final: 0.7202 (pp20) REVERT: C 104 ASN cc_start: 0.8434 (m-40) cc_final: 0.7056 (t0) REVERT: C 211 TYR cc_start: 0.8056 (t80) cc_final: 0.7636 (t80) REVERT: C 216 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8583 (mmtt) REVERT: C 221 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 224 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6539 (tt0) REVERT: D 144 MET cc_start: 0.7966 (mpp) cc_final: 0.7714 (mpp) REVERT: D 210 MET cc_start: 0.8770 (mtm) cc_final: 0.8478 (mtm) REVERT: D 265 ASN cc_start: 0.8383 (t0) cc_final: 0.8000 (t0) REVERT: D 398 THR cc_start: 0.9187 (t) cc_final: 0.8983 (p) REVERT: D 422 CYS cc_start: 0.8108 (t) cc_final: 0.7807 (t) REVERT: E 52 PHE cc_start: 0.7970 (t80) cc_final: 0.7651 (t80) REVERT: E 61 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7613 (mtt-85) REVERT: E 67 LYS cc_start: 0.8917 (ptmt) cc_final: 0.8658 (tppt) REVERT: E 69 TYR cc_start: 0.7108 (m-80) cc_final: 0.6893 (m-80) REVERT: E 120 MET cc_start: 0.8207 (tpp) cc_final: 0.7928 (tpp) REVERT: E 125 PRO cc_start: 0.8757 (Cg_endo) cc_final: 0.7805 (Cg_exo) REVERT: E 174 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: E 184 MET cc_start: 0.7229 (ttp) cc_final: 0.6899 (ptm) REVERT: E 189 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6476 (t0) REVERT: F 101 PHE cc_start: 0.8825 (m-10) cc_final: 0.8415 (m-80) REVERT: F 170 GLN cc_start: 0.8116 (mt0) cc_final: 0.7888 (mt0) REVERT: F 396 MET cc_start: 0.8608 (mmm) cc_final: 0.8357 (mmm) REVERT: F 429 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7784 (t70) REVERT: F 450 MET cc_start: 0.8661 (mmp) cc_final: 0.8228 (mmp) REVERT: G 42 MET cc_start: 0.8840 (tpp) cc_final: 0.8570 (tpp) REVERT: G 62 ARG cc_start: 0.8298 (ptt-90) cc_final: 0.7791 (ptt-90) REVERT: G 136 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7811 (mt-10) REVERT: G 145 MET cc_start: 0.8986 (mmt) cc_final: 0.8710 (mmt) REVERT: G 172 ILE cc_start: 0.9376 (mt) cc_final: 0.9123 (tp) REVERT: G 215 MET cc_start: 0.7388 (ptp) cc_final: 0.7127 (ptp) REVERT: G 269 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7208 (pt0) REVERT: G 391 ILE cc_start: 0.8416 (mm) cc_final: 0.8175 (mm) REVERT: G 434 SER cc_start: 0.9202 (p) cc_final: 0.8815 (t) REVERT: G 471 LYS cc_start: 0.8515 (mttm) cc_final: 0.8235 (mmmm) REVERT: G 567 VAL cc_start: 0.9027 (OUTLIER) cc_final: 0.8691 (p) REVERT: G 618 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8279 (mt-10) REVERT: G 657 ASP cc_start: 0.7497 (t0) cc_final: 0.7083 (t0) REVERT: H 24 GLU cc_start: 0.8404 (tt0) cc_final: 0.8030 (tt0) REVERT: H 32 GLN cc_start: 0.9278 (mt0) cc_final: 0.9031 (mt0) REVERT: H 59 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: H 163 GLN cc_start: 0.8780 (tt0) cc_final: 0.8388 (mt0) REVERT: H 172 MET cc_start: 0.6555 (mmt) cc_final: 0.6135 (mmm) REVERT: H 199 ASP cc_start: 0.7524 (t0) cc_final: 0.7210 (t0) REVERT: H 261 MET cc_start: 0.8165 (mmt) cc_final: 0.7912 (mmt) REVERT: H 282 TYR cc_start: 0.6790 (t80) cc_final: 0.6172 (t80) REVERT: I 36 TYR cc_start: 0.8783 (p90) cc_final: 0.8222 (p90) REVERT: I 72 MET cc_start: 0.9120 (tpp) cc_final: 0.8850 (tpp) REVERT: I 185 TYR cc_start: 0.8509 (m-10) cc_final: 0.8283 (m-80) REVERT: I 195 ASP cc_start: 0.8925 (t0) cc_final: 0.8711 (m-30) REVERT: I 206 GLN cc_start: 0.8940 (tp40) cc_final: 0.8473 (tm-30) REVERT: I 208 ASP cc_start: 0.8269 (t70) cc_final: 0.7186 (t70) REVERT: P 332 LEU cc_start: 0.7987 (tp) cc_final: 0.7605 (tt) REVERT: P 361 TRP cc_start: 0.8077 (m100) cc_final: 0.7706 (m100) REVERT: Q 107 TRP cc_start: 0.8787 (p90) cc_final: 0.8360 (p90) REVERT: Q 119 ASP cc_start: 0.8388 (t0) cc_final: 0.7832 (p0) REVERT: Q 160 TYR cc_start: 0.8369 (t80) cc_final: 0.7762 (t80) REVERT: Q 164 PHE cc_start: 0.7701 (m-80) cc_final: 0.5980 (m-80) REVERT: R 96 ASP cc_start: 0.7390 (t0) cc_final: 0.7137 (t0) REVERT: S 31 GLN cc_start: 0.9064 (tp40) cc_final: 0.8592 (pm20) REVERT: S 40 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7970 (ttm-80) REVERT: T 120 MET cc_start: 0.7951 (tmm) cc_final: 0.7391 (tmm) REVERT: T 124 ASP cc_start: 0.7482 (m-30) cc_final: 0.6770 (m-30) REVERT: T 134 ASP cc_start: 0.8204 (m-30) cc_final: 0.7843 (p0) REVERT: T 136 GLU cc_start: 0.8191 (mp0) cc_final: 0.7983 (pm20) REVERT: V 47 TYR cc_start: 0.8649 (m-80) cc_final: 0.8122 (m-80) REVERT: W 53 MET cc_start: 0.9139 (mtt) cc_final: 0.8731 (mtt) REVERT: W 58 THR cc_start: 0.8465 (m) cc_final: 0.8133 (p) REVERT: W 123 SER cc_start: 0.8846 (m) cc_final: 0.8466 (p) REVERT: X 32 TYR cc_start: 0.8699 (t80) cc_final: 0.8459 (t80) REVERT: X 44 MET cc_start: 0.8964 (tpp) cc_final: 0.8576 (tpp) REVERT: X 90 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8752 (t70) REVERT: Z 21 TYR cc_start: 0.7488 (p90) cc_final: 0.6873 (p90) REVERT: Z 24 ASN cc_start: 0.8333 (t0) cc_final: 0.7971 (t0) REVERT: Z 116 TRP cc_start: 0.8673 (t-100) cc_final: 0.8252 (t-100) REVERT: Z 125 TYR cc_start: 0.8754 (m-80) cc_final: 0.8447 (m-80) REVERT: Z 134 SER cc_start: 0.9374 (t) cc_final: 0.9083 (p) REVERT: a 2 TRP cc_start: 0.8563 (p-90) cc_final: 0.8241 (p-90) REVERT: a 23 THR cc_start: 0.9267 (m) cc_final: 0.8938 (p) REVERT: a 34 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7584 (ptpt) REVERT: a 46 TYR cc_start: 0.8907 (t80) cc_final: 0.8704 (t80) REVERT: b 32 MET cc_start: 0.9158 (mmt) cc_final: 0.8900 (mmt) REVERT: b 78 LEU cc_start: 0.8947 (mp) cc_final: 0.8675 (mp) outliers start: 155 outliers final: 79 residues processed: 1103 average time/residue: 0.2096 time to fit residues: 380.6082 Evaluate side-chains 970 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 879 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 200 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 40 ARG Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 34 LYS Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 198 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 362 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 408 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 159 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN W 94 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.086806 restraints weight = 89063.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089629 restraints weight = 42599.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091463 restraints weight = 25948.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092647 restraints weight = 18738.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093403 restraints weight = 15172.561| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34905 Z= 0.154 Angle : 0.890 73.721 47336 Z= 0.357 Chirality : 0.045 0.275 5163 Planarity : 0.005 0.121 5997 Dihedral : 9.738 159.859 4920 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 4.53 % Allowed : 21.11 % Favored : 74.35 % Cbeta Deviations : 0.00 % 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: -0.40 (0.13), residues: 4153 helix: 0.76 (0.12), residues: 1872 sheet: -0.96 (0.27), residues: 364 loop : -1.13 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 59 TYR 0.034 0.002 TYR F 63 PHE 0.050 0.002 PHE A 62 TRP 0.017 0.001 TRP I 63 HIS 0.012 0.001 HIS q 135 Details of bonding type rmsd covalent geometry : bond 0.00355 (34864) covalent geometry : angle 0.70320 (47244) SS BOND : bond 0.00358 ( 4) SS BOND : angle 2.10547 ( 8) hydrogen bonds : bond 0.04428 ( 1417) hydrogen bonds : angle 5.09018 ( 4128) metal coordination : bond 0.01430 ( 37) metal coordination : angle 12.94581 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 946 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: A 8 PHE cc_start: 0.8351 (m-80) cc_final: 0.7781 (m-10) REVERT: A 19 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8349 (tp) REVERT: A 27 MET cc_start: 0.7345 (ptt) cc_final: 0.7041 (mtm) REVERT: A 38 GLU cc_start: 0.7557 (tp30) cc_final: 0.6824 (mm-30) REVERT: A 48 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7523 (mtm-85) REVERT: A 53 MET cc_start: 0.7874 (ppp) cc_final: 0.7461 (ppp) REVERT: A 83 LYS cc_start: 0.8383 (mmtm) cc_final: 0.7746 (mtmt) REVERT: A 99 SER cc_start: 0.8941 (t) cc_final: 0.8737 (p) REVERT: B 79 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8117 (t0) REVERT: B 220 ILE cc_start: 0.9443 (tp) cc_final: 0.9221 (tp) REVERT: C 104 ASN cc_start: 0.8364 (m-40) cc_final: 0.7115 (t0) REVERT: C 211 TYR cc_start: 0.8098 (t80) cc_final: 0.7724 (t80) REVERT: C 221 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8031 (mt-10) REVERT: D 265 ASN cc_start: 0.8437 (t0) cc_final: 0.8038 (t0) REVERT: E 67 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8648 (tppt) REVERT: E 91 TRP cc_start: 0.7484 (m100) cc_final: 0.6372 (m-10) REVERT: E 120 MET cc_start: 0.8161 (tpp) cc_final: 0.7885 (tpp) REVERT: E 174 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: E 189 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6641 (t0) REVERT: E 192 TYR cc_start: 0.8562 (m-80) cc_final: 0.7856 (m-80) REVERT: E 200 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8087 (tp) REVERT: F 53 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7086 (mt) REVERT: F 63 TYR cc_start: 0.8844 (t80) cc_final: 0.8465 (t80) REVERT: F 101 PHE cc_start: 0.8850 (m-10) cc_final: 0.8439 (m-80) REVERT: F 170 GLN cc_start: 0.8218 (mt0) cc_final: 0.7946 (mt0) REVERT: F 275 LEU cc_start: 0.8539 (mm) cc_final: 0.8142 (mm) REVERT: F 396 MET cc_start: 0.8528 (mmm) cc_final: 0.8323 (mmm) REVERT: F 450 MET cc_start: 0.8691 (mmp) cc_final: 0.8375 (mmp) REVERT: G 42 MET cc_start: 0.8842 (tpp) cc_final: 0.8603 (tpp) REVERT: G 114 GLU cc_start: 0.8128 (tt0) cc_final: 0.7540 (tt0) REVERT: G 136 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7954 (mt-10) REVERT: G 145 MET cc_start: 0.8949 (mmt) cc_final: 0.8653 (mmt) REVERT: G 172 ILE cc_start: 0.9391 (mt) cc_final: 0.9128 (tp) REVERT: G 269 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7374 (pt0) REVERT: G 381 LEU cc_start: 0.9006 (mp) cc_final: 0.8801 (mt) REVERT: G 471 LYS cc_start: 0.8560 (mttm) cc_final: 0.8269 (mmmm) REVERT: G 567 VAL cc_start: 0.9057 (p) cc_final: 0.8750 (p) REVERT: G 640 ASP cc_start: 0.7559 (p0) cc_final: 0.7302 (p0) REVERT: G 657 ASP cc_start: 0.7477 (t0) cc_final: 0.7010 (t0) REVERT: G 663 ASN cc_start: 0.7115 (m-40) cc_final: 0.6642 (m-40) REVERT: H 24 GLU cc_start: 0.8462 (tt0) cc_final: 0.8115 (tt0) REVERT: H 32 GLN cc_start: 0.9237 (mt0) cc_final: 0.8973 (mt0) REVERT: H 34 ARG cc_start: 0.8711 (ptt-90) cc_final: 0.8427 (ptt-90) REVERT: H 59 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: H 163 GLN cc_start: 0.8740 (tt0) cc_final: 0.8353 (mt0) REVERT: H 181 MET cc_start: 0.8333 (mtt) cc_final: 0.8099 (mtt) REVERT: H 199 ASP cc_start: 0.7480 (t0) cc_final: 0.7094 (t0) REVERT: H 261 MET cc_start: 0.8333 (mmt) cc_final: 0.8058 (mmt) REVERT: H 286 MET cc_start: 0.7754 (tpp) cc_final: 0.7500 (tpp) REVERT: H 292 ASN cc_start: 0.8603 (m-40) cc_final: 0.8321 (m-40) REVERT: H 307 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8487 (tp) REVERT: I 36 TYR cc_start: 0.8699 (p90) cc_final: 0.8070 (p90) REVERT: I 177 THR cc_start: 0.8054 (p) cc_final: 0.7758 (t) REVERT: I 206 GLN cc_start: 0.8921 (tp40) cc_final: 0.8550 (tm-30) REVERT: I 208 ASP cc_start: 0.8302 (t70) cc_final: 0.7312 (t70) REVERT: P 97 MET cc_start: 0.7572 (ptp) cc_final: 0.7364 (ptp) REVERT: P 174 MET cc_start: 0.7082 (mtt) cc_final: 0.6769 (mtt) REVERT: P 350 ILE cc_start: 0.9321 (tt) cc_final: 0.9097 (mt) REVERT: Q 69 GLU cc_start: 0.7300 (tp30) cc_final: 0.7095 (tp30) REVERT: Q 70 GLU cc_start: 0.7229 (tp30) cc_final: 0.6882 (tp30) REVERT: Q 74 THR cc_start: 0.7882 (p) cc_final: 0.7653 (p) REVERT: Q 106 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8597 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8475 (t0) cc_final: 0.7756 (p0) REVERT: Q 123 ASN cc_start: 0.8555 (m110) cc_final: 0.8316 (m110) REVERT: Q 160 TYR cc_start: 0.8288 (t80) cc_final: 0.7873 (t80) REVERT: Q 164 PHE cc_start: 0.7518 (m-80) cc_final: 0.5870 (m-80) REVERT: R 47 ARG cc_start: 0.7378 (mtm110) cc_final: 0.6695 (ptt180) REVERT: S 31 GLN cc_start: 0.8989 (tp40) cc_final: 0.8594 (pm20) REVERT: W 37 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8883 (mt-10) REVERT: W 45 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8578 (tp30) REVERT: W 58 THR cc_start: 0.8629 (m) cc_final: 0.8344 (p) REVERT: W 123 SER cc_start: 0.8866 (m) cc_final: 0.8484 (p) REVERT: X 32 TYR cc_start: 0.8760 (t80) cc_final: 0.8542 (t80) REVERT: X 44 MET cc_start: 0.8937 (tpp) cc_final: 0.8574 (tpp) REVERT: Z 21 TYR cc_start: 0.7627 (p90) cc_final: 0.6799 (p90) REVERT: Z 24 ASN cc_start: 0.8231 (t0) cc_final: 0.7782 (t0) REVERT: Z 125 TYR cc_start: 0.8748 (m-80) cc_final: 0.8421 (m-80) REVERT: a 2 TRP cc_start: 0.8718 (p-90) cc_final: 0.8456 (p-90) REVERT: a 23 THR cc_start: 0.9322 (m) cc_final: 0.9001 (p) REVERT: b 32 MET cc_start: 0.9206 (mmt) cc_final: 0.8885 (mmt) REVERT: b 78 LEU cc_start: 0.8962 (mp) cc_final: 0.8731 (mp) REVERT: q 34 ARG cc_start: 0.6571 (mtp85) cc_final: 0.6287 (mtp85) REVERT: q 54 GLN cc_start: 0.7431 (tp40) cc_final: 0.6869 (tp40) REVERT: q 93 MET cc_start: 0.7235 (tmm) cc_final: 0.6859 (ptp) REVERT: r 109 ASP cc_start: 0.6050 (p0) cc_final: 0.5314 (p0) outliers start: 165 outliers final: 96 residues processed: 1041 average time/residue: 0.2033 time to fit residues: 350.0477 Evaluate side-chains 961 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 855 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 ASP Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 329 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 ASN W 94 GLN a 44 GLN q 13 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084067 restraints weight = 90176.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086763 restraints weight = 42913.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088532 restraints weight = 26413.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089695 restraints weight = 19204.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090419 restraints weight = 15594.396| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34905 Z= 0.188 Angle : 0.894 75.735 47336 Z= 0.355 Chirality : 0.046 0.288 5163 Planarity : 0.005 0.123 5997 Dihedral : 9.572 160.279 4916 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.24 % Favored : 95.74 % Rotamer: Outliers : 5.33 % Allowed : 21.33 % Favored : 73.34 % Cbeta Deviations : 0.00 % 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: -0.31 (0.13), residues: 4153 helix: 0.85 (0.12), residues: 1872 sheet: -1.13 (0.27), residues: 352 loop : -1.05 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 80 TYR 0.035 0.002 TYR B 170 PHE 0.031 0.002 PHE A 62 TRP 0.021 0.001 TRP I 63 HIS 0.008 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00437 (34864) covalent geometry : angle 0.69704 (47244) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.73231 ( 8) hydrogen bonds : bond 0.04276 ( 1417) hydrogen bonds : angle 5.03656 ( 4128) metal coordination : bond 0.01990 ( 37) metal coordination : angle 13.28785 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 918 time to evaluate : 1.411 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 8 PHE cc_start: 0.8373 (m-80) cc_final: 0.7855 (m-10) REVERT: A 19 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 27 MET cc_start: 0.7429 (ptt) cc_final: 0.6955 (mtm) REVERT: A 33 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7303 (ttpt) REVERT: A 38 GLU cc_start: 0.7672 (tp30) cc_final: 0.7359 (tp30) REVERT: A 53 MET cc_start: 0.7868 (ppp) cc_final: 0.7411 (ppp) REVERT: A 83 LYS cc_start: 0.8486 (mmtm) cc_final: 0.7971 (pttt) REVERT: B 79 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 166 ASN cc_start: 0.8981 (m-40) cc_final: 0.8624 (m110) REVERT: C 100 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8087 (ttp-170) REVERT: C 104 ASN cc_start: 0.8486 (m-40) cc_final: 0.7265 (t0) REVERT: C 166 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 211 TYR cc_start: 0.8404 (t80) cc_final: 0.7918 (t80) REVERT: C 216 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8391 (mmtt) REVERT: D 107 ARG cc_start: 0.8722 (mmt90) cc_final: 0.8521 (mmm160) REVERT: D 265 ASN cc_start: 0.8546 (t0) cc_final: 0.8115 (t0) REVERT: D 356 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8685 (pp) REVERT: E 67 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8627 (mmtt) REVERT: E 69 TYR cc_start: 0.7056 (m-80) cc_final: 0.6739 (t80) REVERT: E 89 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.6786 (t0) REVERT: E 91 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.6305 (m-10) REVERT: E 120 MET cc_start: 0.8183 (tpp) cc_final: 0.7809 (tpp) REVERT: E 192 TYR cc_start: 0.8489 (m-80) cc_final: 0.8223 (m-80) REVERT: F 101 PHE cc_start: 0.8925 (m-10) cc_final: 0.8558 (m-80) REVERT: F 136 HIS cc_start: 0.8380 (m-70) cc_final: 0.7701 (t-90) REVERT: F 450 MET cc_start: 0.8727 (mmp) cc_final: 0.8457 (mmp) REVERT: G 62 ARG cc_start: 0.8566 (ptt-90) cc_final: 0.7825 (ptt-90) REVERT: G 114 GLU cc_start: 0.8352 (tt0) cc_final: 0.7801 (tt0) REVERT: G 136 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7984 (mt-10) REVERT: G 145 MET cc_start: 0.8925 (mmt) cc_final: 0.8614 (mmt) REVERT: G 161 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: G 172 ILE cc_start: 0.9426 (mt) cc_final: 0.9147 (tp) REVERT: G 269 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: G 381 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8869 (mt) REVERT: G 567 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8806 (p) REVERT: G 657 ASP cc_start: 0.7505 (t0) cc_final: 0.7039 (t0) REVERT: H 24 GLU cc_start: 0.8453 (tt0) cc_final: 0.8177 (tt0) REVERT: H 34 ARG cc_start: 0.8771 (ptt-90) cc_final: 0.8485 (ptt-90) REVERT: H 86 TRP cc_start: 0.8893 (m100) cc_final: 0.8545 (m100) REVERT: H 155 LEU cc_start: 0.9181 (mt) cc_final: 0.8839 (tp) REVERT: H 163 GLN cc_start: 0.8775 (tt0) cc_final: 0.8393 (mt0) REVERT: H 199 ASP cc_start: 0.7608 (t0) cc_final: 0.7195 (t0) REVERT: H 260 MET cc_start: 0.8598 (tmm) cc_final: 0.8370 (tmm) REVERT: H 271 LEU cc_start: 0.9506 (mt) cc_final: 0.9173 (mt) REVERT: H 292 ASN cc_start: 0.8990 (m-40) cc_final: 0.8607 (m-40) REVERT: I 206 GLN cc_start: 0.9017 (tp40) cc_final: 0.8531 (tm-30) REVERT: I 208 ASP cc_start: 0.8340 (t70) cc_final: 0.7383 (t70) REVERT: P 174 MET cc_start: 0.7317 (mtt) cc_final: 0.6938 (mtt) REVERT: P 350 ILE cc_start: 0.9366 (tt) cc_final: 0.9143 (mt) REVERT: Q 69 GLU cc_start: 0.7339 (tp30) cc_final: 0.7086 (tp30) REVERT: Q 70 GLU cc_start: 0.7253 (tp30) cc_final: 0.6832 (tp30) REVERT: Q 74 THR cc_start: 0.7968 (p) cc_final: 0.7628 (p) REVERT: Q 106 ARG cc_start: 0.8943 (mtt-85) cc_final: 0.8569 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8463 (t0) cc_final: 0.7548 (p0) REVERT: Q 160 TYR cc_start: 0.8368 (t80) cc_final: 0.8063 (t80) REVERT: Q 164 PHE cc_start: 0.7608 (m-80) cc_final: 0.6156 (m-80) REVERT: R 47 ARG cc_start: 0.7627 (mtm110) cc_final: 0.6790 (ptt180) REVERT: S 18 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7813 (mp0) REVERT: S 31 GLN cc_start: 0.9015 (tp40) cc_final: 0.8645 (pm20) REVERT: S 80 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (m110) REVERT: T 97 LYS cc_start: 0.7271 (ttpt) cc_final: 0.7069 (ttpt) REVERT: T 99 SER cc_start: 0.7994 (m) cc_final: 0.7405 (p) REVERT: T 123 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7774 (mm-30) REVERT: V 87 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8604 (tp30) REVERT: W 58 THR cc_start: 0.8828 (m) cc_final: 0.8545 (p) REVERT: W 120 ASP cc_start: 0.7533 (p0) cc_final: 0.7309 (p0) REVERT: W 123 SER cc_start: 0.8881 (m) cc_final: 0.8449 (p) REVERT: W 126 TYR cc_start: 0.9078 (m-10) cc_final: 0.8479 (m-80) REVERT: X 44 MET cc_start: 0.8950 (tpp) cc_final: 0.8636 (tpp) REVERT: Z 10 MET cc_start: 0.8402 (mmm) cc_final: 0.8100 (mmt) REVERT: Z 21 TYR cc_start: 0.7956 (p90) cc_final: 0.7059 (p90) REVERT: Z 24 ASN cc_start: 0.8354 (t0) cc_final: 0.8148 (t0) REVERT: Z 125 TYR cc_start: 0.8840 (m-80) cc_final: 0.8529 (m-80) REVERT: a 2 TRP cc_start: 0.8866 (p-90) cc_final: 0.8324 (p-90) REVERT: a 23 THR cc_start: 0.9344 (m) cc_final: 0.9014 (p) REVERT: b 16 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6535 (tt0) REVERT: q 54 GLN cc_start: 0.7206 (tp40) cc_final: 0.6981 (tp40) REVERT: q 81 MET cc_start: 0.8255 (mtt) cc_final: 0.8044 (mtt) REVERT: q 93 MET cc_start: 0.7245 (tmm) cc_final: 0.7037 (mtp) REVERT: q 132 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7395 (tmmt) REVERT: r 109 ASP cc_start: 0.6154 (p0) cc_final: 0.5472 (p0) REVERT: s 85 LEU cc_start: 0.7147 (tp) cc_final: 0.6301 (mt) outliers start: 194 outliers final: 122 residues processed: 1027 average time/residue: 0.2074 time to fit residues: 352.8720 Evaluate side-chains 992 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 858 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER 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 185 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 91 TRP Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 276 LEU Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 163 ASN Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 ASP Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 136 GLU Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 44 TYR Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 132 LYS Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 361 optimal weight: 5.9990 chunk 386 optimal weight: 0.2980 chunk 202 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 343 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN W 102 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.103150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085153 restraints weight = 88674.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087801 restraints weight = 42135.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089537 restraints weight = 25790.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090651 restraints weight = 18657.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.091358 restraints weight = 15090.788| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34905 Z= 0.153 Angle : 0.879 74.657 47336 Z= 0.349 Chirality : 0.045 0.278 5163 Planarity : 0.005 0.124 5997 Dihedral : 9.461 161.703 4916 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 4.06 % Allowed : 23.50 % Favored : 72.43 % Cbeta Deviations : 0.00 % 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: -0.20 (0.13), residues: 4153 helix: 0.93 (0.12), residues: 1880 sheet: -0.98 (0.27), residues: 358 loop : -1.00 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 48 TYR 0.028 0.002 TYR F 63 PHE 0.029 0.001 PHE A 62 TRP 0.026 0.001 TRP H 179 HIS 0.007 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00354 (34864) covalent geometry : angle 0.68665 (47244) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.55716 ( 8) hydrogen bonds : bond 0.04088 ( 1417) hydrogen bonds : angle 4.94882 ( 4128) metal coordination : bond 0.01495 ( 37) metal coordination : angle 13.05077 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 916 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: A 8 PHE cc_start: 0.8338 (m-80) cc_final: 0.7805 (m-10) REVERT: A 19 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 27 MET cc_start: 0.7133 (ptt) cc_final: 0.6924 (mtm) REVERT: A 38 GLU cc_start: 0.7631 (tp30) cc_final: 0.7140 (tp30) REVERT: A 53 MET cc_start: 0.7791 (ppp) cc_final: 0.7353 (ppp) REVERT: A 83 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8106 (pttt) REVERT: B 79 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7968 (t0) REVERT: B 161 MET cc_start: 0.8208 (tpp) cc_final: 0.7979 (tpp) REVERT: B 166 ASN cc_start: 0.8895 (m-40) cc_final: 0.8621 (m110) REVERT: C 100 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8081 (ttp-170) REVERT: C 104 ASN cc_start: 0.8334 (m-40) cc_final: 0.7169 (t0) REVERT: C 211 TYR cc_start: 0.8402 (t80) cc_final: 0.7899 (t80) REVERT: C 216 LYS cc_start: 0.8533 (mmtt) cc_final: 0.8323 (mmtt) REVERT: D 83 ASN cc_start: 0.7762 (p0) cc_final: 0.7423 (p0) REVERT: D 193 ASP cc_start: 0.8807 (m-30) cc_final: 0.8482 (m-30) REVERT: D 265 ASN cc_start: 0.8610 (t0) cc_final: 0.8228 (t0) REVERT: E 67 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8670 (mmtt) REVERT: E 120 MET cc_start: 0.8109 (tpp) cc_final: 0.7788 (tpp) REVERT: E 192 TYR cc_start: 0.8575 (m-80) cc_final: 0.7958 (m-80) REVERT: F 53 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.6996 (mt) REVERT: F 63 TYR cc_start: 0.8758 (t80) cc_final: 0.8429 (t80) REVERT: F 101 PHE cc_start: 0.8895 (m-10) cc_final: 0.8560 (m-80) REVERT: F 136 HIS cc_start: 0.8282 (m-70) cc_final: 0.7763 (t-90) REVERT: F 290 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7541 (mm-30) REVERT: F 450 MET cc_start: 0.8613 (mmp) cc_final: 0.8406 (mmp) REVERT: F 452 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8146 (mmp80) REVERT: G 42 MET cc_start: 0.8949 (tpp) cc_final: 0.8470 (tpp) REVERT: G 62 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.7870 (ptt-90) REVERT: G 114 GLU cc_start: 0.8269 (tt0) cc_final: 0.7774 (tt0) REVERT: G 136 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7832 (mt-10) REVERT: G 145 MET cc_start: 0.8825 (mmt) cc_final: 0.8524 (mmt) REVERT: G 161 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: G 172 ILE cc_start: 0.9394 (mt) cc_final: 0.9176 (tp) REVERT: G 269 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7174 (pt0) REVERT: G 329 MET cc_start: 0.8204 (mmm) cc_final: 0.7042 (mmm) REVERT: G 381 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8803 (mt) REVERT: G 567 VAL cc_start: 0.9176 (OUTLIER) cc_final: 0.8860 (p) REVERT: G 657 ASP cc_start: 0.7401 (t0) cc_final: 0.6904 (t0) REVERT: H 32 GLN cc_start: 0.9227 (mt0) cc_final: 0.8769 (mt0) REVERT: H 34 ARG cc_start: 0.8713 (ptt-90) cc_final: 0.8361 (ptt-90) REVERT: H 86 TRP cc_start: 0.8921 (m100) cc_final: 0.8641 (m100) REVERT: H 163 GLN cc_start: 0.8696 (tt0) cc_final: 0.8365 (mt0) REVERT: H 181 MET cc_start: 0.8327 (mtt) cc_final: 0.8075 (mtt) REVERT: H 184 MET cc_start: 0.9084 (mmm) cc_final: 0.8788 (mtp) REVERT: H 199 ASP cc_start: 0.7526 (t0) cc_final: 0.6802 (t0) REVERT: H 202 GLU cc_start: 0.6699 (tp30) cc_final: 0.5895 (tt0) REVERT: H 204 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7347 (tm-30) REVERT: H 241 ILE cc_start: 0.9397 (mm) cc_final: 0.9180 (mt) REVERT: H 260 MET cc_start: 0.8655 (tmm) cc_final: 0.8228 (tmm) REVERT: H 271 LEU cc_start: 0.9448 (mt) cc_final: 0.9123 (mt) REVERT: H 292 ASN cc_start: 0.8935 (m-40) cc_final: 0.8663 (m-40) REVERT: I 36 TYR cc_start: 0.8581 (p90) cc_final: 0.7952 (p90) REVERT: I 76 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7309 (t80) REVERT: I 177 THR cc_start: 0.8279 (p) cc_final: 0.8047 (t) REVERT: I 181 GLU cc_start: 0.8161 (mp0) cc_final: 0.7827 (mp0) REVERT: I 206 GLN cc_start: 0.8963 (tp40) cc_final: 0.8536 (tm-30) REVERT: I 208 ASP cc_start: 0.8303 (t70) cc_final: 0.7419 (t70) REVERT: P 174 MET cc_start: 0.7265 (mtt) cc_final: 0.6963 (mtt) REVERT: Q 57 GLU cc_start: 0.8162 (tp30) cc_final: 0.7156 (mp0) REVERT: Q 69 GLU cc_start: 0.7366 (tp30) cc_final: 0.7106 (tp30) REVERT: Q 70 GLU cc_start: 0.7200 (tp30) cc_final: 0.6755 (tp30) REVERT: Q 74 THR cc_start: 0.8069 (p) cc_final: 0.7667 (p) REVERT: Q 106 ARG cc_start: 0.8866 (mtt-85) cc_final: 0.8502 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8466 (t0) cc_final: 0.7582 (p0) REVERT: Q 160 TYR cc_start: 0.8372 (t80) cc_final: 0.8051 (t80) REVERT: Q 164 PHE cc_start: 0.7653 (m-80) cc_final: 0.6294 (m-80) REVERT: R 47 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7066 (ptt180) REVERT: R 95 LEU cc_start: 0.8512 (tp) cc_final: 0.7964 (tp) REVERT: S 31 GLN cc_start: 0.8948 (tp40) cc_final: 0.8665 (pm20) REVERT: S 62 GLN cc_start: 0.8555 (pm20) cc_final: 0.8232 (pm20) REVERT: T 99 SER cc_start: 0.7913 (m) cc_final: 0.7327 (p) REVERT: V 87 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: W 45 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: W 58 THR cc_start: 0.8810 (m) cc_final: 0.8552 (p) REVERT: W 123 SER cc_start: 0.8853 (m) cc_final: 0.8427 (p) REVERT: W 126 TYR cc_start: 0.9098 (m-10) cc_final: 0.8576 (m-80) REVERT: Z 21 TYR cc_start: 0.8015 (p90) cc_final: 0.7139 (p90) REVERT: Z 24 ASN cc_start: 0.8381 (t0) cc_final: 0.8156 (t0) REVERT: a 23 THR cc_start: 0.9358 (m) cc_final: 0.9010 (p) REVERT: b 16 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6549 (tt0) REVERT: b 32 MET cc_start: 0.9239 (mmt) cc_final: 0.8914 (mmt) REVERT: q 54 GLN cc_start: 0.7455 (tp40) cc_final: 0.7150 (tp40) REVERT: q 81 MET cc_start: 0.8324 (mtt) cc_final: 0.8098 (mtt) REVERT: r 109 ASP cc_start: 0.6205 (p0) cc_final: 0.5509 (p0) REVERT: s 85 LEU cc_start: 0.7193 (tp) cc_final: 0.6384 (mt) outliers start: 148 outliers final: 107 residues processed: 996 average time/residue: 0.2052 time to fit residues: 338.6110 Evaluate side-chains 973 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 855 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 381 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 528 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 117 THR Chi-restraints excluded: chain Q residue 163 ASN Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 114 ASP Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 132 LYS Chi-restraints excluded: chain r residue 101 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 366 optimal weight: 0.6980 chunk 200 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 357 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 190 ASN ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085829 restraints weight = 89179.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088494 restraints weight = 42259.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090237 restraints weight = 25763.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091370 restraints weight = 18585.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092082 restraints weight = 14975.812| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34905 Z= 0.152 Angle : 0.883 73.833 47336 Z= 0.348 Chirality : 0.045 0.281 5163 Planarity : 0.005 0.125 5997 Dihedral : 9.280 161.895 4916 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 4.23 % Allowed : 23.75 % Favored : 72.02 % Cbeta Deviations : 0.00 % 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: -0.18 (0.13), residues: 4153 helix: 0.94 (0.12), residues: 1879 sheet: -0.96 (0.27), residues: 357 loop : -0.99 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 153 TYR 0.040 0.002 TYR E 69 PHE 0.031 0.001 PHE A 62 TRP 0.021 0.001 TRP I 63 HIS 0.006 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00358 (34864) covalent geometry : angle 0.68948 (47244) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.52431 ( 8) hydrogen bonds : bond 0.03994 ( 1417) hydrogen bonds : angle 4.91142 ( 4128) metal coordination : bond 0.01340 ( 37) metal coordination : angle 13.09303 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 893 time to evaluate : 1.364 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: A 8 PHE cc_start: 0.8294 (m-80) cc_final: 0.7771 (m-10) REVERT: A 19 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 38 GLU cc_start: 0.7597 (tp30) cc_final: 0.7136 (tp30) REVERT: A 53 MET cc_start: 0.7745 (ppp) cc_final: 0.7480 (ppp) REVERT: A 83 LYS cc_start: 0.8385 (mmtm) cc_final: 0.8175 (pttt) REVERT: B 79 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8086 (t0) REVERT: B 166 ASN cc_start: 0.8857 (m-40) cc_final: 0.8589 (m110) REVERT: C 100 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.8132 (ttp-170) REVERT: C 104 ASN cc_start: 0.8321 (m-40) cc_final: 0.7102 (t0) REVERT: C 185 ARG cc_start: 0.8650 (ptp90) cc_final: 0.8397 (ptp90) REVERT: C 211 TYR cc_start: 0.8479 (t80) cc_final: 0.8042 (t80) REVERT: D 83 ASN cc_start: 0.7644 (p0) cc_final: 0.7339 (p0) REVERT: D 104 GLU cc_start: 0.7868 (tt0) cc_final: 0.7600 (tt0) REVERT: D 107 ARG cc_start: 0.8630 (mmt90) cc_final: 0.8393 (mmm160) REVERT: D 123 LEU cc_start: 0.8934 (tp) cc_final: 0.8730 (tp) REVERT: D 193 ASP cc_start: 0.8781 (m-30) cc_final: 0.8418 (m-30) REVERT: D 265 ASN cc_start: 0.8744 (t0) cc_final: 0.8118 (t0) REVERT: D 356 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8744 (pp) REVERT: E 68 ASN cc_start: 0.8614 (t0) cc_final: 0.8280 (t0) REVERT: E 69 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.7211 (t80) REVERT: E 120 MET cc_start: 0.8127 (tpp) cc_final: 0.7863 (ttm) REVERT: E 184 MET cc_start: 0.6334 (ptm) cc_final: 0.5738 (ptt) REVERT: F 53 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.6971 (mt) REVERT: F 63 TYR cc_start: 0.8770 (t80) cc_final: 0.8488 (t80) REVERT: F 101 PHE cc_start: 0.8879 (m-10) cc_final: 0.8532 (m-80) REVERT: F 136 HIS cc_start: 0.8203 (m-70) cc_final: 0.7871 (t-90) REVERT: F 170 GLN cc_start: 0.8375 (mt0) cc_final: 0.8104 (mt0) REVERT: F 290 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7592 (mm-30) REVERT: G 62 ARG cc_start: 0.8531 (ptt-90) cc_final: 0.7866 (ptt-90) REVERT: G 97 MET cc_start: 0.8147 (mtp) cc_final: 0.7826 (mtm) REVERT: G 114 GLU cc_start: 0.8258 (tt0) cc_final: 0.7775 (tt0) REVERT: G 136 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7907 (mt-10) REVERT: G 145 MET cc_start: 0.8794 (mmt) cc_final: 0.8519 (mmt) REVERT: G 172 ILE cc_start: 0.9389 (mt) cc_final: 0.9178 (tp) REVERT: G 213 MET cc_start: 0.8605 (ppp) cc_final: 0.8092 (ppp) REVERT: G 269 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: G 329 MET cc_start: 0.8220 (mmm) cc_final: 0.7158 (mmm) REVERT: G 567 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8831 (p) REVERT: G 657 ASP cc_start: 0.7416 (t0) cc_final: 0.6928 (t0) REVERT: G 663 ASN cc_start: 0.6920 (m-40) cc_final: 0.6494 (m-40) REVERT: H 32 GLN cc_start: 0.9230 (mt0) cc_final: 0.8845 (mt0) REVERT: H 86 TRP cc_start: 0.8945 (m100) cc_final: 0.8670 (m100) REVERT: H 163 GLN cc_start: 0.8676 (tt0) cc_final: 0.8324 (mt0) REVERT: H 181 MET cc_start: 0.8309 (mtt) cc_final: 0.8061 (mtt) REVERT: H 184 MET cc_start: 0.9164 (mmm) cc_final: 0.8822 (mmm) REVERT: H 199 ASP cc_start: 0.7544 (t0) cc_final: 0.6764 (t0) REVERT: H 202 GLU cc_start: 0.6633 (tp30) cc_final: 0.6071 (tt0) REVERT: H 204 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 214 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8327 (mm-30) REVERT: H 260 MET cc_start: 0.8724 (tmm) cc_final: 0.8514 (tmm) REVERT: H 292 ASN cc_start: 0.8999 (m-40) cc_final: 0.8780 (m-40) REVERT: I 36 TYR cc_start: 0.8402 (p90) cc_final: 0.7888 (p90) REVERT: I 76 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7395 (t80) REVERT: I 177 THR cc_start: 0.8407 (p) cc_final: 0.8170 (t) REVERT: I 206 GLN cc_start: 0.8961 (tp40) cc_final: 0.8427 (tm-30) REVERT: I 208 ASP cc_start: 0.8253 (t70) cc_final: 0.7376 (t70) REVERT: P 337 ASP cc_start: 0.7926 (m-30) cc_final: 0.7713 (m-30) REVERT: Q 69 GLU cc_start: 0.7444 (tp30) cc_final: 0.7179 (tp30) REVERT: Q 70 GLU cc_start: 0.7244 (tp30) cc_final: 0.6799 (tp30) REVERT: Q 74 THR cc_start: 0.8095 (p) cc_final: 0.7681 (p) REVERT: Q 106 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8508 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8398 (t0) cc_final: 0.7523 (p0) REVERT: R 47 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7131 (ptt180) REVERT: R 95 LEU cc_start: 0.8461 (tp) cc_final: 0.8106 (tp) REVERT: S 31 GLN cc_start: 0.8919 (tp40) cc_final: 0.8693 (pm20) REVERT: S 66 TRP cc_start: 0.8614 (m100) cc_final: 0.8286 (m100) REVERT: T 99 SER cc_start: 0.7981 (m) cc_final: 0.7382 (p) REVERT: V 47 TYR cc_start: 0.8682 (m-80) cc_final: 0.8048 (m-80) REVERT: V 87 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8530 (tp30) REVERT: W 45 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8501 (tp30) REVERT: W 58 THR cc_start: 0.8852 (m) cc_final: 0.8605 (p) REVERT: W 123 SER cc_start: 0.8748 (m) cc_final: 0.8180 (p) REVERT: W 126 TYR cc_start: 0.9109 (m-10) cc_final: 0.8616 (m-80) REVERT: Z 21 TYR cc_start: 0.8116 (p90) cc_final: 0.7191 (p90) REVERT: Z 24 ASN cc_start: 0.8427 (t0) cc_final: 0.8186 (t0) REVERT: Z 133 MET cc_start: 0.7703 (ttt) cc_final: 0.7453 (tmm) REVERT: a 2 TRP cc_start: 0.8772 (p-90) cc_final: 0.8503 (p-90) REVERT: a 6 LEU cc_start: 0.9367 (mm) cc_final: 0.9113 (mm) REVERT: a 11 ILE cc_start: 0.9089 (mm) cc_final: 0.8844 (tp) REVERT: a 23 THR cc_start: 0.9352 (m) cc_final: 0.8986 (p) REVERT: b 16 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6624 (tt0) REVERT: b 32 MET cc_start: 0.9260 (mmt) cc_final: 0.8941 (mmt) REVERT: r 109 ASP cc_start: 0.6236 (p0) cc_final: 0.5554 (p0) REVERT: s 85 LEU cc_start: 0.7216 (tp) cc_final: 0.6438 (mt) outliers start: 154 outliers final: 109 residues processed: 986 average time/residue: 0.2070 time to fit residues: 339.1158 Evaluate side-chains 959 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 840 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 528 LEU Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 97 ILE Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 94 THR Chi-restraints excluded: chain q residue 132 LYS Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 29 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 407 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 376 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 ASN W 73 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.100501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.081956 restraints weight = 91216.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084627 restraints weight = 42988.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086405 restraints weight = 26365.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087555 restraints weight = 19053.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.088281 restraints weight = 15433.111| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 34905 Z= 0.204 Angle : 0.922 76.073 47336 Z= 0.367 Chirality : 0.046 0.277 5163 Planarity : 0.005 0.126 5997 Dihedral : 9.293 159.028 4916 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 4.28 % Allowed : 24.27 % Favored : 71.44 % Cbeta Deviations : 0.00 % 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: -0.23 (0.13), residues: 4153 helix: 0.89 (0.12), residues: 1880 sheet: -1.08 (0.27), residues: 373 loop : -0.97 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 48 TYR 0.026 0.002 TYR I 185 PHE 0.024 0.002 PHE A 62 TRP 0.029 0.002 TRP I 63 HIS 0.007 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00477 (34864) covalent geometry : angle 0.72167 (47244) SS BOND : bond 0.00278 ( 4) SS BOND : angle 1.57862 ( 8) hydrogen bonds : bond 0.04143 ( 1417) hydrogen bonds : angle 4.99669 ( 4128) metal coordination : bond 0.02158 ( 37) metal coordination : angle 13.64303 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 855 time to evaluate : 1.403 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: A 8 PHE cc_start: 0.8349 (m-80) cc_final: 0.7861 (m-10) REVERT: A 19 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8374 (tp) REVERT: A 38 GLU cc_start: 0.7597 (tp30) cc_final: 0.7090 (tp30) REVERT: A 42 ASP cc_start: 0.8916 (p0) cc_final: 0.8666 (p0) REVERT: A 53 MET cc_start: 0.7827 (ppp) cc_final: 0.7483 (ppp) REVERT: A 83 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8219 (pttt) REVERT: B 83 ASN cc_start: 0.8782 (m-40) cc_final: 0.8284 (m-40) REVERT: B 166 ASN cc_start: 0.9037 (m-40) cc_final: 0.8601 (m110) REVERT: B 201 LEU cc_start: 0.9076 (tt) cc_final: 0.8767 (tt) REVERT: C 100 ARG cc_start: 0.8481 (ttp-170) cc_final: 0.8195 (ttp-170) REVERT: C 104 ASN cc_start: 0.8576 (m-40) cc_final: 0.7282 (t0) REVERT: C 185 ARG cc_start: 0.8708 (ptp90) cc_final: 0.8463 (ptp90) REVERT: C 211 TYR cc_start: 0.8577 (t80) cc_final: 0.8195 (t80) REVERT: C 216 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8491 (mmtt) REVERT: D 83 ASN cc_start: 0.7656 (p0) cc_final: 0.7303 (p0) REVERT: D 123 LEU cc_start: 0.9067 (tp) cc_final: 0.8853 (tp) REVERT: D 193 ASP cc_start: 0.8825 (m-30) cc_final: 0.8455 (m-30) REVERT: D 261 MET cc_start: 0.9098 (tpp) cc_final: 0.8858 (mmp) REVERT: D 265 ASN cc_start: 0.8882 (t0) cc_final: 0.8159 (t0) REVERT: D 356 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8755 (pp) REVERT: E 69 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6918 (t80) REVERT: E 112 TYR cc_start: 0.9367 (m-80) cc_final: 0.8624 (m-80) REVERT: E 113 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8401 (mt-10) REVERT: E 120 MET cc_start: 0.8266 (tpp) cc_final: 0.7809 (ttm) REVERT: E 184 MET cc_start: 0.5983 (ptm) cc_final: 0.5702 (ptt) REVERT: E 189 ASP cc_start: 0.6420 (t0) cc_final: 0.6068 (t0) REVERT: F 53 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7161 (mt) REVERT: F 63 TYR cc_start: 0.8888 (t80) cc_final: 0.8631 (t80) REVERT: F 101 PHE cc_start: 0.8871 (m-10) cc_final: 0.8518 (m-80) REVERT: F 136 HIS cc_start: 0.8151 (m-70) cc_final: 0.7808 (t-90) REVERT: F 170 GLN cc_start: 0.8477 (mt0) cc_final: 0.8172 (mt0) REVERT: F 290 GLU cc_start: 0.8657 (mt-10) cc_final: 0.7750 (mm-30) REVERT: F 390 ASP cc_start: 0.8103 (t0) cc_final: 0.7800 (t0) REVERT: F 429 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7711 (t0) REVERT: F 450 MET cc_start: 0.8553 (mmp) cc_final: 0.8227 (mmp) REVERT: G 97 MET cc_start: 0.8249 (mtp) cc_final: 0.7917 (mtm) REVERT: G 114 GLU cc_start: 0.8444 (tt0) cc_final: 0.8168 (tt0) REVERT: G 136 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7883 (mt-10) REVERT: G 145 MET cc_start: 0.8894 (mmt) cc_final: 0.8679 (mmt) REVERT: G 161 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: G 172 ILE cc_start: 0.9462 (mt) cc_final: 0.9157 (tp) REVERT: G 215 MET cc_start: 0.8039 (mtm) cc_final: 0.7804 (mtt) REVERT: G 269 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: G 382 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8084 (ttm-80) REVERT: G 567 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8768 (p) REVERT: G 657 ASP cc_start: 0.7603 (t0) cc_final: 0.7178 (t0) REVERT: H 32 GLN cc_start: 0.9316 (mt0) cc_final: 0.8972 (mt0) REVERT: H 53 MET cc_start: 0.8912 (tpp) cc_final: 0.8583 (ttm) REVERT: H 86 TRP cc_start: 0.9182 (m100) cc_final: 0.8889 (m100) REVERT: H 146 MET cc_start: 0.9011 (mmt) cc_final: 0.8254 (tpp) REVERT: H 163 GLN cc_start: 0.8857 (tt0) cc_final: 0.8419 (mt0) REVERT: H 184 MET cc_start: 0.9163 (mmm) cc_final: 0.8600 (mmm) REVERT: H 185 TRP cc_start: 0.8922 (t-100) cc_final: 0.8403 (t-100) REVERT: H 199 ASP cc_start: 0.7696 (t0) cc_final: 0.7113 (t0) REVERT: H 202 GLU cc_start: 0.6961 (tp30) cc_final: 0.6622 (tt0) REVERT: H 204 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7348 (tm-30) REVERT: H 214 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8402 (mm-30) REVERT: H 260 MET cc_start: 0.8898 (tmm) cc_final: 0.8680 (tmm) REVERT: H 292 ASN cc_start: 0.9065 (m-40) cc_final: 0.8829 (m-40) REVERT: I 36 TYR cc_start: 0.8428 (p90) cc_final: 0.7811 (p90) REVERT: I 72 MET cc_start: 0.9312 (tpp) cc_final: 0.8892 (tpp) REVERT: I 76 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7462 (t80) REVERT: I 208 ASP cc_start: 0.8374 (t70) cc_final: 0.7363 (t70) REVERT: P 55 VAL cc_start: 0.8923 (t) cc_final: 0.8675 (p) REVERT: P 68 TYR cc_start: 0.9182 (m-10) cc_final: 0.8960 (m-10) REVERT: P 154 GLN cc_start: 0.8292 (tp40) cc_final: 0.7982 (tp40) REVERT: P 332 LEU cc_start: 0.8399 (tp) cc_final: 0.8108 (tt) REVERT: P 337 ASP cc_start: 0.8180 (m-30) cc_final: 0.7955 (m-30) REVERT: Q 69 GLU cc_start: 0.7490 (tp30) cc_final: 0.7233 (tp30) REVERT: Q 70 GLU cc_start: 0.7360 (tp30) cc_final: 0.6877 (tp30) REVERT: Q 74 THR cc_start: 0.8045 (p) cc_final: 0.7584 (p) REVERT: Q 106 ARG cc_start: 0.8940 (mtt-85) cc_final: 0.8334 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8285 (t0) cc_final: 0.7446 (p0) REVERT: R 47 ARG cc_start: 0.7670 (mtm110) cc_final: 0.6984 (ptt180) REVERT: R 95 LEU cc_start: 0.8476 (tp) cc_final: 0.7934 (tp) REVERT: S 31 GLN cc_start: 0.8998 (tp40) cc_final: 0.8663 (pm20) REVERT: S 66 TRP cc_start: 0.8675 (m100) cc_final: 0.8318 (m100) REVERT: T 92 LYS cc_start: 0.8533 (tttm) cc_final: 0.8224 (tttm) REVERT: T 99 SER cc_start: 0.8093 (m) cc_final: 0.7469 (p) REVERT: V 87 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: W 37 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8852 (mt-10) REVERT: W 43 TYR cc_start: 0.8578 (t80) cc_final: 0.7829 (t80) REVERT: W 45 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: W 58 THR cc_start: 0.9043 (m) cc_final: 0.8810 (p) REVERT: W 120 ASP cc_start: 0.8212 (p0) cc_final: 0.7908 (p0) REVERT: W 126 TYR cc_start: 0.9155 (m-10) cc_final: 0.8741 (m-80) REVERT: X 85 TYR cc_start: 0.8267 (t80) cc_final: 0.7611 (t80) REVERT: Z 21 TYR cc_start: 0.8364 (p90) cc_final: 0.7399 (p90) REVERT: Z 24 ASN cc_start: 0.8595 (t0) cc_final: 0.8354 (t0) REVERT: a 2 TRP cc_start: 0.8835 (p-90) cc_final: 0.8579 (p90) REVERT: a 11 ILE cc_start: 0.9127 (mm) cc_final: 0.8859 (tp) REVERT: a 23 THR cc_start: 0.9348 (m) cc_final: 0.8987 (p) REVERT: b 16 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6618 (tt0) REVERT: b 32 MET cc_start: 0.9410 (mmt) cc_final: 0.8980 (mmt) REVERT: s 85 LEU cc_start: 0.7305 (tp) cc_final: 0.6511 (mt) outliers start: 156 outliers final: 113 residues processed: 936 average time/residue: 0.1987 time to fit residues: 310.6901 Evaluate side-chains 934 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 809 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 133 VAL 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 185 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 429 ASP Chi-restraints excluded: chain G residue 30 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 242 VAL Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 117 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain q residue 132 LYS Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 301 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 283 optimal weight: 0.0020 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN W 102 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084894 restraints weight = 89812.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087620 restraints weight = 41815.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089433 restraints weight = 25270.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.090569 restraints weight = 18100.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091288 restraints weight = 14599.077| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 34905 Z= 0.139 Angle : 0.892 72.139 47336 Z= 0.355 Chirality : 0.044 0.270 5163 Planarity : 0.005 0.125 5997 Dihedral : 9.134 161.155 4916 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 3.27 % Allowed : 25.70 % Favored : 71.03 % Cbeta Deviations : 0.00 % 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: -0.21 (0.13), residues: 4153 helix: 0.93 (0.12), residues: 1880 sheet: -1.10 (0.26), residues: 364 loop : -0.99 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 61 TYR 0.043 0.002 TYR E 192 PHE 0.042 0.002 PHE A 62 TRP 0.036 0.001 TRP H 179 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00324 (34864) covalent geometry : angle 0.70595 (47244) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.50577 ( 8) hydrogen bonds : bond 0.03949 ( 1417) hydrogen bonds : angle 4.94335 ( 4128) metal coordination : bond 0.01048 ( 37) metal coordination : angle 12.94956 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 895 time to evaluate : 1.354 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: A 8 PHE cc_start: 0.8317 (m-80) cc_final: 0.7843 (m-10) REVERT: A 38 GLU cc_start: 0.7429 (tp30) cc_final: 0.6947 (tp30) REVERT: A 42 ASP cc_start: 0.8903 (p0) cc_final: 0.8419 (p0) REVERT: A 53 MET cc_start: 0.7867 (ppp) cc_final: 0.7478 (ppp) REVERT: A 72 LEU cc_start: 0.9218 (mt) cc_final: 0.8961 (tp) REVERT: A 83 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8262 (pttt) REVERT: B 82 ILE cc_start: 0.8999 (tp) cc_final: 0.8621 (tp) REVERT: B 107 MET cc_start: 0.9329 (ttp) cc_final: 0.8937 (tmm) REVERT: B 166 ASN cc_start: 0.8912 (m-40) cc_final: 0.8533 (m110) REVERT: C 74 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8139 (tm-30) REVERT: C 100 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8097 (ttp-170) REVERT: C 104 ASN cc_start: 0.8322 (m-40) cc_final: 0.7090 (t0) REVERT: C 145 TYR cc_start: 0.9333 (p90) cc_final: 0.9101 (p90) REVERT: C 185 ARG cc_start: 0.8579 (ptp90) cc_final: 0.8357 (ptp90) REVERT: C 211 TYR cc_start: 0.8542 (t80) cc_final: 0.8153 (t80) REVERT: D 83 ASN cc_start: 0.7493 (p0) cc_final: 0.7157 (p0) REVERT: D 123 LEU cc_start: 0.8939 (tp) cc_final: 0.8562 (tp) REVERT: D 193 ASP cc_start: 0.8805 (m-30) cc_final: 0.8445 (m-30) REVERT: D 204 PHE cc_start: 0.9034 (m-80) cc_final: 0.8822 (m-10) REVERT: D 257 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7973 (mt-10) REVERT: D 265 ASN cc_start: 0.8997 (t0) cc_final: 0.8284 (t0) REVERT: D 296 SER cc_start: 0.8995 (m) cc_final: 0.8414 (t) REVERT: D 356 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8728 (pp) REVERT: E 61 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7830 (mtt-85) REVERT: E 69 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6978 (t80) REVERT: E 112 TYR cc_start: 0.9339 (m-80) cc_final: 0.8554 (m-80) REVERT: E 120 MET cc_start: 0.8246 (tpp) cc_final: 0.7863 (ttm) REVERT: E 153 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.7923 (mtm-85) REVERT: E 184 MET cc_start: 0.5926 (ptm) cc_final: 0.5639 (ptt) REVERT: E 189 ASP cc_start: 0.6529 (t0) cc_final: 0.6317 (t0) REVERT: F 53 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7147 (mt) REVERT: F 64 LYS cc_start: 0.6078 (mmtt) cc_final: 0.5787 (tppt) REVERT: F 101 PHE cc_start: 0.8807 (m-10) cc_final: 0.8481 (m-80) REVERT: F 136 HIS cc_start: 0.8046 (m-70) cc_final: 0.7718 (t-90) REVERT: F 170 GLN cc_start: 0.8483 (mt0) cc_final: 0.8149 (mt0) REVERT: F 208 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7908 (tm-30) REVERT: F 290 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7597 (mm-30) REVERT: F 337 MET cc_start: 0.8012 (tpp) cc_final: 0.7747 (tpp) REVERT: F 390 ASP cc_start: 0.8088 (t0) cc_final: 0.7773 (t0) REVERT: F 450 MET cc_start: 0.8523 (mmp) cc_final: 0.8202 (mmp) REVERT: G 97 MET cc_start: 0.8105 (mtp) cc_final: 0.7769 (mtm) REVERT: G 114 GLU cc_start: 0.8416 (tt0) cc_final: 0.8027 (pt0) REVERT: G 136 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7413 (mt-10) REVERT: G 145 MET cc_start: 0.8807 (mmt) cc_final: 0.8582 (mmt) REVERT: G 161 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: G 260 ASN cc_start: 0.9090 (m-40) cc_final: 0.8868 (m-40) REVERT: G 269 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7173 (pt0) REVERT: G 567 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8738 (p) REVERT: G 602 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8258 (ttp-110) REVERT: G 657 ASP cc_start: 0.7583 (t0) cc_final: 0.7187 (t0) REVERT: H 17 MET cc_start: 0.8861 (tmm) cc_final: 0.8579 (tmm) REVERT: H 32 GLN cc_start: 0.9378 (mt0) cc_final: 0.9068 (mt0) REVERT: H 53 MET cc_start: 0.8683 (tpp) cc_final: 0.8323 (ttm) REVERT: H 86 TRP cc_start: 0.9133 (m100) cc_final: 0.8832 (m100) REVERT: H 146 MET cc_start: 0.9081 (mmt) cc_final: 0.8216 (tpp) REVERT: H 163 GLN cc_start: 0.8805 (tt0) cc_final: 0.8364 (mt0) REVERT: H 181 MET cc_start: 0.8179 (mtt) cc_final: 0.7765 (mpt) REVERT: H 184 MET cc_start: 0.9245 (mmm) cc_final: 0.8623 (mmm) REVERT: H 185 TRP cc_start: 0.8798 (t-100) cc_final: 0.8213 (t-100) REVERT: H 199 ASP cc_start: 0.7608 (t0) cc_final: 0.6841 (t0) REVERT: H 202 GLU cc_start: 0.6572 (tp30) cc_final: 0.6206 (tt0) REVERT: H 204 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7225 (tm-30) REVERT: H 214 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8350 (mm-30) REVERT: H 260 MET cc_start: 0.8848 (tmm) cc_final: 0.8254 (tmm) REVERT: H 292 ASN cc_start: 0.9018 (m-40) cc_final: 0.8797 (m-40) REVERT: I 36 TYR cc_start: 0.8288 (p90) cc_final: 0.7834 (p90) REVERT: I 72 MET cc_start: 0.9252 (tpp) cc_final: 0.8821 (tpp) REVERT: I 76 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7599 (t80) REVERT: I 177 THR cc_start: 0.8380 (p) cc_final: 0.7954 (t) REVERT: I 208 ASP cc_start: 0.8349 (t70) cc_final: 0.7440 (t70) REVERT: P 55 VAL cc_start: 0.8879 (t) cc_final: 0.8629 (p) REVERT: P 154 GLN cc_start: 0.8275 (tp40) cc_final: 0.7948 (tp40) REVERT: P 332 LEU cc_start: 0.8415 (tp) cc_final: 0.8052 (tt) REVERT: Q 69 GLU cc_start: 0.7491 (tp30) cc_final: 0.7220 (tp30) REVERT: Q 70 GLU cc_start: 0.7327 (tp30) cc_final: 0.6899 (tp30) REVERT: Q 74 THR cc_start: 0.7979 (p) cc_final: 0.7510 (p) REVERT: Q 106 ARG cc_start: 0.8906 (mtt-85) cc_final: 0.8289 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8246 (t0) cc_final: 0.7505 (p0) REVERT: R 47 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7115 (ptt180) REVERT: R 93 ILE cc_start: 0.9324 (mt) cc_final: 0.8991 (mt) REVERT: R 95 LEU cc_start: 0.8402 (tp) cc_final: 0.7991 (tp) REVERT: S 31 GLN cc_start: 0.8950 (tp40) cc_final: 0.8665 (pm20) REVERT: S 53 ILE cc_start: 0.8577 (mm) cc_final: 0.8280 (tp) REVERT: S 66 TRP cc_start: 0.8549 (m100) cc_final: 0.8115 (m100) REVERT: T 92 LYS cc_start: 0.8533 (tttm) cc_final: 0.8281 (tttm) REVERT: T 99 SER cc_start: 0.8085 (m) cc_final: 0.7475 (p) REVERT: V 87 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: W 37 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8789 (mt-10) REVERT: W 43 TYR cc_start: 0.8281 (t80) cc_final: 0.7971 (t80) REVERT: W 58 THR cc_start: 0.9013 (m) cc_final: 0.8791 (p) REVERT: W 102 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7637 (mm110) REVERT: W 126 TYR cc_start: 0.9135 (m-10) cc_final: 0.8719 (m-80) REVERT: Z 21 TYR cc_start: 0.8439 (p90) cc_final: 0.7379 (p90) REVERT: Z 24 ASN cc_start: 0.8611 (t0) cc_final: 0.8384 (t0) REVERT: Z 133 MET cc_start: 0.7744 (ttt) cc_final: 0.7299 (tmm) REVERT: a 11 ILE cc_start: 0.9075 (mm) cc_final: 0.8764 (tp) REVERT: a 23 THR cc_start: 0.9291 (m) cc_final: 0.8881 (p) REVERT: b 16 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6596 (tt0) REVERT: b 32 MET cc_start: 0.9405 (mmt) cc_final: 0.8986 (mmt) REVERT: b 44 MET cc_start: 0.8409 (ptp) cc_final: 0.8063 (ptp) REVERT: r 109 ASP cc_start: 0.6304 (p0) cc_final: 0.5597 (p0) REVERT: s 85 LEU cc_start: 0.7284 (tp) cc_final: 0.6490 (mt) outliers start: 119 outliers final: 92 residues processed: 961 average time/residue: 0.2124 time to fit residues: 338.8275 Evaluate side-chains 963 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 861 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 133 VAL 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 185 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 555 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain q residue 132 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 126 optimal weight: 4.9990 chunk 218 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 410 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 180 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN ** E 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN H 235 ASN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN W 73 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083309 restraints weight = 90767.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086003 restraints weight = 42647.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087790 restraints weight = 26027.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088909 restraints weight = 18802.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089558 restraints weight = 15270.529| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34905 Z= 0.175 Angle : 0.921 73.693 47336 Z= 0.370 Chirality : 0.046 0.255 5163 Planarity : 0.005 0.126 5997 Dihedral : 9.069 158.537 4916 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 3.08 % Allowed : 26.14 % Favored : 70.79 % Cbeta Deviations : 0.00 % 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: -0.24 (0.13), residues: 4153 helix: 0.89 (0.12), residues: 1867 sheet: -1.17 (0.26), residues: 383 loop : -0.96 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 48 TYR 0.025 0.002 TYR T 85 PHE 0.041 0.002 PHE A 62 TRP 0.030 0.002 TRP H 179 HIS 0.006 0.001 HIS F 457 Details of bonding type rmsd covalent geometry : bond 0.00415 (34864) covalent geometry : angle 0.73242 (47244) SS BOND : bond 0.00244 ( 4) SS BOND : angle 1.56489 ( 8) hydrogen bonds : bond 0.04031 ( 1417) hydrogen bonds : angle 4.97903 ( 4128) metal coordination : bond 0.01647 ( 37) metal coordination : angle 13.26885 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 857 time to evaluate : 1.336 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: A 8 PHE cc_start: 0.8338 (m-80) cc_final: 0.7877 (m-10) REVERT: A 19 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 38 GLU cc_start: 0.7508 (tp30) cc_final: 0.7011 (tp30) REVERT: A 53 MET cc_start: 0.7950 (ppp) cc_final: 0.7615 (ppp) REVERT: A 83 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8333 (pttt) REVERT: B 107 MET cc_start: 0.9365 (ttp) cc_final: 0.8852 (tmm) REVERT: B 166 ASN cc_start: 0.8990 (m-40) cc_final: 0.8700 (m110) REVERT: C 74 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 100 ARG cc_start: 0.8446 (ttp-170) cc_final: 0.8110 (ttp-170) REVERT: C 104 ASN cc_start: 0.8420 (m-40) cc_final: 0.7135 (t0) REVERT: C 185 ARG cc_start: 0.8662 (ptp90) cc_final: 0.8352 (ptp90) REVERT: C 211 TYR cc_start: 0.8595 (t80) cc_final: 0.8232 (t80) REVERT: D 83 ASN cc_start: 0.7536 (p0) cc_final: 0.7206 (p0) REVERT: D 123 LEU cc_start: 0.8991 (tp) cc_final: 0.8672 (tp) REVERT: D 193 ASP cc_start: 0.8775 (m-30) cc_final: 0.8418 (m-30) REVERT: D 204 PHE cc_start: 0.9096 (m-80) cc_final: 0.8864 (m-10) REVERT: D 257 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8032 (mt-10) REVERT: D 265 ASN cc_start: 0.8950 (t0) cc_final: 0.8308 (t0) REVERT: D 356 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8784 (pp) REVERT: E 61 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7801 (mtt-85) REVERT: E 69 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6935 (t80) REVERT: E 120 MET cc_start: 0.8251 (tpp) cc_final: 0.7780 (ttm) REVERT: E 153 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.7922 (mtm-85) REVERT: E 184 MET cc_start: 0.5977 (ptm) cc_final: 0.5680 (ptt) REVERT: F 53 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7238 (mt) REVERT: F 101 PHE cc_start: 0.8455 (m-10) cc_final: 0.8155 (m-80) REVERT: F 136 HIS cc_start: 0.7999 (m-70) cc_final: 0.7672 (t-90) REVERT: F 149 MET cc_start: 0.7230 (mmm) cc_final: 0.6955 (mtt) REVERT: F 170 GLN cc_start: 0.8467 (mt0) cc_final: 0.8118 (mt0) REVERT: F 208 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8012 (tm-30) REVERT: F 281 HIS cc_start: 0.7936 (m170) cc_final: 0.7539 (m170) REVERT: F 290 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7848 (mm-30) REVERT: F 390 ASP cc_start: 0.8093 (t0) cc_final: 0.7786 (t0) REVERT: F 450 MET cc_start: 0.8528 (mmp) cc_final: 0.8182 (mmp) REVERT: G 62 ARG cc_start: 0.8563 (ptt-90) cc_final: 0.7736 (ptt-90) REVERT: G 97 MET cc_start: 0.8167 (mtp) cc_final: 0.7826 (mtm) REVERT: G 114 GLU cc_start: 0.8443 (tt0) cc_final: 0.8147 (pt0) REVERT: G 136 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7468 (mt-10) REVERT: G 161 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: G 260 ASN cc_start: 0.9117 (m-40) cc_final: 0.8888 (m-40) REVERT: G 269 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: G 329 MET cc_start: 0.7771 (mmm) cc_final: 0.7394 (mtp) REVERT: G 567 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8758 (p) REVERT: G 602 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8280 (ttp-110) REVERT: G 657 ASP cc_start: 0.7605 (t0) cc_final: 0.7180 (t0) REVERT: G 666 GLN cc_start: 0.7848 (pm20) cc_final: 0.7528 (pm20) REVERT: H 32 GLN cc_start: 0.9376 (mt0) cc_final: 0.9091 (mt0) REVERT: H 86 TRP cc_start: 0.9137 (m100) cc_final: 0.8745 (m100) REVERT: H 146 MET cc_start: 0.9095 (mmt) cc_final: 0.8424 (tpp) REVERT: H 163 GLN cc_start: 0.8833 (tt0) cc_final: 0.8383 (mt0) REVERT: H 173 TRP cc_start: 0.8890 (m-10) cc_final: 0.8033 (m-90) REVERT: H 181 MET cc_start: 0.8294 (mtt) cc_final: 0.7939 (mtt) REVERT: H 184 MET cc_start: 0.9182 (mmm) cc_final: 0.8585 (mmm) REVERT: H 185 TRP cc_start: 0.8880 (t-100) cc_final: 0.8347 (t-100) REVERT: H 204 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 248 TYR cc_start: 0.7906 (m-10) cc_final: 0.7560 (m-10) REVERT: I 36 TYR cc_start: 0.8277 (p90) cc_final: 0.7778 (p90) REVERT: I 72 MET cc_start: 0.9223 (tpp) cc_final: 0.8825 (tpp) REVERT: I 76 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7644 (t80) REVERT: I 208 ASP cc_start: 0.8371 (t70) cc_final: 0.7353 (t70) REVERT: P 55 VAL cc_start: 0.8924 (t) cc_final: 0.8676 (p) REVERT: P 154 GLN cc_start: 0.8281 (tp40) cc_final: 0.7964 (tp40) REVERT: P 332 LEU cc_start: 0.8406 (tp) cc_final: 0.7914 (tt) REVERT: Q 63 THR cc_start: 0.8251 (p) cc_final: 0.7862 (t) REVERT: Q 69 GLU cc_start: 0.7545 (tp30) cc_final: 0.7295 (tp30) REVERT: Q 70 GLU cc_start: 0.7371 (tp30) cc_final: 0.6936 (tp30) REVERT: Q 74 THR cc_start: 0.8058 (p) cc_final: 0.7575 (p) REVERT: Q 106 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8263 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8244 (t0) cc_final: 0.7484 (p0) REVERT: R 47 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7433 (ptt180) REVERT: R 93 ILE cc_start: 0.9328 (mt) cc_final: 0.9108 (mt) REVERT: S 31 GLN cc_start: 0.8980 (tp40) cc_final: 0.8687 (pm20) REVERT: S 66 TRP cc_start: 0.8573 (m100) cc_final: 0.8173 (m100) REVERT: S 68 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7936 (mtp85) REVERT: T 92 LYS cc_start: 0.8691 (tttm) cc_final: 0.8428 (tttm) REVERT: T 99 SER cc_start: 0.8112 (m) cc_final: 0.7479 (p) REVERT: T 113 LEU cc_start: 0.8787 (mp) cc_final: 0.8544 (mp) REVERT: V 87 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8584 (tp30) REVERT: W 37 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8805 (mt-10) REVERT: W 43 TYR cc_start: 0.8338 (t80) cc_final: 0.8028 (t80) REVERT: W 114 GLU cc_start: 0.7951 (pm20) cc_final: 0.7613 (pm20) REVERT: Z 24 ASN cc_start: 0.8585 (t0) cc_final: 0.8378 (t0) REVERT: Z 133 MET cc_start: 0.7814 (ttt) cc_final: 0.7366 (tmm) REVERT: a 6 LEU cc_start: 0.9321 (mm) cc_final: 0.9086 (mm) REVERT: a 11 ILE cc_start: 0.9061 (mm) cc_final: 0.8757 (tp) REVERT: a 23 THR cc_start: 0.9309 (m) cc_final: 0.8901 (p) REVERT: b 16 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6626 (tt0) REVERT: b 44 MET cc_start: 0.8430 (ptp) cc_final: 0.8078 (ptp) REVERT: q 132 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7408 (tmmt) REVERT: s 85 LEU cc_start: 0.7285 (tp) cc_final: 0.6496 (mt) outliers start: 112 outliers final: 96 residues processed: 916 average time/residue: 0.2089 time to fit residues: 319.8006 Evaluate side-chains 938 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 831 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 83 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 133 VAL 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 185 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 332 CYS Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 TYR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 161 GLU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 670 GLU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 698 ASP Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 160 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain I residue 63 TRP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 79 GLN Chi-restraints excluded: chain P residue 123 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 298 TYR Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 80 SER Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain q residue 132 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 299 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 394 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 190 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 HIS F 376 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN H 292 ASN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083767 restraints weight = 90131.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086462 restraints weight = 42699.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088242 restraints weight = 25992.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089397 restraints weight = 18784.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090115 restraints weight = 15192.813| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34905 Z= 0.156 Angle : 0.917 73.877 47336 Z= 0.368 Chirality : 0.046 0.253 5163 Planarity : 0.006 0.125 5997 Dihedral : 8.959 157.237 4916 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 3.27 % Allowed : 26.17 % Favored : 70.57 % Cbeta Deviations : 0.00 % 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: -0.27 (0.13), residues: 4153 helix: 0.87 (0.12), residues: 1871 sheet: -1.23 (0.26), residues: 370 loop : -0.98 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 224 TYR 0.026 0.002 TYR T 85 PHE 0.031 0.002 PHE T 126 TRP 0.030 0.001 TRP H 179 HIS 0.005 0.001 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00370 (34864) covalent geometry : angle 0.72956 (47244) SS BOND : bond 0.00207 ( 4) SS BOND : angle 1.58025 ( 8) hydrogen bonds : bond 0.03899 ( 1417) hydrogen bonds : angle 4.95219 ( 4128) metal coordination : bond 0.01363 ( 37) metal coordination : angle 13.20278 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8240.67 seconds wall clock time: 142 minutes 36.19 seconds (8556.19 seconds total)