Starting phenix.real_space_refine on Mon Jul 6 06:50:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnp_38510/07_2026/8xnp_38510_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnp_38510/07_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_38510/07_2026/8xnp_38510_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnp_38510/07_2026/8xnp_38510_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnp_38510/07_2026/8xnp_38510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnp_38510/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.11, 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: 3.20 Conformation dependent library (CDL) restraints added in 1.5 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: 1.10 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: 6.14 Time building geometry restraints manager: 4.19 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=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" N VAL F 235 " pdb=" CA VAL F 235 " ideal model delta sigma weight residual 1.459 1.342 0.117 1.26e-02 6.30e+03 8.60e+01 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.180 0.176 2.00e-02 2.50e+03 7.70e+01 ... (remaining 34859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 46469 6.66 - 13.31: 609 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: 20648 34.47 - 68.94: 382 68.94 - 103.42: 35 103.42 - 137.89: 6 137.89 - 172.36: 1 Dihedral angle restraints: 21072 sinusoidal: 8877 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 21069 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: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 38.690 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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= 1.051 Angle : 2.272 52.546 47336 Z= 1.517 Chirality : 0.133 0.914 5163 Planarity : 0.008 0.202 5997 Dihedral : 13.484 172.359 13200 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/Z covalent geometry : bond 0.01468 / 0.94 (34864) covalent geometry : angle 2.14658 / 1.52 (47244) SS BOND : bond 0.03605 / 1.82 ( 4) SS BOND : angle 5.78172 / 2.52 ( 8) hydrogen bonds : bond 0.24566 / 16.19 ( 1417) hydrogen bonds : angle 8.94763 / 6.38 ( 4128) metal coordination : bond 0.52811 / 33.81 ( 37) metal coordination : angle 17.72747 / 13.71 ( 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 : 1.287 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: 0.2163 time to fit residues: 604.4457 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 : 1.331 ------------------------------------------------------------------------------- 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... 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 112 HIS 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 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 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: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087212 restraints weight = 88546.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090018 restraints weight = 41355.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091844 restraints weight = 25043.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093026 restraints weight = 17998.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093773 restraints weight = 14505.527| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 34905 Z= 0.240 Angle : 1.084 72.919 47336 Z= 0.452 Chirality : 0.051 0.257 5163 Planarity : 0.007 0.119 5997 Dihedral : 10.139 165.297 4941 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 4.72 % Allowed : 17.30 % Favored : 77.98 % 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: 0.17 (0.12), residues: 1893 sheet: -1.21 (0.26), residues: 370 loop : -1.44 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 135 TYR 0.047 0.003 TYR E 112 PHE 0.035 0.003 PHE P 64 TRP 0.032 0.002 TRP F 51 HIS 0.014 0.002 HIS P 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (34864) covalent geometry : angle 0.87157 / 0.45 (47244) SS BOND : bond 0.03104 / 1.58 ( 4) SS BOND : angle 3.08086 / 1.52 ( 8) hydrogen bonds : bond 0.05954 / 3.97 ( 1417) hydrogen bonds : angle 5.74463 / 4.06 ( 4128) metal coordination : bond 0.02837 / 1.53 ( 37) metal coordination : angle 15.29003 / 10.68 ( 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 1245 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1073 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9285 (mt) cc_final: 0.8872 (tt) REVERT: A 27 MET cc_start: 0.7679 (ptt) cc_final: 0.7337 (mtm) REVERT: A 53 MET cc_start: 0.7877 (ppp) cc_final: 0.7484 (ppp) REVERT: A 62 PHE cc_start: 0.8905 (t80) cc_final: 0.8678 (t80) REVERT: A 83 LYS cc_start: 0.8371 (mmtm) cc_final: 0.7620 (mtmt) REVERT: A 87 MET cc_start: 0.8526 (ttp) cc_final: 0.8082 (tmm) REVERT: A 88 MET cc_start: 0.8463 (ptm) cc_final: 0.8236 (ttp) REVERT: B 76 THR cc_start: 0.9004 (p) cc_final: 0.8804 (t) REVERT: B 133 VAL cc_start: 0.9254 (t) cc_final: 0.9041 (p) REVERT: B 141 MET cc_start: 0.8896 (tpt) cc_final: 0.8637 (tpt) REVERT: B 147 LYS cc_start: 0.8887 (tptm) cc_final: 0.8552 (tptp) REVERT: B 161 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7615 (ttt) REVERT: B 170 TYR cc_start: 0.9051 (t80) cc_final: 0.8792 (t80) REVERT: B 201 LEU cc_start: 0.9463 (tp) cc_final: 0.8772 (tp) REVERT: B 207 GLN cc_start: 0.8482 (tt0) cc_final: 0.8191 (tt0) REVERT: B 211 LYS cc_start: 0.8969 (tttp) cc_final: 0.8718 (tttm) REVERT: B 215 GLU cc_start: 0.8529 (pt0) cc_final: 0.8324 (pt0) REVERT: C 166 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 216 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8402 (mmtt) REVERT: C 224 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6740 (tt0) REVERT: D 84 PHE cc_start: 0.9186 (t80) cc_final: 0.8902 (t80) REVERT: D 144 MET cc_start: 0.8031 (mpp) cc_final: 0.7702 (mpp) REVERT: D 210 MET cc_start: 0.8836 (mtm) cc_final: 0.8614 (mtm) REVERT: D 265 ASN cc_start: 0.8382 (t0) cc_final: 0.8053 (t0) REVERT: D 311 TYR cc_start: 0.8729 (m-80) cc_final: 0.8272 (m-80) REVERT: D 398 THR cc_start: 0.9221 (t) cc_final: 0.8954 (p) REVERT: E 54 PHE cc_start: 0.8354 (m-80) cc_final: 0.7860 (m-80) REVERT: E 67 LYS cc_start: 0.8905 (ptmt) cc_final: 0.8665 (mmtt) REVERT: E 69 TYR cc_start: 0.7218 (m-80) cc_final: 0.6810 (m-80) REVERT: E 120 MET cc_start: 0.8397 (tpp) cc_final: 0.7887 (mmm) REVERT: E 125 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.7635 (Cg_exo) REVERT: E 168 PHE cc_start: 0.7606 (m-80) cc_final: 0.6623 (m-10) REVERT: E 174 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: E 184 MET cc_start: 0.7248 (ttp) cc_final: 0.6907 (ptm) REVERT: E 189 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6035 (t0) REVERT: F 61 ASP cc_start: 0.6350 (p0) cc_final: 0.6095 (p0) REVERT: F 170 GLN cc_start: 0.7753 (mt0) cc_final: 0.7268 (mt0) REVERT: F 208 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8162 (tm-30) REVERT: F 396 MET cc_start: 0.8792 (mmm) cc_final: 0.8586 (mmm) REVERT: F 429 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7683 (t70) REVERT: G 62 ARG cc_start: 0.8320 (ptt-90) cc_final: 0.7809 (ptt-90) REVERT: G 111 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8239 (tptp) REVERT: G 114 GLU cc_start: 0.8024 (tt0) cc_final: 0.7591 (pt0) REVERT: G 172 ILE cc_start: 0.9378 (mt) cc_final: 0.9116 (tp) REVERT: G 391 ILE cc_start: 0.8510 (mm) cc_final: 0.8223 (mm) REVERT: G 434 SER cc_start: 0.9263 (p) cc_final: 0.8894 (t) REVERT: G 471 LYS cc_start: 0.8561 (mttp) cc_final: 0.8141 (mmmm) REVERT: G 640 ASP cc_start: 0.7822 (p0) cc_final: 0.7616 (p0) REVERT: G 657 ASP cc_start: 0.7476 (t0) cc_final: 0.7030 (t0) REVERT: H 24 GLU cc_start: 0.8615 (tt0) cc_final: 0.8399 (tt0) REVERT: H 31 MET cc_start: 0.9238 (mtp) cc_final: 0.8548 (mtp) REVERT: H 170 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7782 (mt-10) REVERT: H 190 LEU cc_start: 0.9028 (mt) cc_final: 0.8809 (mt) REVERT: H 199 ASP cc_start: 0.7797 (t0) cc_final: 0.7318 (t0) REVERT: I 59 ARG cc_start: 0.7545 (ttm110) cc_final: 0.7055 (ttp-110) REVERT: I 128 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9077 (mp) REVERT: I 139 SER cc_start: 0.8601 (t) cc_final: 0.8295 (p) REVERT: I 182 GLU cc_start: 0.8133 (tt0) cc_final: 0.7782 (tt0) REVERT: I 208 ASP cc_start: 0.8176 (t70) cc_final: 0.6982 (t70) REVERT: P 97 MET cc_start: 0.8341 (ptp) cc_final: 0.7961 (ptp) REVERT: P 332 LEU cc_start: 0.8179 (tp) cc_final: 0.7779 (tt) REVERT: Q 69 GLU cc_start: 0.7428 (tp30) cc_final: 0.7095 (tp30) REVERT: Q 107 TRP cc_start: 0.8854 (p90) cc_final: 0.8580 (p90) REVERT: Q 128 PHE cc_start: 0.8374 (m-80) cc_final: 0.8168 (m-80) REVERT: Q 139 GLU cc_start: 0.8774 (tp30) cc_final: 0.8263 (mm-30) REVERT: Q 145 TYR cc_start: 0.8858 (p90) cc_final: 0.8613 (p90) REVERT: Q 159 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (p) REVERT: Q 160 TYR cc_start: 0.8536 (t80) cc_final: 0.7776 (t80) REVERT: Q 164 PHE cc_start: 0.7823 (m-80) cc_final: 0.6048 (m-80) REVERT: R 48 PHE cc_start: 0.6871 (m-80) cc_final: 0.6587 (m-80) REVERT: R 96 ASP cc_start: 0.7558 (t0) cc_final: 0.7167 (t0) REVERT: S 31 GLN cc_start: 0.9071 (tp40) cc_final: 0.8573 (pm20) REVERT: T 99 SER cc_start: 0.8089 (m) cc_final: 0.7523 (p) REVERT: T 146 ASP cc_start: 0.9023 (m-30) cc_final: 0.8666 (m-30) REVERT: V 64 ASP cc_start: 0.7705 (t0) cc_final: 0.7392 (t0) REVERT: V 73 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8057 (mp10) REVERT: W 53 MET cc_start: 0.9140 (mtt) cc_final: 0.8893 (mtt) REVERT: W 55 LEU cc_start: 0.8417 (mp) cc_final: 0.8193 (mp) REVERT: X 32 TYR cc_start: 0.8699 (t80) cc_final: 0.8498 (t80) REVERT: X 44 MET cc_start: 0.8967 (tpp) cc_final: 0.8531 (tpp) REVERT: X 46 CYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4635 (m) REVERT: X 117 TRP cc_start: 0.8054 (m-10) cc_final: 0.7813 (m-10) REVERT: Z 24 ASN cc_start: 0.8260 (t0) cc_final: 0.7847 (t0) REVERT: Z 125 TYR cc_start: 0.8591 (m-80) cc_final: 0.8380 (m-80) REVERT: a 2 TRP cc_start: 0.8484 (p-90) cc_final: 0.8090 (p-90) REVERT: a 34 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8019 (ptpt) REVERT: a 38 VAL cc_start: 0.9143 (t) cc_final: 0.8680 (p) REVERT: a 54 ILE cc_start: 0.8797 (mm) cc_final: 0.8541 (mm) REVERT: a 66 LEU cc_start: 0.9151 (pp) cc_final: 0.8928 (tt) REVERT: b 32 MET cc_start: 0.9188 (mmt) cc_final: 0.8915 (mmt) REVERT: b 44 MET cc_start: 0.8318 (mtp) cc_final: 0.7287 (ptp) REVERT: b 78 LEU cc_start: 0.8819 (mp) cc_final: 0.8614 (mp) REVERT: q 34 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6621 (mtp85) REVERT: q 93 MET cc_start: 0.7151 (tmm) cc_final: 0.6773 (tmm) outliers start: 172 outliers final: 85 residues processed: 1171 average time/residue: 0.1982 time to fit residues: 383.0437 Evaluate side-chains 977 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 884 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 C residue 154 SER 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 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: 10.0000 chunk 75 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 377 optimal weight: 0.0040 chunk 60 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 362 optimal weight: 3.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 E 130 HIS ** 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 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 72 HIS P 93 HIS P 171 ASN P 285 HIS ** Q 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087270 restraints weight = 90137.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090244 restraints weight = 39833.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092151 restraints weight = 23235.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093408 restraints weight = 16308.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094202 restraints weight = 12913.539| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34905 Z= 0.165 Angle : 0.941 72.221 47336 Z= 0.377 Chirality : 0.046 0.207 5163 Planarity : 0.005 0.121 5997 Dihedral : 9.834 163.139 4937 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 4.42 % Allowed : 19.85 % Favored : 75.73 % 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: -0.61 (0.13), residues: 4153 helix: 0.57 (0.12), residues: 1879 sheet: -1.09 (0.26), residues: 364 loop : -1.22 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG r 12 TYR 0.034 0.002 TYR E 112 PHE 0.029 0.002 PHE H 270 TRP 0.030 0.002 TRP Z 116 HIS 0.008 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (34864) covalent geometry : angle 0.74099 / 0.37 (47244) SS BOND : bond 0.00495 / 0.25 ( 4) SS BOND : angle 2.20889 / 1.09 ( 8) hydrogen bonds : bond 0.05000 / 3.34 ( 1417) hydrogen bonds : angle 5.27851 / 3.72 ( 4128) metal coordination : bond 0.01695 / 1.04 ( 37) metal coordination : angle 13.77800 / 9.77 ( 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 1147 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 986 time to evaluate : 1.035 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: 0.9351 (mt) cc_final: 0.9007 (tt) REVERT: A 19 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 27 MET cc_start: 0.7356 (ptt) cc_final: 0.7041 (mtm) REVERT: A 53 MET cc_start: 0.7812 (ppp) cc_final: 0.7518 (ppp) REVERT: A 83 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7673 (mtmt) REVERT: A 87 MET cc_start: 0.8489 (ttp) cc_final: 0.8019 (tmm) REVERT: B 147 LYS cc_start: 0.8761 (tptm) cc_final: 0.8537 (tptp) REVERT: B 161 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7538 (ttt) REVERT: B 170 TYR cc_start: 0.9025 (t80) cc_final: 0.8804 (t80) REVERT: B 188 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (t0) REVERT: B 201 LEU cc_start: 0.9355 (tp) cc_final: 0.8596 (tp) REVERT: B 207 GLN cc_start: 0.8533 (tt0) cc_final: 0.8299 (tt0) REVERT: C 104 ASN cc_start: 0.8458 (m-40) cc_final: 0.7082 (t0) REVERT: C 211 TYR cc_start: 0.7995 (t80) cc_final: 0.7605 (t80) REVERT: C 216 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8468 (mmtt) REVERT: C 224 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6579 (tt0) REVERT: D 210 MET cc_start: 0.8762 (mtm) cc_final: 0.8515 (mtm) REVERT: D 265 ASN cc_start: 0.8404 (t0) cc_final: 0.8041 (t0) REVERT: D 375 MET cc_start: 0.8219 (tpp) cc_final: 0.8006 (tpp) REVERT: D 398 THR cc_start: 0.9172 (t) cc_final: 0.8952 (p) REVERT: E 61 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7630 (mtt-85) REVERT: E 67 LYS cc_start: 0.8916 (ptmt) cc_final: 0.8656 (tppt) REVERT: E 69 TYR cc_start: 0.7090 (m-80) cc_final: 0.6851 (m-80) REVERT: E 120 MET cc_start: 0.8203 (tpp) cc_final: 0.7690 (mmm) REVERT: E 125 PRO cc_start: 0.8784 (Cg_endo) cc_final: 0.7870 (Cg_exo) REVERT: E 174 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: E 184 MET cc_start: 0.7194 (ttp) cc_final: 0.6940 (ptm) REVERT: E 189 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6454 (t0) REVERT: F 101 PHE cc_start: 0.8853 (m-10) cc_final: 0.8410 (m-80) REVERT: F 170 GLN cc_start: 0.8133 (mt0) cc_final: 0.7817 (mt0) REVERT: F 396 MET cc_start: 0.8659 (mmm) cc_final: 0.8415 (mmm) REVERT: F 429 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7457 (t0) REVERT: F 450 MET cc_start: 0.8649 (mmp) cc_final: 0.8191 (mmp) REVERT: G 42 MET cc_start: 0.8867 (tpp) cc_final: 0.8611 (tpp) REVERT: G 62 ARG cc_start: 0.8304 (ptt-90) cc_final: 0.7790 (ptt-90) REVERT: G 136 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7907 (mt-10) REVERT: G 145 MET cc_start: 0.8960 (mmt) cc_final: 0.8713 (mmt) REVERT: G 172 ILE cc_start: 0.9376 (mt) cc_final: 0.9164 (tp) REVERT: G 269 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7143 (pt0) REVERT: G 391 ILE cc_start: 0.8508 (mm) cc_final: 0.8275 (mm) REVERT: G 434 SER cc_start: 0.9220 (p) cc_final: 0.8839 (t) REVERT: G 471 LYS cc_start: 0.8514 (mttm) cc_final: 0.8230 (mmmm) REVERT: G 567 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8733 (p) REVERT: G 657 ASP cc_start: 0.7484 (t0) cc_final: 0.7076 (t0) REVERT: H 24 GLU cc_start: 0.8458 (tt0) cc_final: 0.8154 (tt0) REVERT: H 32 GLN cc_start: 0.9161 (mt0) cc_final: 0.8799 (mt0) REVERT: H 59 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: H 163 GLN cc_start: 0.8805 (tt0) cc_final: 0.8429 (mt0) REVERT: H 172 MET cc_start: 0.6551 (mmt) cc_final: 0.6119 (mmm) REVERT: H 199 ASP cc_start: 0.7632 (t0) cc_final: 0.7289 (t0) REVERT: H 261 MET cc_start: 0.8172 (mmt) cc_final: 0.7912 (mmt) REVERT: H 282 TYR cc_start: 0.6796 (t80) cc_final: 0.6166 (t80) REVERT: I 36 TYR cc_start: 0.8832 (p90) cc_final: 0.8295 (p90) REVERT: I 72 MET cc_start: 0.9185 (tpp) cc_final: 0.8756 (tpp) REVERT: I 185 TYR cc_start: 0.8554 (m-10) cc_final: 0.8303 (m-80) REVERT: I 190 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9024 (mp) REVERT: I 206 GLN cc_start: 0.8952 (tp40) cc_final: 0.8517 (tm-30) REVERT: I 208 ASP cc_start: 0.8252 (t70) cc_final: 0.7204 (t70) REVERT: P 92 MET cc_start: 0.8426 (mmm) cc_final: 0.8081 (mmt) REVERT: P 326 ASP cc_start: 0.7188 (m-30) cc_final: 0.6955 (m-30) REVERT: P 332 LEU cc_start: 0.8069 (tp) cc_final: 0.7687 (tt) REVERT: Q 107 TRP cc_start: 0.8814 (p90) cc_final: 0.8405 (p90) REVERT: Q 160 TYR cc_start: 0.8445 (t80) cc_final: 0.7830 (t80) REVERT: Q 164 PHE cc_start: 0.7719 (m-80) cc_final: 0.6034 (m-80) REVERT: R 96 ASP cc_start: 0.7448 (t0) cc_final: 0.7182 (t0) REVERT: S 16 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7714 (pp) REVERT: S 31 GLN cc_start: 0.9071 (tp40) cc_final: 0.8594 (pm20) REVERT: S 69 TYR cc_start: 0.8401 (m-80) cc_final: 0.7807 (m-80) REVERT: S 75 LYS cc_start: 0.8894 (mttt) cc_final: 0.8579 (mtmt) REVERT: T 136 GLU cc_start: 0.8243 (mp0) cc_final: 0.8003 (pm20) REVERT: V 47 TYR cc_start: 0.8674 (m-80) cc_final: 0.8125 (m-80) REVERT: W 53 MET cc_start: 0.9138 (mtt) cc_final: 0.8833 (mtt) REVERT: W 58 THR cc_start: 0.8446 (m) cc_final: 0.8103 (p) REVERT: W 123 SER cc_start: 0.8830 (m) cc_final: 0.8457 (p) REVERT: X 32 TYR cc_start: 0.8723 (t80) cc_final: 0.8453 (t80) REVERT: X 44 MET cc_start: 0.8965 (tpp) cc_final: 0.8559 (tpp) REVERT: Z 21 TYR cc_start: 0.7403 (p90) cc_final: 0.6693 (p90) REVERT: Z 24 ASN cc_start: 0.8329 (t0) cc_final: 0.7998 (t0) REVERT: Z 116 TRP cc_start: 0.8605 (t-100) cc_final: 0.8151 (t-100) REVERT: Z 125 TYR cc_start: 0.8767 (m-80) cc_final: 0.8461 (m-80) REVERT: Z 134 SER cc_start: 0.9369 (t) cc_final: 0.9083 (p) REVERT: a 2 TRP cc_start: 0.8522 (p-90) cc_final: 0.8191 (p-90) REVERT: a 4 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8556 (mp0) REVERT: a 38 VAL cc_start: 0.9152 (t) cc_final: 0.8784 (p) REVERT: a 46 TYR cc_start: 0.8945 (t80) cc_final: 0.8743 (t80) REVERT: b 32 MET cc_start: 0.9135 (mmt) cc_final: 0.8826 (mmt) REVERT: b 78 LEU cc_start: 0.8938 (mp) cc_final: 0.8654 (mp) REVERT: r 109 ASP cc_start: 0.5770 (p0) cc_final: 0.5009 (p0) outliers start: 161 outliers final: 90 residues processed: 1078 average time/residue: 0.1936 time to fit residues: 345.4512 Evaluate side-chains 970 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 869 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 18 ILE 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 D residue 416 SER Chi-restraints excluded: chain E residue 89 ASN Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 122 ASN 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 E residue 244 VAL 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 424 ILE 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 290 THR Chi-restraints excluded: chain G residue 386 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 G residue 689 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 59 GLU 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 111 LEU 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 H residue 301 CYS 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 I residue 190 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 80 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 Q residue 103 THR Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain T residue 128 PHE 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 Z residue 62 ILE Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain Z residue 117 VAL 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 b residue 45 ILE 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: 8.9990 chunk 252 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 148 optimal weight: 0.9990 chunk 362 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 408 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** F 418 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS H 235 ASN ** 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** ** Q 123 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085967 restraints weight = 88740.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088740 restraints weight = 41820.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090541 restraints weight = 25363.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091703 restraints weight = 18293.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092430 restraints weight = 14769.124| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34905 Z= 0.166 Angle : 0.897 73.417 47336 Z= 0.359 Chirality : 0.045 0.275 5163 Planarity : 0.005 0.121 5997 Dihedral : 9.682 159.787 4937 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 4.26 % Allowed : 21.20 % Favored : 74.55 % 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: -0.43 (0.13), residues: 4153 helix: 0.74 (0.12), residues: 1868 sheet: -1.07 (0.26), residues: 372 loop : -1.13 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG q 88 TYR 0.033 0.002 TYR F 157 PHE 0.042 0.002 PHE A 62 TRP 0.022 0.001 TRP E 91 HIS 0.007 0.001 HIS F 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (34864) covalent geometry : angle 0.70569 / 0.36 (47244) SS BOND : bond 0.00285 / 0.15 ( 4) SS BOND : angle 2.09960 / 1.02 ( 8) hydrogen bonds : bond 0.04562 / 3.06 ( 1417) hydrogen bonds : angle 5.13945 / 3.63 ( 4128) metal coordination : bond 0.01608 / 1.02 ( 37) metal coordination : angle 13.14103 / 9.43 ( 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 1097 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 942 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8368 (tp) REVERT: A 27 MET cc_start: 0.7252 (ptt) cc_final: 0.6922 (mtm) REVERT: A 38 GLU cc_start: 0.7586 (tp30) cc_final: 0.6916 (mm-30) REVERT: A 53 MET cc_start: 0.7814 (ppp) cc_final: 0.7378 (ppp) REVERT: A 83 LYS cc_start: 0.8401 (mmtm) cc_final: 0.7739 (mtmt) REVERT: A 87 MET cc_start: 0.8621 (ttp) cc_final: 0.8350 (tmm) REVERT: A 99 SER cc_start: 0.8957 (t) cc_final: 0.8697 (p) REVERT: A 104 TYR cc_start: 0.9094 (t80) cc_final: 0.8890 (t80) REVERT: B 79 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (t0) REVERT: B 83 ASN cc_start: 0.9129 (m-40) cc_final: 0.8925 (m-40) REVERT: B 161 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: B 170 TYR cc_start: 0.9092 (t80) cc_final: 0.8821 (t80) REVERT: B 201 LEU cc_start: 0.9344 (tp) cc_final: 0.8575 (tp) REVERT: B 207 GLN cc_start: 0.8513 (tt0) cc_final: 0.8167 (tt0) REVERT: B 218 LEU cc_start: 0.9066 (mt) cc_final: 0.8830 (mt) REVERT: B 220 ILE cc_start: 0.9436 (tp) cc_final: 0.9232 (tp) REVERT: C 104 ASN cc_start: 0.8436 (m-40) cc_final: 0.7153 (t0) REVERT: C 211 TYR cc_start: 0.8176 (t80) cc_final: 0.7787 (t80) REVERT: D 208 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8057 (tp30) REVERT: D 265 ASN cc_start: 0.8447 (t0) cc_final: 0.8062 (t0) REVERT: D 398 THR cc_start: 0.9185 (t) cc_final: 0.8978 (p) REVERT: E 61 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7544 (mtt-85) REVERT: E 67 LYS cc_start: 0.8928 (ptmt) cc_final: 0.8657 (tppt) REVERT: E 91 TRP cc_start: 0.7497 (m100) cc_final: 0.6296 (m-10) REVERT: E 120 MET cc_start: 0.8208 (tpp) cc_final: 0.7898 (tpp) REVERT: E 189 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6547 (t0) REVERT: E 200 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (tp) REVERT: F 101 PHE cc_start: 0.8873 (m-10) cc_final: 0.8465 (m-80) REVERT: F 170 GLN cc_start: 0.8064 (mt0) cc_final: 0.7696 (mt0) REVERT: F 275 LEU cc_start: 0.8558 (mm) cc_final: 0.8164 (mm) REVERT: F 396 MET cc_start: 0.8593 (mmm) cc_final: 0.8383 (mmm) REVERT: F 450 MET cc_start: 0.8700 (mmp) cc_final: 0.8365 (mmp) REVERT: G 42 MET cc_start: 0.8837 (tpp) cc_final: 0.8602 (tpp) REVERT: G 62 ARG cc_start: 0.8413 (ptt-90) cc_final: 0.7761 (ptt-90) REVERT: G 114 GLU cc_start: 0.8138 (tt0) cc_final: 0.7811 (pt0) REVERT: G 136 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7603 (mt-10) REVERT: G 145 MET cc_start: 0.8952 (mmt) cc_final: 0.8672 (mmt) REVERT: G 172 ILE cc_start: 0.9418 (mt) cc_final: 0.9136 (tp) REVERT: G 269 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7023 (pt0) REVERT: G 471 LYS cc_start: 0.8572 (mttm) cc_final: 0.8258 (mmmm) REVERT: G 567 VAL cc_start: 0.9068 (p) cc_final: 0.8762 (p) REVERT: G 657 ASP cc_start: 0.7490 (t0) cc_final: 0.7033 (t0) REVERT: H 24 GLU cc_start: 0.8502 (tt0) cc_final: 0.8139 (tt0) REVERT: H 32 GLN cc_start: 0.9136 (mt0) cc_final: 0.8825 (mt0) REVERT: H 59 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: H 163 GLN cc_start: 0.8799 (tt0) cc_final: 0.8427 (mt0) REVERT: H 199 ASP cc_start: 0.7560 (t0) cc_final: 0.7183 (t0) REVERT: H 202 GLU cc_start: 0.6776 (tp30) cc_final: 0.6502 (tp30) REVERT: H 261 MET cc_start: 0.8329 (mmt) cc_final: 0.8107 (mmt) REVERT: I 36 TYR cc_start: 0.8813 (p90) cc_final: 0.8172 (p90) REVERT: I 70 LEU cc_start: 0.9408 (mt) cc_final: 0.9162 (mt) REVERT: I 177 THR cc_start: 0.8081 (p) cc_final: 0.7717 (t) REVERT: I 182 GLU cc_start: 0.8365 (tt0) cc_final: 0.8140 (tt0) REVERT: I 206 GLN cc_start: 0.8956 (tp40) cc_final: 0.8545 (tm-30) REVERT: I 208 ASP cc_start: 0.8296 (t70) cc_final: 0.7276 (t70) REVERT: P 97 MET cc_start: 0.7707 (ptp) cc_final: 0.7479 (ptp) REVERT: P 174 MET cc_start: 0.7268 (mtt) cc_final: 0.6930 (mtt) REVERT: Q 69 GLU cc_start: 0.7294 (tp30) cc_final: 0.7082 (tp30) REVERT: Q 70 GLU cc_start: 0.7255 (tp30) cc_final: 0.7027 (tp30) REVERT: Q 106 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.8605 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8472 (t0) cc_final: 0.7800 (p0) REVERT: Q 160 TYR cc_start: 0.8394 (t80) cc_final: 0.7930 (t80) REVERT: Q 164 PHE cc_start: 0.7553 (m-80) cc_final: 0.6013 (m-80) REVERT: R 47 ARG cc_start: 0.7554 (mtm110) cc_final: 0.6850 (ptt180) REVERT: S 31 GLN cc_start: 0.9034 (tp40) cc_final: 0.8613 (pm20) REVERT: S 64 LYS cc_start: 0.6655 (pttm) cc_final: 0.6417 (pttm) REVERT: T 123 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7873 (mt-10) REVERT: T 139 MET cc_start: 0.8173 (mmt) cc_final: 0.7776 (mmt) REVERT: W 58 THR cc_start: 0.8645 (m) cc_final: 0.8357 (p) REVERT: W 123 SER cc_start: 0.8870 (m) cc_final: 0.8489 (p) REVERT: X 44 MET cc_start: 0.8926 (tpp) cc_final: 0.8561 (tpp) REVERT: Z 21 TYR cc_start: 0.7746 (p90) cc_final: 0.6877 (p90) REVERT: Z 24 ASN cc_start: 0.8209 (t0) cc_final: 0.7778 (t0) REVERT: Z 125 TYR cc_start: 0.8745 (m-80) cc_final: 0.8489 (m-80) REVERT: a 2 TRP cc_start: 0.8568 (p-90) cc_final: 0.8306 (p-90) REVERT: a 4 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8476 (mp0) REVERT: b 32 MET cc_start: 0.9174 (mmt) cc_final: 0.8883 (mmt) REVERT: b 78 LEU cc_start: 0.8968 (mp) cc_final: 0.8761 (mp) REVERT: q 93 MET cc_start: 0.7214 (tmm) cc_final: 0.6741 (ptp) REVERT: r 109 ASP cc_start: 0.6099 (p0) cc_final: 0.5374 (p0) outliers start: 155 outliers final: 97 residues processed: 1032 average time/residue: 0.1968 time to fit residues: 338.3759 Evaluate side-chains 962 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 858 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 86 THR 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 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 C residue 78 SER 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 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 384 LEU Chi-restraints excluded: chain D residue 416 SER 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 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 30 ASN Chi-restraints excluded: chain G residue 66 HIS Chi-restraints excluded: chain G residue 126 LEU 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 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 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 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 285 LEU Chi-restraints excluded: chain H residue 301 CYS 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 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 108 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain S residue 21 VAL 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 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 95 GLU 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 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 q residue 80 SER Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU 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: 8.9990 chunk 275 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 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 140 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** 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 ** 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 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085928 restraints weight = 89538.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088665 restraints weight = 42658.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.090459 restraints weight = 26173.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091614 restraints weight = 18977.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092361 restraints weight = 15433.645| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34905 Z= 0.149 Angle : 0.870 73.679 47336 Z= 0.347 Chirality : 0.045 0.276 5163 Planarity : 0.005 0.123 5997 Dihedral : 9.496 160.926 4936 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 4.48 % Allowed : 22.21 % Favored : 73.31 % 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: 0.84 (0.12), residues: 1865 sheet: -1.08 (0.27), residues: 355 loop : -1.05 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 44 TYR 0.028 0.002 TYR E 192 PHE 0.027 0.002 PHE A 62 TRP 0.018 0.001 TRP I 63 HIS 0.008 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (34864) covalent geometry : angle 0.68275 / 0.34 (47244) SS BOND : bond 0.00758 / 0.36 ( 4) SS BOND : angle 1.71572 / 0.87 ( 8) hydrogen bonds : bond 0.04249 / 2.83 ( 1417) hydrogen bonds : angle 5.02278 / 3.55 ( 4128) metal coordination : bond 0.01419 / 0.95 ( 37) metal coordination : angle 12.79538 / 9.22 ( 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 1086 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 923 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8374 (m-80) cc_final: 0.7803 (m-10) REVERT: A 19 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 27 MET cc_start: 0.7136 (ptt) cc_final: 0.6862 (mtm) REVERT: A 38 GLU cc_start: 0.7675 (tp30) cc_final: 0.7257 (tp30) REVERT: A 53 MET cc_start: 0.7846 (ppp) cc_final: 0.7457 (ppp) REVERT: A 83 LYS cc_start: 0.8369 (mmtm) cc_final: 0.7796 (pttt) REVERT: A 87 MET cc_start: 0.8534 (ttp) cc_final: 0.8332 (tmm) REVERT: B 79 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: B 93 MET cc_start: 0.8372 (ttp) cc_final: 0.8126 (ttt) REVERT: B 147 LYS cc_start: 0.8701 (tptp) cc_final: 0.8380 (tptp) REVERT: B 170 TYR cc_start: 0.9139 (t80) cc_final: 0.8796 (t80) REVERT: B 207 GLN cc_start: 0.8512 (tt0) cc_final: 0.8127 (tt0) REVERT: B 220 ILE cc_start: 0.9405 (tp) cc_final: 0.9188 (tp) REVERT: C 104 ASN cc_start: 0.8250 (m-40) cc_final: 0.7115 (t0) REVERT: C 166 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7960 (mt-10) REVERT: C 211 TYR cc_start: 0.8303 (t80) cc_final: 0.7924 (t80) REVERT: C 216 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8258 (mmtt) REVERT: D 193 ASP cc_start: 0.8740 (m-30) cc_final: 0.8420 (m-30) REVERT: D 257 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7893 (mt-10) REVERT: D 265 ASN cc_start: 0.8503 (t0) cc_final: 0.8138 (t0) REVERT: E 67 LYS cc_start: 0.8932 (ptmt) cc_final: 0.8619 (tppt) REVERT: E 68 ASN cc_start: 0.8388 (t0) cc_final: 0.8130 (t0) REVERT: E 69 TYR cc_start: 0.7112 (m-80) cc_final: 0.6643 (t80) REVERT: E 89 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6767 (t0) REVERT: E 91 TRP cc_start: 0.7398 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: E 120 MET cc_start: 0.8147 (tpp) cc_final: 0.7800 (tpp) REVERT: E 189 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6789 (t0) REVERT: E 192 TYR cc_start: 0.8475 (m-80) cc_final: 0.8182 (m-80) REVERT: E 200 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8234 (tp) REVERT: F 53 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.6982 (mt) REVERT: F 101 PHE cc_start: 0.8909 (m-10) cc_final: 0.8536 (m-80) REVERT: F 136 HIS cc_start: 0.8330 (m-70) cc_final: 0.7620 (t-90) REVERT: F 275 LEU cc_start: 0.8492 (mm) cc_final: 0.8269 (mm) REVERT: F 450 MET cc_start: 0.8688 (mmp) cc_final: 0.8442 (mmp) REVERT: F 452 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8128 (mmp80) REVERT: G 42 MET cc_start: 0.8854 (tpp) cc_final: 0.8647 (tpp) REVERT: G 62 ARG cc_start: 0.8462 (ptt-90) cc_final: 0.7912 (ptt-90) REVERT: G 114 GLU cc_start: 0.8070 (tt0) cc_final: 0.7771 (pt0) REVERT: G 136 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7819 (mt-10) REVERT: G 145 MET cc_start: 0.8864 (mmt) cc_final: 0.8525 (mmt) REVERT: G 161 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: G 172 ILE cc_start: 0.9378 (mt) cc_final: 0.9149 (tp) REVERT: G 239 THR cc_start: 0.8571 (p) cc_final: 0.8178 (t) REVERT: G 269 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: G 282 ASN cc_start: 0.6931 (p0) cc_final: 0.6579 (p0) REVERT: G 567 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8837 (p) REVERT: G 657 ASP cc_start: 0.7410 (t0) cc_final: 0.6915 (t0) REVERT: G 663 ASN cc_start: 0.7135 (m-40) cc_final: 0.6667 (m-40) REVERT: H 17 MET cc_start: 0.8931 (tmm) cc_final: 0.8696 (tmm) REVERT: H 24 GLU cc_start: 0.8332 (tt0) cc_final: 0.8100 (tt0) REVERT: H 32 GLN cc_start: 0.9137 (mt0) cc_final: 0.8896 (mt0) REVERT: H 59 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7043 (tp30) REVERT: H 163 GLN cc_start: 0.8734 (tt0) cc_final: 0.8361 (mt0) REVERT: H 184 MET cc_start: 0.8785 (mtp) cc_final: 0.8542 (mmm) REVERT: H 199 ASP cc_start: 0.7479 (t0) cc_final: 0.7059 (t0) REVERT: H 260 MET cc_start: 0.8512 (tmm) cc_final: 0.8285 (tmm) REVERT: H 271 LEU cc_start: 0.9446 (mt) cc_final: 0.9070 (mt) REVERT: H 292 ASN cc_start: 0.8819 (m-40) cc_final: 0.8538 (m-40) REVERT: I 36 TYR cc_start: 0.8754 (p90) cc_final: 0.8132 (p90) REVERT: I 206 GLN cc_start: 0.8923 (tp40) cc_final: 0.8478 (tm-30) REVERT: I 208 ASP cc_start: 0.8270 (t70) cc_final: 0.7333 (t70) REVERT: P 174 MET cc_start: 0.7239 (mtt) cc_final: 0.6901 (mtt) REVERT: Q 69 GLU cc_start: 0.7367 (tp30) cc_final: 0.7129 (tp30) REVERT: Q 70 GLU cc_start: 0.7331 (tp30) cc_final: 0.7052 (tp30) REVERT: Q 99 MET cc_start: 0.8833 (ttp) cc_final: 0.8468 (ttp) REVERT: Q 106 ARG cc_start: 0.8880 (mtt-85) cc_final: 0.8582 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8458 (t0) cc_final: 0.7638 (p0) REVERT: Q 160 TYR cc_start: 0.8322 (t80) cc_final: 0.7972 (t80) REVERT: Q 164 PHE cc_start: 0.7576 (m-80) cc_final: 0.6074 (m-80) REVERT: R 47 ARG cc_start: 0.7620 (mtm110) cc_final: 0.6896 (ptt180) REVERT: S 31 GLN cc_start: 0.8979 (tp40) cc_final: 0.8643 (pm20) REVERT: S 68 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.4327 (mmm160) REVERT: S 75 LYS cc_start: 0.8841 (mttt) cc_final: 0.8506 (mtpt) REVERT: T 139 MET cc_start: 0.8265 (mmt) cc_final: 0.8018 (mmt) REVERT: V 87 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: W 58 THR cc_start: 0.8728 (m) cc_final: 0.8451 (p) REVERT: W 120 ASP cc_start: 0.7468 (p0) cc_final: 0.7266 (p0) REVERT: W 123 SER cc_start: 0.8849 (m) cc_final: 0.8435 (p) REVERT: X 44 MET cc_start: 0.8873 (tpp) cc_final: 0.8568 (tpp) REVERT: Z 10 MET cc_start: 0.8311 (mmm) cc_final: 0.8062 (mmt) REVERT: Z 21 TYR cc_start: 0.7804 (p90) cc_final: 0.6992 (p90) REVERT: Z 24 ASN cc_start: 0.8266 (t0) cc_final: 0.8058 (t0) REVERT: Z 125 TYR cc_start: 0.8745 (m-80) cc_final: 0.8473 (m-80) REVERT: a 2 TRP cc_start: 0.8625 (p-90) cc_final: 0.8090 (p-90) REVERT: b 16 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6553 (tt0) REVERT: b 32 MET cc_start: 0.9196 (mmt) cc_final: 0.8888 (mmt) REVERT: q 81 MET cc_start: 0.8274 (mtt) cc_final: 0.8071 (mtt) REVERT: q 93 MET cc_start: 0.7288 (tmm) cc_final: 0.6843 (ptp) REVERT: r 109 ASP cc_start: 0.6017 (p0) cc_final: 0.5356 (p0) REVERT: s 85 LEU cc_start: 0.7200 (tp) cc_final: 0.6460 (mt) outliers start: 163 outliers final: 103 residues processed: 1019 average time/residue: 0.1922 time to fit residues: 325.4213 Evaluate side-chains 976 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 859 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 86 THR 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 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 78 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 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 E residue 39 VAL 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 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 205 ILE 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 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 386 LEU Chi-restraints excluded: chain G residue 388 ASN Chi-restraints excluded: chain G residue 403 VAL 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 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 126 LYS Chi-restraints excluded: chain H residue 160 TYR 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 301 CYS 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 167 VAL 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 P residue 324 ILE Chi-restraints excluded: chain Q residue 108 GLU 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 68 ARG 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 V residue 87 GLU 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 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 55 SER Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU 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: 4.9990 chunk 386 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** E 186 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS W 73 ASN W 102 GLN a 44 GLN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** 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 = 0.3526 r_free = 0.3526 target = 0.098973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080741 restraints weight = 90645.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.083331 restraints weight = 43172.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085039 restraints weight = 26427.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086154 restraints weight = 19161.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086854 restraints weight = 15536.821| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 34905 Z= 0.267 Angle : 0.998 80.022 47336 Z= 0.391 Chirality : 0.049 0.286 5163 Planarity : 0.006 0.126 5997 Dihedral : 9.750 159.764 4936 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 5.33 % Allowed : 22.65 % 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: -0.41 (0.13), residues: 4153 helix: 0.74 (0.12), residues: 1870 sheet: -1.19 (0.27), residues: 371 loop : -1.05 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 26 TYR 0.032 0.002 TYR I 185 PHE 0.024 0.002 PHE A 62 TRP 0.027 0.002 TRP I 63 HIS 0.010 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (34864) covalent geometry : angle 0.76172 / 0.39 (47244) SS BOND : bond 0.00276 / 0.14 ( 4) SS BOND : angle 1.75176 / 0.92 ( 8) hydrogen bonds : bond 0.04586 / 3.06 ( 1417) hydrogen bonds : angle 5.23028 / 3.70 ( 4128) metal coordination : bond 0.03023 / 1.81 ( 37) metal coordination : angle 15.32222 / 10.47 ( 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 1056 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 862 time to evaluate : 1.341 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 27 MET cc_start: 0.7270 (ptt) cc_final: 0.6977 (mtm) REVERT: A 38 GLU cc_start: 0.7946 (tp30) cc_final: 0.7517 (tp30) REVERT: A 51 PHE cc_start: 0.8313 (t80) cc_final: 0.8020 (t80) REVERT: A 53 MET cc_start: 0.7951 (ppp) cc_final: 0.7439 (ppp) REVERT: A 83 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8118 (pttt) REVERT: A 87 MET cc_start: 0.8765 (ttp) cc_final: 0.8458 (tmm) REVERT: B 79 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8115 (t0) REVERT: B 166 ASN cc_start: 0.9096 (m-40) cc_final: 0.8825 (m110) REVERT: B 170 TYR cc_start: 0.9348 (t80) cc_final: 0.8851 (t80) REVERT: B 220 ILE cc_start: 0.9474 (tp) cc_final: 0.9256 (tp) REVERT: C 100 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.7936 (ttp80) REVERT: C 104 ASN cc_start: 0.8758 (m-40) cc_final: 0.7516 (t0) REVERT: C 149 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9085 (pp) REVERT: C 166 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 211 TYR cc_start: 0.8557 (t80) cc_final: 0.8159 (t80) REVERT: D 104 GLU cc_start: 0.7912 (tt0) cc_final: 0.7704 (tt0) REVERT: D 265 ASN cc_start: 0.8812 (t0) cc_final: 0.8086 (t0) REVERT: D 282 ASP cc_start: 0.9005 (t0) cc_final: 0.8795 (t0) REVERT: D 356 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8724 (pp) REVERT: E 67 LYS cc_start: 0.8871 (ptmt) cc_final: 0.8548 (mmtt) REVERT: E 68 ASN cc_start: 0.8621 (t0) cc_final: 0.8253 (t0) REVERT: E 91 TRP cc_start: 0.7647 (OUTLIER) cc_final: 0.7342 (t60) REVERT: E 120 MET cc_start: 0.8295 (tpp) cc_final: 0.7826 (tpp) REVERT: F 53 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7198 (mt) REVERT: F 101 PHE cc_start: 0.8900 (m-10) cc_final: 0.8512 (m-80) REVERT: F 136 HIS cc_start: 0.8342 (m-70) cc_final: 0.7578 (t-90) REVERT: F 290 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7494 (tp30) REVERT: F 390 ASP cc_start: 0.8081 (t0) cc_final: 0.7779 (t0) REVERT: F 450 MET cc_start: 0.8657 (mmp) cc_final: 0.8407 (mmp) REVERT: G 114 GLU cc_start: 0.8415 (tt0) cc_final: 0.8119 (pt0) REVERT: G 136 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7837 (mt-10) REVERT: G 172 ILE cc_start: 0.9480 (mt) cc_final: 0.9147 (tp) REVERT: G 269 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: G 657 ASP cc_start: 0.7644 (t0) cc_final: 0.7218 (t0) REVERT: H 24 GLU cc_start: 0.8583 (tt0) cc_final: 0.8219 (tt0) REVERT: H 32 GLN cc_start: 0.9270 (mt0) cc_final: 0.8967 (mt0) REVERT: H 86 TRP cc_start: 0.9197 (m100) cc_final: 0.8721 (m100) REVERT: H 163 GLN cc_start: 0.8806 (tt0) cc_final: 0.8444 (mt0) REVERT: H 199 ASP cc_start: 0.7877 (t0) cc_final: 0.7452 (t0) REVERT: H 260 MET cc_start: 0.8771 (tmm) cc_final: 0.8380 (tmm) REVERT: H 271 LEU cc_start: 0.9516 (mt) cc_final: 0.9161 (mt) REVERT: I 70 LEU cc_start: 0.9451 (mt) cc_final: 0.9198 (mt) REVERT: I 72 MET cc_start: 0.9329 (tpp) cc_final: 0.9017 (tpp) REVERT: I 185 TYR cc_start: 0.8629 (m-80) cc_final: 0.8321 (m-80) REVERT: I 206 GLN cc_start: 0.9175 (tp40) cc_final: 0.8527 (tm-30) REVERT: I 208 ASP cc_start: 0.8445 (t70) cc_final: 0.7567 (t70) REVERT: P 174 MET cc_start: 0.7512 (mtt) cc_final: 0.7129 (mtt) REVERT: Q 70 GLU cc_start: 0.7438 (tp30) cc_final: 0.7077 (tp30) REVERT: Q 106 ARG cc_start: 0.8977 (mtt-85) cc_final: 0.8420 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8407 (t0) cc_final: 0.7514 (p0) REVERT: Q 160 TYR cc_start: 0.8639 (t80) cc_final: 0.8327 (t80) REVERT: Q 164 PHE cc_start: 0.7646 (m-80) cc_final: 0.6679 (m-80) REVERT: R 47 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7111 (ptt180) REVERT: R 95 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8143 (tp) REVERT: S 18 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: S 31 GLN cc_start: 0.9069 (tp40) cc_final: 0.8656 (pm20) REVERT: S 64 LYS cc_start: 0.6397 (pttm) cc_final: 0.6182 (pttm) REVERT: T 99 SER cc_start: 0.8080 (m) cc_final: 0.7476 (p) REVERT: T 136 GLU cc_start: 0.8659 (pm20) cc_final: 0.8427 (pm20) REVERT: V 87 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8564 (tp30) REVERT: W 27 ASP cc_start: 0.9131 (p0) cc_final: 0.8389 (p0) REVERT: W 30 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: W 58 THR cc_start: 0.9036 (m) cc_final: 0.8804 (p) REVERT: W 126 TYR cc_start: 0.9154 (m-10) cc_final: 0.8716 (m-80) REVERT: Z 21 TYR cc_start: 0.8281 (p90) cc_final: 0.7363 (p90) REVERT: Z 24 ASN cc_start: 0.8447 (t0) cc_final: 0.8222 (t0) REVERT: Z 65 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9181 (tp) REVERT: a 1 MET cc_start: 0.7285 (mmp) cc_final: 0.6391 (mmt) REVERT: a 2 TRP cc_start: 0.8693 (p-90) cc_final: 0.8176 (p-90) REVERT: a 11 ILE cc_start: 0.9259 (mm) cc_final: 0.8956 (tp) REVERT: q 81 MET cc_start: 0.8261 (mtt) cc_final: 0.8055 (mtt) REVERT: q 88 ARG cc_start: 0.8421 (ptm160) cc_final: 0.8049 (ptm-80) outliers start: 194 outliers final: 137 residues processed: 971 average time/residue: 0.2087 time to fit residues: 336.6303 Evaluate side-chains 948 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 800 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR 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 130 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 78 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 149 LEU 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 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 82 LEU 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 182 ILE Chi-restraints excluded: chain F residue 205 ILE 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 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 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 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 H residue 7 LEU Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 100 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 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 35 THR 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 161 VAL 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 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 R residue 33 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain S residue 18 GLU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 68 ARG 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 V residue 12 VAL Chi-restraints excluded: chain V residue 16 VAL 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 V residue 87 GLU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 115 THR Chi-restraints excluded: chain X residue 46 CYS 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 65 LEU 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 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain q residue 37 THR Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain q residue 138 VAL Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 101 MET Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 366 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 193 optimal weight: 0.2980 chunk 357 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 380 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** 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** Q 92 ASN W 73 ASN W 102 GLN ** q 13 GLN ** 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 = 0.3572 r_free = 0.3572 target = 0.101585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083457 restraints weight = 89247.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086098 restraints weight = 42605.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087820 restraints weight = 26150.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.088931 restraints weight = 18935.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089565 restraints weight = 15372.577| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34905 Z= 0.146 Angle : 0.902 75.238 47336 Z= 0.354 Chirality : 0.045 0.285 5163 Planarity : 0.005 0.124 5997 Dihedral : 9.519 163.005 4936 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 3.62 % Allowed : 24.77 % Favored : 71.61 % 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: -0.25 (0.13), residues: 4153 helix: 0.87 (0.12), residues: 1877 sheet: -1.10 (0.28), residues: 347 loop : -0.99 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG W 44 TYR 0.034 0.002 TYR E 69 PHE 0.032 0.002 PHE A 62 TRP 0.021 0.001 TRP I 63 HIS 0.011 0.001 HIS F 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (34864) covalent geometry : angle 0.69891 / 0.35 (47244) SS BOND : bond 0.00227 / 0.12 ( 4) SS BOND : angle 1.50345 / 0.77 ( 8) hydrogen bonds : bond 0.04113 / 2.75 ( 1417) hydrogen bonds : angle 4.97437 / 3.52 ( 4128) metal coordination : bond 0.01200 / 0.80 ( 37) metal coordination : angle 13.54243 / 9.53 ( 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 1030 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 898 time to evaluate : 1.229 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: 0.8234 (m-80) cc_final: 0.7762 (m-10) REVERT: A 19 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 38 GLU cc_start: 0.7640 (tp30) cc_final: 0.6579 (mm-30) REVERT: A 42 ASP cc_start: 0.8959 (p0) cc_final: 0.8669 (p0) REVERT: A 48 ARG cc_start: 0.8662 (tpp80) cc_final: 0.8384 (ttm-80) REVERT: A 53 MET cc_start: 0.7852 (ppp) cc_final: 0.7398 (ppp) REVERT: A 83 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8258 (pttt) REVERT: A 87 MET cc_start: 0.8588 (ttp) cc_final: 0.8343 (tmm) REVERT: B 79 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7932 (t0) REVERT: B 138 THR cc_start: 0.9436 (p) cc_final: 0.9196 (p) REVERT: B 166 ASN cc_start: 0.8957 (m-40) cc_final: 0.8725 (m110) REVERT: B 170 TYR cc_start: 0.9175 (t80) cc_final: 0.8821 (t80) REVERT: B 220 ILE cc_start: 0.9484 (tp) cc_final: 0.9264 (tp) REVERT: C 100 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.8073 (ttp-170) REVERT: C 104 ASN cc_start: 0.8483 (m-40) cc_final: 0.7335 (t0) REVERT: C 149 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (pp) REVERT: C 166 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 185 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8323 (ptp90) REVERT: C 211 TYR cc_start: 0.8522 (t80) cc_final: 0.8138 (t80) REVERT: C 216 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8314 (mmtt) REVERT: D 83 ASN cc_start: 0.7737 (p0) cc_final: 0.6567 (p0) REVERT: D 257 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8003 (mt-10) REVERT: D 265 ASN cc_start: 0.8811 (t0) cc_final: 0.8338 (t0) REVERT: D 266 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8303 (ttm110) REVERT: D 356 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8756 (pp) REVERT: E 67 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8532 (mmtt) REVERT: E 69 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.7177 (t80) REVERT: E 91 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.7252 (t60) REVERT: E 120 MET cc_start: 0.8107 (tpp) cc_final: 0.7781 (ttm) REVERT: F 53 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7106 (mt) REVERT: F 101 PHE cc_start: 0.8876 (m-10) cc_final: 0.8605 (m-80) REVERT: F 136 HIS cc_start: 0.8269 (m-70) cc_final: 0.7705 (t-90) REVERT: F 290 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7643 (mm-30) REVERT: F 390 ASP cc_start: 0.7913 (t0) cc_final: 0.7618 (t0) REVERT: F 450 MET cc_start: 0.8666 (mmp) cc_final: 0.8438 (mmp) REVERT: G 42 MET cc_start: 0.9011 (tpp) cc_final: 0.8501 (tpp) REVERT: G 114 GLU cc_start: 0.8087 (tt0) cc_final: 0.7740 (pt0) REVERT: G 136 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7693 (mt-10) REVERT: G 172 ILE cc_start: 0.9411 (mt) cc_final: 0.9211 (tp) REVERT: G 269 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: G 329 MET cc_start: 0.8060 (mmm) cc_final: 0.7358 (mmt) REVERT: G 567 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8853 (p) REVERT: G 657 ASP cc_start: 0.7505 (t0) cc_final: 0.7088 (t0) REVERT: H 24 GLU cc_start: 0.8363 (tt0) cc_final: 0.8097 (tt0) REVERT: H 61 MET cc_start: 0.7633 (mmm) cc_final: 0.6806 (tpt) REVERT: H 86 TRP cc_start: 0.9140 (m100) cc_final: 0.8658 (m100) REVERT: H 146 MET cc_start: 0.8569 (tpp) cc_final: 0.7702 (tpp) REVERT: H 163 GLN cc_start: 0.8694 (tt0) cc_final: 0.8339 (mt0) REVERT: H 184 MET cc_start: 0.9000 (mmm) cc_final: 0.8726 (mmm) REVERT: H 185 TRP cc_start: 0.8831 (t-100) cc_final: 0.8571 (t-100) REVERT: H 199 ASP cc_start: 0.7598 (t0) cc_final: 0.6855 (t0) REVERT: H 202 GLU cc_start: 0.7272 (tp30) cc_final: 0.6595 (tt0) REVERT: H 204 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7245 (tm-30) REVERT: H 253 GLU cc_start: 0.8773 (mp0) cc_final: 0.8555 (mp0) REVERT: H 271 LEU cc_start: 0.9396 (mt) cc_final: 0.9114 (mt) REVERT: H 284 GLN cc_start: 0.8812 (tp40) cc_final: 0.8519 (tp-100) REVERT: I 72 MET cc_start: 0.9168 (tpp) cc_final: 0.8850 (tpp) REVERT: I 76 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7329 (t80) REVERT: I 208 ASP cc_start: 0.8313 (t70) cc_final: 0.7415 (t70) REVERT: P 332 LEU cc_start: 0.8596 (tp) cc_final: 0.8139 (tt) REVERT: Q 70 GLU cc_start: 0.7366 (tp30) cc_final: 0.7060 (tp30) REVERT: Q 99 MET cc_start: 0.8725 (ttp) cc_final: 0.8415 (ttm) REVERT: Q 106 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8426 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8324 (t0) cc_final: 0.7387 (p0) REVERT: R 47 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7036 (ptt180) REVERT: S 31 GLN cc_start: 0.8933 (tp40) cc_final: 0.8679 (pm20) REVERT: S 66 TRP cc_start: 0.8476 (m100) cc_final: 0.8191 (m100) REVERT: T 99 SER cc_start: 0.8133 (m) cc_final: 0.7527 (p) REVERT: T 117 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7591 (mt-10) REVERT: T 123 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7706 (mt-10) REVERT: T 130 ILE cc_start: 0.9123 (mp) cc_final: 0.8875 (mp) REVERT: V 47 TYR cc_start: 0.8692 (m-80) cc_final: 0.8150 (m-80) REVERT: V 87 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8492 (tp30) REVERT: W 27 ASP cc_start: 0.9091 (p0) cc_final: 0.8735 (p0) REVERT: W 30 GLU cc_start: 0.8634 (pt0) cc_final: 0.8384 (pm20) REVERT: W 43 TYR cc_start: 0.8471 (t80) cc_final: 0.8100 (t80) REVERT: W 126 TYR cc_start: 0.9141 (m-10) cc_final: 0.8680 (m-80) REVERT: Z 21 TYR cc_start: 0.8310 (p90) cc_final: 0.7350 (p90) REVERT: Z 24 ASN cc_start: 0.8390 (t0) cc_final: 0.8163 (t0) REVERT: Z 65 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9222 (tp) REVERT: a 1 MET cc_start: 0.7120 (mmp) cc_final: 0.6728 (mmt) REVERT: a 2 TRP cc_start: 0.8614 (p-90) cc_final: 0.8164 (p-90) REVERT: a 11 ILE cc_start: 0.9157 (mm) cc_final: 0.8882 (tp) REVERT: b 16 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6595 (tt0) REVERT: b 32 MET cc_start: 0.9284 (mmt) cc_final: 0.8976 (mmt) REVERT: q 81 MET cc_start: 0.8322 (mtt) cc_final: 0.8071 (mtt) REVERT: q 132 LYS cc_start: 0.8109 (tmmt) cc_final: 0.7560 (pttp) REVERT: r 109 ASP cc_start: 0.6314 (p0) cc_final: 0.5662 (p0) REVERT: s 85 LEU cc_start: 0.7426 (tp) cc_final: 0.6590 (mt) outliers start: 132 outliers final: 91 residues processed: 971 average time/residue: 0.2042 time to fit residues: 327.3691 Evaluate side-chains 937 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 834 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 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 78 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 149 LEU 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 341 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 416 SER Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 69 TYR Chi-restraints excluded: chain E residue 91 TRP 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 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 351 THR 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 224 ASP 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 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 301 CYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP 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 207 PHE Chi-restraints excluded: chain P residue 291 TYR Chi-restraints excluded: chain P residue 307 LEU 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 38 VAL 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 57 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 96 THR 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 129 THR Chi-restraints excluded: chain Z residue 65 LEU 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 99 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain s residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 29 optimal weight: 0.3980 chunk 250 optimal weight: 6.9990 chunk 295 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 251 optimal weight: 0.7980 chunk 407 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 376 optimal weight: 0.0770 chunk 285 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN B 151 GLN B 207 GLN C 122 GLN D 112 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** E 186 GLN E 190 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 ASN ** 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 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084461 restraints weight = 89821.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087108 restraints weight = 42310.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088856 restraints weight = 25802.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089981 restraints weight = 18583.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090666 restraints weight = 15000.729| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6709 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= 0.144 Angle : 0.903 74.170 47336 Z= 0.358 Chirality : 0.045 0.278 5163 Planarity : 0.005 0.125 5997 Dihedral : 9.370 162.318 4936 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 3.68 % Allowed : 25.34 % Favored : 70.98 % 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: -0.22 (0.13), residues: 4153 helix: 0.94 (0.12), residues: 1866 sheet: -1.12 (0.26), residues: 370 loop : -1.00 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 126 TYR 0.032 0.002 TYR E 192 PHE 0.032 0.002 PHE A 62 TRP 0.031 0.001 TRP H 179 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (34864) covalent geometry : angle 0.70944 / 0.35 (47244) SS BOND : bond 0.00211 / 0.11 ( 4) SS BOND : angle 1.52148 / 0.78 ( 8) hydrogen bonds : bond 0.04039 / 2.68 ( 1417) hydrogen bonds : angle 4.97196 / 3.52 ( 4128) metal coordination : bond 0.01073 / 0.70 ( 37) metal coordination : angle 13.28389 / 9.47 ( 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 1023 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 889 time to evaluate : 1.351 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 8 PHE cc_start: 0.8257 (m-80) cc_final: 0.7806 (m-10) REVERT: A 19 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8354 (tp) REVERT: A 38 GLU cc_start: 0.7555 (tp30) cc_final: 0.6333 (mm-30) REVERT: A 42 ASP cc_start: 0.8844 (p0) cc_final: 0.8628 (p0) REVERT: A 48 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8335 (ttm-80) REVERT: A 53 MET cc_start: 0.7840 (ppp) cc_final: 0.7461 (ppp) REVERT: A 72 LEU cc_start: 0.9255 (mt) cc_final: 0.9010 (tp) REVERT: A 83 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8178 (pttt) REVERT: A 87 MET cc_start: 0.8698 (ttp) cc_final: 0.8445 (tmm) REVERT: B 79 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (t0) REVERT: B 138 THR cc_start: 0.9405 (p) cc_final: 0.9187 (p) REVERT: B 161 MET cc_start: 0.8469 (tpp) cc_final: 0.8084 (tpt) REVERT: B 166 ASN cc_start: 0.8936 (m-40) cc_final: 0.8671 (m110) REVERT: B 170 TYR cc_start: 0.9237 (t80) cc_final: 0.8812 (t80) REVERT: B 173 TYR cc_start: 0.8919 (m-80) cc_final: 0.8684 (m-80) REVERT: B 220 ILE cc_start: 0.9488 (tp) cc_final: 0.9245 (tp) REVERT: C 104 ASN cc_start: 0.8459 (m-40) cc_final: 0.7156 (t0) REVERT: C 166 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 185 ARG cc_start: 0.8618 (ptp90) cc_final: 0.8356 (ptp90) REVERT: C 211 TYR cc_start: 0.8430 (t80) cc_final: 0.8010 (t80) REVERT: C 216 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8308 (mmtt) REVERT: D 83 ASN cc_start: 0.7589 (p0) cc_final: 0.6404 (p0) REVERT: D 104 GLU cc_start: 0.7857 (tt0) cc_final: 0.7657 (tt0) REVERT: D 257 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8006 (mt-10) REVERT: D 265 ASN cc_start: 0.8910 (t0) cc_final: 0.8203 (t0) REVERT: D 266 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8192 (ttm110) REVERT: D 296 SER cc_start: 0.9008 (m) cc_final: 0.8357 (t) REVERT: D 356 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8733 (pp) REVERT: D 443 MET cc_start: 0.7318 (mtm) cc_final: 0.7084 (mtm) REVERT: E 67 LYS cc_start: 0.8647 (ptmt) cc_final: 0.8419 (mmtt) REVERT: E 69 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6970 (t80) REVERT: E 91 TRP cc_start: 0.7528 (OUTLIER) cc_final: 0.7247 (t60) REVERT: E 120 MET cc_start: 0.8181 (tpp) cc_final: 0.7741 (ttm) REVERT: E 153 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8281 (mtm-85) REVERT: E 192 TYR cc_start: 0.8534 (m-80) cc_final: 0.8151 (m-80) REVERT: F 53 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7096 (mt) REVERT: F 101 PHE cc_start: 0.8834 (m-10) cc_final: 0.8516 (m-80) REVERT: F 136 HIS cc_start: 0.8116 (m-70) cc_final: 0.7725 (t-90) REVERT: F 290 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7610 (mm-30) REVERT: F 390 ASP cc_start: 0.8034 (t0) cc_final: 0.7717 (t0) REVERT: F 429 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7076 (t0) REVERT: F 450 MET cc_start: 0.8703 (mmp) cc_final: 0.8476 (mmp) REVERT: G 42 MET cc_start: 0.8996 (tpp) cc_final: 0.8729 (mmm) REVERT: G 114 GLU cc_start: 0.8150 (tt0) cc_final: 0.7665 (pt0) REVERT: G 136 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7424 (mt-10) REVERT: G 269 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7068 (pt0) REVERT: G 329 MET cc_start: 0.8067 (mmm) cc_final: 0.7464 (mmt) REVERT: G 567 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8718 (p) REVERT: G 618 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8201 (mt-10) REVERT: G 657 ASP cc_start: 0.7577 (t0) cc_final: 0.7130 (t0) REVERT: G 666 GLN cc_start: 0.7672 (pm20) cc_final: 0.7432 (pm20) REVERT: H 17 MET cc_start: 0.8866 (tmm) cc_final: 0.8576 (tmm) REVERT: H 24 GLU cc_start: 0.8499 (tt0) cc_final: 0.8171 (tt0) REVERT: H 32 GLN cc_start: 0.9230 (mt0) cc_final: 0.8895 (mt0) REVERT: H 53 MET cc_start: 0.8973 (tpp) cc_final: 0.8442 (ttm) REVERT: H 86 TRP cc_start: 0.9073 (m100) cc_final: 0.8451 (m100) REVERT: H 146 MET cc_start: 0.8578 (tpp) cc_final: 0.7815 (tpp) REVERT: H 163 GLN cc_start: 0.8799 (tt0) cc_final: 0.8391 (mt0) REVERT: H 184 MET cc_start: 0.9142 (mmm) cc_final: 0.8802 (mmm) REVERT: H 185 TRP cc_start: 0.8770 (t-100) cc_final: 0.8532 (t-100) REVERT: H 199 ASP cc_start: 0.7657 (t0) cc_final: 0.7031 (t0) REVERT: H 202 GLU cc_start: 0.7152 (tp30) cc_final: 0.6530 (tt0) REVERT: H 204 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7139 (tm-30) REVERT: I 36 TYR cc_start: 0.8742 (p90) cc_final: 0.8250 (p90) REVERT: I 72 MET cc_start: 0.9227 (tpp) cc_final: 0.8882 (tpp) REVERT: I 76 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7606 (t80) REVERT: I 206 GLN cc_start: 0.9093 (tp40) cc_final: 0.8477 (tm-30) REVERT: I 208 ASP cc_start: 0.8420 (t70) cc_final: 0.7437 (t70) REVERT: P 55 VAL cc_start: 0.8907 (t) cc_final: 0.8659 (p) REVERT: P 332 LEU cc_start: 0.8578 (tp) cc_final: 0.8095 (tt) REVERT: Q 70 GLU cc_start: 0.7521 (tp30) cc_final: 0.7287 (tp30) REVERT: Q 106 ARG cc_start: 0.8926 (mtt-85) cc_final: 0.8380 (mtt-85) REVERT: R 47 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7038 (ptt180) REVERT: R 93 ILE cc_start: 0.9364 (mt) cc_final: 0.9032 (mt) REVERT: R 95 LEU cc_start: 0.8352 (tp) cc_final: 0.7853 (tp) REVERT: S 31 GLN cc_start: 0.8959 (tp40) cc_final: 0.8682 (pm20) REVERT: S 66 TRP cc_start: 0.8492 (m100) cc_final: 0.8187 (m100) REVERT: T 92 LYS cc_start: 0.8495 (tttm) cc_final: 0.8034 (tmtt) REVERT: T 99 SER cc_start: 0.8140 (m) cc_final: 0.7471 (p) REVERT: T 117 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7640 (mt-10) REVERT: T 136 GLU cc_start: 0.8656 (pm20) cc_final: 0.8444 (pm20) REVERT: V 87 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: W 27 ASP cc_start: 0.9099 (p0) cc_final: 0.8509 (p0) REVERT: W 30 GLU cc_start: 0.8732 (pt0) cc_final: 0.8380 (pm20) REVERT: W 43 TYR cc_start: 0.8407 (t80) cc_final: 0.8106 (t80) REVERT: W 120 ASP cc_start: 0.8163 (p0) cc_final: 0.7960 (p0) REVERT: W 126 TYR cc_start: 0.9116 (m-10) cc_final: 0.8663 (m-80) REVERT: Z 21 TYR cc_start: 0.8398 (p90) cc_final: 0.7375 (p90) REVERT: Z 24 ASN cc_start: 0.8474 (t0) cc_final: 0.8061 (t0) REVERT: Z 65 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9199 (tp) REVERT: Z 133 MET cc_start: 0.7823 (ttt) cc_final: 0.7342 (tmm) REVERT: Z 143 TYR cc_start: 0.8086 (p90) cc_final: 0.7865 (p90) REVERT: a 1 MET cc_start: 0.7088 (mmp) cc_final: 0.6815 (mmt) REVERT: a 2 TRP cc_start: 0.8546 (p-90) cc_final: 0.8235 (p-90) REVERT: a 11 ILE cc_start: 0.9054 (mm) cc_final: 0.8711 (tp) REVERT: b 16 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6605 (tt0) REVERT: b 32 MET cc_start: 0.9368 (mmt) cc_final: 0.8987 (mmt) REVERT: b 44 MET cc_start: 0.8420 (ptp) cc_final: 0.8047 (ptp) REVERT: q 54 GLN cc_start: 0.7216 (tp40) cc_final: 0.7015 (tp40) REVERT: q 93 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6997 (mtm) REVERT: q 132 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7704 (pttp) REVERT: r 109 ASP cc_start: 0.6368 (p0) cc_final: 0.5692 (p0) REVERT: s 85 LEU cc_start: 0.7350 (tp) cc_final: 0.6544 (mt) outliers start: 134 outliers final: 91 residues processed: 960 average time/residue: 0.2056 time to fit residues: 327.5603 Evaluate side-chains 948 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 844 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 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 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 78 SER 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 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 416 SER 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 91 TRP 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 158 ILE 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 429 ASP 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 254 MET 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 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 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 240 ILE Chi-restraints excluded: chain H residue 301 CYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP 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 291 TYR Chi-restraints excluded: chain P residue 307 LEU 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 38 VAL Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 128 PHE 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 115 THR Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 65 LEU 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 93 MET Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU 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: 0.5980 chunk 234 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN B 151 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** 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 ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** q 13 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.101486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.083248 restraints weight = 90076.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085964 restraints weight = 41817.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087724 restraints weight = 25253.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.088847 restraints weight = 18168.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089494 restraints weight = 14694.231| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34905 Z= 0.162 Angle : 0.913 74.697 47336 Z= 0.362 Chirality : 0.045 0.269 5163 Planarity : 0.005 0.125 5997 Dihedral : 9.136 159.219 4932 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 3.40 % Allowed : 26.00 % Favored : 70.59 % 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: -0.22 (0.13), residues: 4153 helix: 0.96 (0.12), residues: 1859 sheet: -1.17 (0.26), residues: 381 loop : -1.00 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 68 TYR 0.031 0.002 TYR I 185 PHE 0.031 0.002 PHE A 62 TRP 0.027 0.001 TRP H 179 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (34864) covalent geometry : angle 0.71673 / 0.36 (47244) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 1.45133 / 0.75 ( 8) hydrogen bonds : bond 0.04015 / 2.66 ( 1417) hydrogen bonds : angle 4.95916 / 3.52 ( 4128) metal coordination : bond 0.01497 / 0.94 ( 37) metal coordination : angle 13.45503 / 9.57 ( 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 999 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 875 time to evaluate : 1.368 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: 0.8264 (m-80) cc_final: 0.7817 (m-10) REVERT: A 19 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 53 MET cc_start: 0.7846 (ppp) cc_final: 0.7482 (ppp) REVERT: A 83 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8269 (pttt) REVERT: A 87 MET cc_start: 0.8755 (ttp) cc_final: 0.8485 (tmm) REVERT: B 79 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7882 (t0) REVERT: B 122 ARG cc_start: 0.8350 (tpt170) cc_final: 0.7953 (tpp-160) REVERT: B 138 THR cc_start: 0.9407 (p) cc_final: 0.9202 (p) REVERT: B 147 LYS cc_start: 0.8901 (tppt) cc_final: 0.8352 (tttm) REVERT: B 166 ASN cc_start: 0.8969 (m-40) cc_final: 0.8722 (m110) REVERT: B 170 TYR cc_start: 0.9286 (t80) cc_final: 0.8788 (t80) REVERT: B 173 TYR cc_start: 0.8943 (m-80) cc_final: 0.8716 (m-80) REVERT: B 220 ILE cc_start: 0.9498 (tp) cc_final: 0.9244 (tp) REVERT: C 104 ASN cc_start: 0.8483 (m-40) cc_final: 0.7207 (t0) REVERT: C 166 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 185 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8071 (ptp-170) REVERT: C 211 TYR cc_start: 0.8474 (t80) cc_final: 0.8088 (t80) REVERT: C 216 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8424 (mmtt) REVERT: D 265 ASN cc_start: 0.8961 (t0) cc_final: 0.8246 (t0) REVERT: D 296 SER cc_start: 0.8987 (m) cc_final: 0.8438 (t) REVERT: D 356 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8745 (pp) REVERT: E 67 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8409 (mmtt) REVERT: E 69 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6952 (t80) REVERT: E 91 TRP cc_start: 0.7567 (OUTLIER) cc_final: 0.7279 (t60) REVERT: E 153 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8271 (mtm-85) REVERT: E 189 ASP cc_start: 0.6431 (t0) cc_final: 0.6205 (t0) REVERT: E 192 TYR cc_start: 0.8596 (m-80) cc_final: 0.7951 (m-10) REVERT: F 53 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7196 (mt) REVERT: F 101 PHE cc_start: 0.8776 (m-10) cc_final: 0.8434 (m-80) REVERT: F 136 HIS cc_start: 0.8005 (m-70) cc_final: 0.7622 (t-90) REVERT: F 290 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7763 (mm-30) REVERT: F 390 ASP cc_start: 0.8097 (t0) cc_final: 0.7777 (t0) REVERT: F 429 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.6999 (t0) REVERT: F 433 TRP cc_start: 0.8967 (m-10) cc_final: 0.8754 (m-10) REVERT: F 450 MET cc_start: 0.8691 (mmp) cc_final: 0.8451 (mmp) REVERT: G 42 MET cc_start: 0.9060 (tpp) cc_final: 0.8793 (mmm) REVERT: G 114 GLU cc_start: 0.8178 (tt0) cc_final: 0.7697 (pt0) REVERT: G 136 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7391 (mt-10) REVERT: G 260 ASN cc_start: 0.9113 (m-40) cc_final: 0.8910 (m-40) REVERT: G 269 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7077 (pt0) REVERT: G 329 MET cc_start: 0.8104 (mmm) cc_final: 0.7464 (mmt) REVERT: G 567 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8714 (p) REVERT: G 618 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8140 (mt-10) REVERT: G 657 ASP cc_start: 0.7636 (t0) cc_final: 0.7210 (t0) REVERT: H 17 MET cc_start: 0.8875 (tmm) cc_final: 0.8572 (tmm) REVERT: H 25 ARG cc_start: 0.8726 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: H 32 GLN cc_start: 0.9230 (mt0) cc_final: 0.8818 (mt0) REVERT: H 53 MET cc_start: 0.9064 (tpp) cc_final: 0.8563 (ttm) REVERT: H 86 TRP cc_start: 0.9127 (m100) cc_final: 0.8458 (m100) REVERT: H 146 MET cc_start: 0.8598 (tpp) cc_final: 0.7789 (tpp) REVERT: H 163 GLN cc_start: 0.8833 (tt0) cc_final: 0.8466 (mt0) REVERT: H 184 MET cc_start: 0.9167 (mmm) cc_final: 0.8721 (mmm) REVERT: H 199 ASP cc_start: 0.7640 (t0) cc_final: 0.6920 (t0) REVERT: H 202 GLU cc_start: 0.7183 (tp30) cc_final: 0.6717 (tt0) REVERT: H 204 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7199 (tm-30) REVERT: H 248 TYR cc_start: 0.7936 (m-10) cc_final: 0.7593 (m-10) REVERT: I 36 TYR cc_start: 0.8767 (p90) cc_final: 0.8260 (p90) REVERT: I 72 MET cc_start: 0.9235 (tpp) cc_final: 0.8830 (tpp) REVERT: I 76 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7579 (t80) REVERT: I 181 GLU cc_start: 0.8232 (mp0) cc_final: 0.7991 (mp0) REVERT: I 206 GLN cc_start: 0.9140 (tp40) cc_final: 0.8509 (tm-30) REVERT: I 208 ASP cc_start: 0.8471 (t70) cc_final: 0.7515 (t70) REVERT: P 55 VAL cc_start: 0.8937 (t) cc_final: 0.8697 (p) REVERT: P 332 LEU cc_start: 0.8600 (tp) cc_final: 0.8109 (tt) REVERT: Q 70 GLU cc_start: 0.7574 (tp30) cc_final: 0.7303 (tp30) REVERT: Q 106 ARG cc_start: 0.8933 (mtt-85) cc_final: 0.8338 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8106 (t70) cc_final: 0.7651 (p0) REVERT: Q 124 MET cc_start: 0.8253 (mmm) cc_final: 0.8015 (tpp) REVERT: R 47 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7014 (ptt180) REVERT: R 93 ILE cc_start: 0.9354 (mt) cc_final: 0.9139 (mt) REVERT: R 95 LEU cc_start: 0.8367 (tp) cc_final: 0.7632 (pp) REVERT: S 31 GLN cc_start: 0.8976 (tp40) cc_final: 0.8706 (pm20) REVERT: S 62 GLN cc_start: 0.8796 (pm20) cc_final: 0.8385 (pp30) REVERT: S 66 TRP cc_start: 0.8608 (m100) cc_final: 0.8280 (m100) REVERT: T 92 LYS cc_start: 0.8546 (tttm) cc_final: 0.8312 (tttm) REVERT: T 99 SER cc_start: 0.8134 (m) cc_final: 0.7588 (p) REVERT: T 117 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7612 (mt-10) REVERT: V 85 GLU cc_start: 0.9052 (pt0) cc_final: 0.8746 (pt0) REVERT: V 87 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8497 (tp30) REVERT: W 27 ASP cc_start: 0.9097 (p0) cc_final: 0.8555 (p0) REVERT: W 30 GLU cc_start: 0.8759 (pt0) cc_final: 0.8455 (pm20) REVERT: W 37 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8848 (mt-10) REVERT: W 43 TYR cc_start: 0.8522 (t80) cc_final: 0.8228 (t80) REVERT: W 120 ASP cc_start: 0.8101 (p0) cc_final: 0.7868 (p0) REVERT: W 126 TYR cc_start: 0.9135 (m-10) cc_final: 0.8769 (m-80) REVERT: Z 21 TYR cc_start: 0.8471 (p90) cc_final: 0.7583 (p90) REVERT: Z 24 ASN cc_start: 0.8503 (t0) cc_final: 0.8273 (t0) REVERT: Z 65 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9107 (tp) REVERT: a 1 MET cc_start: 0.6994 (mmp) cc_final: 0.6779 (mmt) REVERT: a 2 TRP cc_start: 0.8623 (p-90) cc_final: 0.8037 (p-90) REVERT: a 11 ILE cc_start: 0.9017 (mm) cc_final: 0.8716 (tp) REVERT: a 54 ILE cc_start: 0.8704 (mm) cc_final: 0.8403 (mm) REVERT: b 16 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6640 (tt0) REVERT: b 32 MET cc_start: 0.9399 (mmt) cc_final: 0.8989 (mmt) REVERT: b 44 MET cc_start: 0.8416 (ptp) cc_final: 0.8082 (ptp) REVERT: q 132 LYS cc_start: 0.8324 (tmmt) cc_final: 0.7930 (pttp) REVERT: s 85 LEU cc_start: 0.7354 (tp) cc_final: 0.6553 (mt) outliers start: 124 outliers final: 100 residues processed: 940 average time/residue: 0.1997 time to fit residues: 312.5269 Evaluate side-chains 953 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 841 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 98 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 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 78 SER 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 99 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 158 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 D residue 416 SER 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 91 TRP 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 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 429 ASP 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 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 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 301 CYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP 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 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 38 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 53 MET Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 96 THR 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 129 THR Chi-restraints excluded: chain Z residue 65 LEU 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 99 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 126 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 410 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 266 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN E 47 ASN E 190 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** q 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080494 restraints weight = 91620.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083133 restraints weight = 42673.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084837 restraints weight = 25875.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085949 restraints weight = 18702.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.086662 restraints weight = 15147.797| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.7033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 34905 Z= 0.247 Angle : 0.988 77.921 47336 Z= 0.396 Chirality : 0.049 0.265 5163 Planarity : 0.005 0.125 5997 Dihedral : 9.267 154.463 4932 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.62 % Allowed : 26.14 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 4153 helix: 0.75 (0.12), residues: 1872 sheet: -1.36 (0.26), residues: 384 loop : -1.05 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 72 TYR 0.037 0.002 TYR I 185 PHE 0.027 0.002 PHE A 62 TRP 0.025 0.002 TRP H 179 HIS 0.015 0.001 HIS F 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (34864) covalent geometry : angle 0.77855 / 0.39 (47244) SS BOND : bond 0.00193 / 0.10 ( 4) SS BOND : angle 1.63334 / 0.86 ( 8) hydrogen bonds : bond 0.04316 / 2.85 ( 1417) hydrogen bonds : angle 5.11364 / 3.64 ( 4128) metal coordination : bond 0.02617 / 1.59 ( 37) metal coordination : angle 14.43669 / 10.06 ( 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 964 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 832 time to evaluate : 1.286 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: 0.8320 (m-80) cc_final: 0.7838 (m-10) REVERT: A 19 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8395 (tp) REVERT: A 38 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 42 ASP cc_start: 0.8769 (p0) cc_final: 0.8508 (p0) REVERT: A 53 MET cc_start: 0.7882 (ppp) cc_final: 0.7525 (ppp) REVERT: A 72 LEU cc_start: 0.9293 (mt) cc_final: 0.9064 (tp) REVERT: A 83 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8353 (pttt) REVERT: A 87 MET cc_start: 0.8815 (ttp) cc_final: 0.8495 (tmm) REVERT: B 79 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8064 (t0) REVERT: B 147 LYS cc_start: 0.8968 (tppt) cc_final: 0.8410 (tttm) REVERT: B 161 MET cc_start: 0.8711 (tpp) cc_final: 0.8229 (tpt) REVERT: B 166 ASN cc_start: 0.9091 (m-40) cc_final: 0.8816 (m110) REVERT: B 170 TYR cc_start: 0.9375 (t80) cc_final: 0.8789 (t80) REVERT: B 220 ILE cc_start: 0.9513 (tp) cc_final: 0.9257 (tp) REVERT: C 100 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8132 (ttp-170) REVERT: C 104 ASN cc_start: 0.8697 (m-40) cc_final: 0.7288 (t0) REVERT: C 166 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8121 (mt-10) REVERT: C 185 ARG cc_start: 0.8695 (ptp90) cc_final: 0.8124 (ptp-170) REVERT: C 211 TYR cc_start: 0.8642 (t80) cc_final: 0.8225 (t80) REVERT: D 83 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7731 (p0) REVERT: D 265 ASN cc_start: 0.9038 (t0) cc_final: 0.8419 (t0) REVERT: D 356 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8799 (pp) REVERT: E 67 LYS cc_start: 0.8617 (ptmt) cc_final: 0.8337 (mmtt) REVERT: E 69 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6923 (t80) REVERT: E 91 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.7290 (t60) REVERT: E 120 MET cc_start: 0.7985 (ttm) cc_final: 0.7724 (ttm) REVERT: E 121 TYR cc_start: 0.8886 (m-80) cc_final: 0.8621 (m-10) REVERT: E 153 ARG cc_start: 0.8704 (mtp180) cc_final: 0.8328 (mtm-85) REVERT: E 192 TYR cc_start: 0.8545 (m-80) cc_final: 0.8053 (m-80) REVERT: F 53 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7237 (mt) REVERT: F 101 PHE cc_start: 0.8819 (m-10) cc_final: 0.8467 (m-80) REVERT: F 136 HIS cc_start: 0.8078 (m-70) cc_final: 0.7635 (t-90) REVERT: F 170 GLN cc_start: 0.8265 (mt0) cc_final: 0.8032 (mt0) REVERT: F 290 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7623 (tp30) REVERT: F 390 ASP cc_start: 0.8165 (t0) cc_final: 0.7907 (t0) REVERT: F 429 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7148 (t0) REVERT: F 450 MET cc_start: 0.8704 (mmp) cc_final: 0.8461 (mmp) REVERT: G 62 ARG cc_start: 0.8607 (ptt-90) cc_final: 0.8257 (ptt90) REVERT: G 136 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 161 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: G 269 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7127 (pt0) REVERT: G 329 MET cc_start: 0.8191 (mmm) cc_final: 0.7429 (mmt) REVERT: G 567 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8845 (p) REVERT: G 657 ASP cc_start: 0.7714 (t0) cc_final: 0.7289 (t0) REVERT: H 32 GLN cc_start: 0.9236 (mt0) cc_final: 0.8781 (mt0) REVERT: H 79 LEU cc_start: 0.9197 (tp) cc_final: 0.8970 (tp) REVERT: H 163 GLN cc_start: 0.8835 (tt0) cc_final: 0.8542 (mt0) REVERT: H 173 TRP cc_start: 0.9007 (m-10) cc_final: 0.8752 (m-10) REVERT: H 184 MET cc_start: 0.9168 (mmm) cc_final: 0.8547 (mmm) REVERT: H 199 ASP cc_start: 0.7878 (t0) cc_final: 0.7115 (t0) REVERT: H 202 GLU cc_start: 0.7495 (tp30) cc_final: 0.7168 (tt0) REVERT: H 248 TYR cc_start: 0.7968 (m-10) cc_final: 0.7606 (m-10) REVERT: H 253 GLU cc_start: 0.8715 (mp0) cc_final: 0.8319 (mp0) REVERT: I 36 TYR cc_start: 0.8907 (p90) cc_final: 0.8292 (p90) REVERT: I 50 MET cc_start: 0.8146 (pmm) cc_final: 0.7528 (tpp) REVERT: I 72 MET cc_start: 0.9195 (tpp) cc_final: 0.8811 (tpp) REVERT: I 76 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7414 (t80) REVERT: I 206 GLN cc_start: 0.9173 (tp40) cc_final: 0.8943 (tp40) REVERT: I 208 ASP cc_start: 0.8520 (t70) cc_final: 0.7691 (t70) REVERT: P 55 VAL cc_start: 0.9054 (t) cc_final: 0.8809 (p) REVERT: P 154 GLN cc_start: 0.8387 (tp40) cc_final: 0.8083 (tp40) REVERT: Q 70 GLU cc_start: 0.7579 (tp30) cc_final: 0.7264 (tp30) REVERT: Q 106 ARG cc_start: 0.8946 (mtt-85) cc_final: 0.8350 (mtt-85) REVERT: Q 119 ASP cc_start: 0.8149 (t70) cc_final: 0.7680 (p0) REVERT: Q 124 MET cc_start: 0.8324 (mmm) cc_final: 0.8043 (tpp) REVERT: R 47 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7165 (ptt180) REVERT: R 93 ILE cc_start: 0.9410 (mt) cc_final: 0.9197 (mt) REVERT: R 95 LEU cc_start: 0.8315 (tp) cc_final: 0.8086 (tp) REVERT: S 31 GLN cc_start: 0.9010 (tp40) cc_final: 0.8694 (pm20) REVERT: S 62 GLN cc_start: 0.8785 (pm20) cc_final: 0.8370 (pp30) REVERT: S 66 TRP cc_start: 0.8669 (m100) cc_final: 0.8302 (m100) REVERT: S 68 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7580 (ttt90) REVERT: T 92 LYS cc_start: 0.8572 (tttm) cc_final: 0.8346 (tttm) REVERT: T 99 SER cc_start: 0.8068 (m) cc_final: 0.7696 (p) REVERT: T 117 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7738 (mt-10) REVERT: V 85 GLU cc_start: 0.9088 (pt0) cc_final: 0.8821 (pt0) REVERT: V 87 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8509 (tp30) REVERT: W 27 ASP cc_start: 0.9063 (p0) cc_final: 0.8522 (p0) REVERT: W 30 GLU cc_start: 0.8774 (pt0) cc_final: 0.8473 (pm20) REVERT: W 43 TYR cc_start: 0.8646 (t80) cc_final: 0.8285 (t80) REVERT: W 120 ASP cc_start: 0.8136 (p0) cc_final: 0.7906 (p0) REVERT: X 19 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8612 (ptpp) REVERT: Z 65 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9056 (tp) REVERT: a 1 MET cc_start: 0.6942 (mmp) cc_final: 0.6697 (mmt) REVERT: a 2 TRP cc_start: 0.8727 (p-90) cc_final: 0.8240 (p-90) REVERT: b 16 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6619 (tt0) REVERT: b 44 MET cc_start: 0.8518 (ptp) cc_final: 0.8135 (ptp) REVERT: q 34 ARG cc_start: 0.6660 (mtp85) cc_final: 0.6375 (mtp85) REVERT: s 85 LEU cc_start: 0.7430 (tp) cc_final: 0.6621 (mt) outliers start: 132 outliers final: 108 residues processed: 907 average time/residue: 0.1952 time to fit residues: 294.5648 Evaluate side-chains 926 residues out of total 3642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 804 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 98 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 163 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 93 ILE 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 83 ASN 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 270 ASN 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 416 SER Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 69 TYR 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 190 ASN Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 182 ILE 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 429 ASP 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 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 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 301 CYS Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 63 TRP 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 I residue 184 LEU Chi-restraints excluded: chain I residue 193 ASN 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 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 38 VAL Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 87 GLU Chi-restraints excluded: chain W residue 53 MET Chi-restraints excluded: chain W residue 58 THR 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 129 THR Chi-restraints excluded: chain Z residue 65 LEU 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 b residue 31 ILE Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain q residue 65 THR Chi-restraints excluded: chain q residue 99 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain s residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 299 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 224 optimal weight: 0.9980 chunk 198 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 394 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN E 47 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** r 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.100988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082916 restraints weight = 89754.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085600 restraints weight = 41628.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087356 restraints weight = 25109.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.088481 restraints weight = 18029.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.089187 restraints weight = 14533.539| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.7165 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= 0.151 Angle : 0.941 74.263 47336 Z= 0.377 Chirality : 0.046 0.331 5163 Planarity : 0.006 0.137 5997 Dihedral : 9.121 156.154 4932 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.29 % Favored : 95.67 % Rotamer: Outliers : 3.13 % Allowed : 26.83 % Favored : 70.04 % 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: 0.75 (0.12), residues: 1868 sheet: -1.28 (0.27), residues: 370 loop : -1.04 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG r 6 TYR 0.032 0.002 TYR E 192 PHE 0.031 0.002 PHE A 62 TRP 0.037 0.002 TRP H 179 HIS 0.006 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (34864) covalent geometry : angle 0.75012 / 0.37 (47244) SS BOND : bond 0.00160 / 0.08 ( 4) SS BOND : angle 1.61884 / 0.83 ( 8) hydrogen bonds : bond 0.04117 / 2.71 ( 1417) hydrogen bonds : angle 5.01701 / 3.56 ( 4128) metal coordination : bond 0.01183 / 0.78 ( 37) metal coordination : angle 13.50695 / 9.57 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7964.37 seconds wall clock time: 137 minutes 50.85 seconds (8270.85 seconds total)