Starting phenix.real_space_refine on Tue May 5 23:18:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibe_35341/05_2026/8ibe_35341_neut.cif" } resolution = 3.3 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= 0.086 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 245 5.16 5 C 21935 2.51 5 N 5816 2.21 5 O 6218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34255 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 2 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1643 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: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2532 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1025 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain breaks: 1 Chain: "r" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 10, 'TRANS': 73} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 104 Unusual residues: {'PC1': 2, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 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: "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 1045 SG CYS B 99 79.971 62.744 106.538 1.00 29.52 S ATOM 1051 SG CYS B 100 79.374 57.575 104.034 1.00 30.11 S ATOM 1548 SG CYS B 164 76.984 57.987 108.072 1.00 28.96 S ATOM 1778 SG CYS B 194 83.306 58.362 108.837 1.00 29.28 S ATOM 7560 SG CYS E 134 140.655 53.627 151.637 1.00 56.01 S ATOM 7594 SG CYS E 139 143.458 55.400 150.700 1.00 56.50 S ATOM 7878 SG CYS E 175 138.393 57.247 154.160 1.00 54.42 S ATOM 7901 SG CYS E 179 141.619 59.144 153.879 1.00 57.95 S ATOM 11431 SG CYS F 425 122.072 62.914 154.351 1.00 45.60 S ATOM 11109 SG CYS F 385 122.108 60.443 148.556 1.00 39.95 S ATOM 11089 SG CYS F 382 117.841 61.596 150.828 1.00 40.29 S ATOM 11070 SG CYS F 379 119.812 57.531 153.685 1.00 43.09 S ATOM 12479 SG CYS G 131 101.752 50.374 137.246 1.00 31.31 S ATOM 12458 SG CYS G 128 103.760 54.215 132.649 1.00 30.26 S ATOM 12519 SG CYS G 137 101.405 56.279 138.666 1.00 33.13 S ATOM 13204 SG CYS G 226 103.276 50.389 145.836 1.00 34.31 S ATOM 12875 SG CYS G 182 106.340 49.003 151.068 1.00 36.31 S ATOM 12851 SG CYS G 179 105.789 54.301 149.048 1.00 35.62 S ATOM 12828 SG CYS G 176 109.244 50.040 146.584 1.00 34.05 S ATOM 11965 SG CYS G 64 107.183 60.345 151.061 1.00 35.53 S ATOM 12051 SG CYS G 75 107.907 62.388 149.395 1.00 36.47 S ATOM 12076 SG CYS G 78 106.769 66.950 151.534 1.00 36.76 S ATOM 12177 SG CYS G 92 104.312 64.874 153.474 1.00 39.04 S ATOM 20407 SG CYS I 152 87.334 52.238 113.229 1.00 27.39 S ATOM 20181 SG CYS I 123 86.976 53.396 118.580 1.00 27.30 S ATOM 20433 SG CYS I 155 89.786 57.064 114.797 1.00 27.04 S ATOM 20454 SG CYS I 158 92.873 51.836 115.712 1.00 26.60 S ATOM 20153 SG CYS I 119 93.115 49.189 122.201 1.00 28.85 S ATOM 20483 SG CYS I 162 99.373 48.897 120.072 1.00 28.07 S ATOM 20111 SG CYS I 113 95.914 44.048 122.447 1.00 28.61 S ATOM 20130 SG CYS I 116 98.409 48.425 126.060 1.00 29.24 S ATOM 24965 SG CYS R 79 112.464 42.148 125.035 1.00 32.60 S ATOM 25141 SG CYS R 104 110.017 40.794 126.493 1.00 32.49 S ATOM 25163 SG CYS R 107 109.353 41.446 123.066 1.00 30.78 S Time building chain proxies: 8.21, per 1000 atoms: 0.24 Number of scatterers: 34255 At special positions: 0 Unit cell: (168.3, 129.8, 202.4, 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 245 16.00 P 12 15.00 O 6218 8.00 N 5816 7.00 C 21935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 164 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7904 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 33 sheets defined 48.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 removed outlier: 3.508A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 removed outlier: 4.083A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 109 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.763A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.912A pdb=" N ASP B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.229A pdb=" N ILE B 184 " --> pdb=" O GLY B 180 " (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: 3.959A 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: 4.321A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.035A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.925A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.736A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 143 through 159 removed outlier: 4.133A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 216 removed outlier: 3.829A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.088A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.750A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.525A pdb=" N LYS D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.677A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.833A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.632A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.614A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.558A 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 133 removed outlier: 4.183A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.033A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.635A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.259A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.600A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.016A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.862A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.061A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.645A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.350A 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: 3.773A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.713A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.931A 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 377 through 381 removed outlier: 4.550A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.588A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.008A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.675A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 2 through 32 removed outlier: 3.605A pdb=" N VAL H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.397A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU H 28 " --> pdb=" O GLU H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 3.902A pdb=" N ALA H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.704A pdb=" N LEU H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 123 removed outlier: 3.671A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 3.518A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.675A pdb=" N LEU H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 191 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.803A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 226 removed outlier: 3.586A pdb=" N PHE H 220 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 252 through 275 removed outlier: 4.396A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 265 " --> pdb=" O MET H 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 273 " --> pdb=" O THR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.607A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 312 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 58 Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.771A pdb=" N MET I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.284A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.590A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 114 through 122 removed outlier: 4.504A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 Processing helix chain 'P' and resid 178 through 195 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.118A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.904A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 333 through 339 removed outlier: 3.989A pdb=" N ASP P 337 " --> pdb=" O PRO P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.284A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.519A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'R' and resid 42 through 49 removed outlier: 4.168A pdb=" N ARG R 47 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.310A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.708A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.680A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.989A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.947A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.544A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.679A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.054A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.894A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.900A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.544A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.659A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.717A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 4 through 13 removed outlier: 4.428A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 27 Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.667A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.579A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.534A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.740A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 28 Processing helix chain 'q' and resid 43 through 45 No H-bonds generated for 'chain 'q' and resid 43 through 45' Processing helix chain 'q' and resid 68 through 72 removed outlier: 4.361A pdb=" N ASN q 72 " --> pdb=" O ASN q 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.201A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.983A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.724A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) Processing helix chain 's' and resid 78 through 88 removed outlier: 3.744A pdb=" N ASN s 84 " --> pdb=" O PHE s 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.138A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 189 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.859A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.398A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.558A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA7, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.566A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.150A 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=AB1, 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=AB2, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.775A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.312A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB7, 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: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.323A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC1, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.573A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC4, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.863A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.848A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.368A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AC8, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD3, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 53 through 57 Processing sheet with id=AD5, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'q' and resid 37 through 41 removed outlier: 3.824A pdb=" N THR q 37 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) 1325 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.33: 10221 1.33 - 1.56: 24333 1.56 - 1.78: 100 1.78 - 2.00: 342 2.00 - 2.23: 80 Bond restraints: 35076 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.648 0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb=" N PRO G 532 " pdb=" CD PRO G 532 " ideal model delta sigma weight residual 1.473 1.296 0.177 1.40e-02 5.10e+03 1.59e+02 bond pdb=" N PRO W 131 " pdb=" CD PRO W 131 " ideal model delta sigma weight residual 1.473 1.299 0.174 1.40e-02 5.10e+03 1.54e+02 bond pdb=" N PRO A 36 " pdb=" CD PRO A 36 " ideal model delta sigma weight residual 1.473 1.318 0.155 1.40e-02 5.10e+03 1.23e+02 bond pdb=" CA7 CDL a 101 " pdb=" OA8 CDL a 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 ... (remaining 35071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 46568 6.18 - 12.35: 748 12.35 - 18.53: 199 18.53 - 24.70: 13 24.70 - 30.88: 3 Bond angle restraints: 47531 Sorted by residual: angle pdb=" N ILE H 231 " pdb=" CA ILE H 231 " pdb=" C ILE H 231 " ideal model delta sigma weight residual 113.42 90.97 22.45 1.17e+00 7.31e-01 3.68e+02 angle pdb=" N CYS B 99 " pdb=" CA CYS B 99 " pdb=" C CYS B 99 " ideal model delta sigma weight residual 113.41 91.45 21.96 1.22e+00 6.72e-01 3.24e+02 angle pdb=" N TYR B 170 " pdb=" CA TYR B 170 " pdb=" C TYR B 170 " ideal model delta sigma weight residual 111.33 89.93 21.40 1.21e+00 6.83e-01 3.13e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.07 25.57 1.52e+00 4.33e-01 2.83e+02 angle pdb=" N ARG B 122 " pdb=" CA ARG B 122 " pdb=" CB ARG B 122 " ideal model delta sigma weight residual 110.04 85.52 24.52 1.47e+00 4.63e-01 2.78e+02 ... (remaining 47526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 20516 27.97 - 55.93: 602 55.93 - 83.90: 60 83.90 - 111.86: 9 111.86 - 139.83: 5 Dihedral angle restraints: 21192 sinusoidal: 8933 harmonic: 12259 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 171.70 -78.70 1 1.00e+01 1.00e-02 7.72e+01 dihedral pdb=" C PHE a 3 " pdb=" N PHE a 3 " pdb=" CA PHE a 3 " pdb=" CB PHE a 3 " ideal model delta harmonic sigma weight residual -122.60 -101.77 -20.83 0 2.50e+00 1.60e-01 6.94e+01 dihedral pdb=" C ASP D 359 " pdb=" N ASP D 359 " pdb=" CA ASP D 359 " pdb=" CB ASP D 359 " ideal model delta harmonic sigma weight residual -122.60 -103.66 -18.94 0 2.50e+00 1.60e-01 5.74e+01 ... (remaining 21189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4677 0.190 - 0.381: 448 0.381 - 0.571: 41 0.571 - 0.762: 3 0.762 - 0.952: 24 Chirality restraints: 5193 Sorted by residual: chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.60 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb="FE4 SF4 G 801 " pdb=" S1 SF4 G 801 " pdb=" S2 SF4 G 801 " pdb=" S3 SF4 G 801 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 5190 not shown) Planarity restraints: 6033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 400 " 0.340 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C23 UQ9 H 400 " -0.505 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 400 " -0.106 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 400 " 0.153 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 400 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 H 400 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C13 UQ9 H 400 " -0.501 2.00e-02 2.50e+03 pdb=" C14 UQ9 H 400 " -0.103 2.00e-02 2.50e+03 pdb=" C15 UQ9 H 400 " 0.116 2.00e-02 2.50e+03 pdb=" C16 UQ9 H 400 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 400 " 0.020 2.00e-02 2.50e+03 1.35e-01 5.51e+02 pdb=" C1M UQ9 H 400 " 0.130 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 400 " -0.064 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 400 " 0.057 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 400 " -0.041 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 400 " 0.029 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 400 " -0.006 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 400 " -0.073 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 400 " -0.237 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 400 " 0.270 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 400 " -0.208 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 400 " 0.123 2.00e-02 2.50e+03 ... (remaining 6030 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 39 2.26 - 2.92: 17385 2.92 - 3.58: 52372 3.58 - 4.24: 86369 4.24 - 4.90: 143511 Nonbonded interactions: 299676 Sorted by model distance: nonbonded pdb=" O ASP D 360 " pdb=" OD1 ASP D 360 " model vdw 1.601 3.040 nonbonded pdb=" O ILE G 130 " pdb=" NH1 ARG I 140 " model vdw 1.891 3.120 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 3.040 nonbonded pdb=" O GLY H 203 " pdb=" O LEU H 207 " model vdw 1.962 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 1.998 3.040 ... (remaining 299671 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 individual isotropic 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: 5.330 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.850 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:2.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 1.241 35117 Z= 1.045 Angle : 2.266 56.972 47623 Z= 1.499 Chirality : 0.128 0.952 5193 Planarity : 0.010 0.290 6033 Dihedral : 13.092 139.825 13276 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 45.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 0.49 % Allowed : 7.42 % Favored : 92.09 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.12), residues: 4167 helix: -1.80 (0.11), residues: 1763 sheet: -2.02 (0.27), residues: 329 loop : -2.43 (0.12), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 68 TYR 0.067 0.003 TYR D 135 PHE 0.052 0.003 PHE a 3 TRP 0.034 0.002 TRP G 285 HIS 0.011 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01520 (35076) covalent geometry : angle 2.16060 (47531) SS BOND : bond 0.00814 ( 4) SS BOND : angle 1.32585 ( 8) hydrogen bonds : bond 0.25022 ( 1325) hydrogen bonds : angle 9.67443 ( 3771) metal coordination : bond 0.46129 ( 37) metal coordination : angle 16.38195 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 1336 time to evaluate : 1.448 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: B 164 CYS cc_start: 0.7157 (p) cc_final: 0.6866 (p) REVERT: C 143 LYS cc_start: 0.8934 (ptpt) cc_final: 0.8485 (pttp) REVERT: D 145 MET cc_start: 0.8375 (mtt) cc_final: 0.7852 (mtt) REVERT: D 185 MET cc_start: 0.8685 (tpt) cc_final: 0.7598 (tpt) REVERT: D 215 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7537 (tt0) REVERT: E 105 GLN cc_start: 0.8209 (mp10) cc_final: 0.7950 (mp10) REVERT: E 146 SER cc_start: 0.8600 (t) cc_final: 0.8368 (t) REVERT: E 238 LYS cc_start: 0.7518 (mmmt) cc_final: 0.7040 (mptt) REVERT: F 112 TYR cc_start: 0.8151 (m-80) cc_final: 0.7911 (m-10) REVERT: G 97 MET cc_start: 0.6730 (mtp) cc_final: 0.6455 (mtp) REVERT: G 307 VAL cc_start: 0.9172 (p) cc_final: 0.8864 (m) REVERT: G 315 THR cc_start: 0.8561 (m) cc_final: 0.8123 (p) REVERT: G 530 TYR cc_start: 0.8502 (m-80) cc_final: 0.8230 (m-80) REVERT: G 663 ASN cc_start: 0.7039 (p0) cc_final: 0.6677 (p0) REVERT: H 163 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7881 (tm-30) REVERT: I 56 ASN cc_start: 0.7512 (t0) cc_final: 0.7192 (t0) REVERT: I 59 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7257 (tmm-80) REVERT: P 171 ASN cc_start: 0.8282 (p0) cc_final: 0.7925 (p0) REVERT: P 238 GLN cc_start: 0.7644 (mt0) cc_final: 0.7304 (mt0) REVERT: S 57 GLU cc_start: 0.7183 (mm-30) cc_final: 0.5901 (mm-30) REVERT: S 64 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7710 (mtmm) REVERT: T 115 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8811 (tm-30) REVERT: T 122 MET cc_start: 0.8264 (mmt) cc_final: 0.7768 (mmt) REVERT: T 126 PHE cc_start: 0.6808 (m-80) cc_final: 0.6559 (m-10) REVERT: T 143 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7796 (tp30) REVERT: W 49 THR cc_start: 0.8995 (p) cc_final: 0.8750 (m) REVERT: W 78 ASP cc_start: 0.8287 (t0) cc_final: 0.8016 (t0) REVERT: W 127 MET cc_start: 0.7031 (ptm) cc_final: 0.6802 (ptp) REVERT: X 35 GLN cc_start: 0.7709 (mp-120) cc_final: 0.7126 (mp10) REVERT: X 125 LEU cc_start: 0.8326 (mt) cc_final: 0.8091 (mp) REVERT: a 34 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7808 (mtmm) REVERT: a 47 LEU cc_start: 0.8652 (mp) cc_final: 0.8111 (mp) REVERT: a 48 MET cc_start: 0.8143 (ttm) cc_final: 0.7839 (ttm) outliers start: 18 outliers final: 0 residues processed: 1343 average time/residue: 0.2275 time to fit residues: 481.2945 Evaluate side-chains 874 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 874 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 102 HIS C 130 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 147 ASN D 149 GLN D 182 ASN D 234 GLN D 270 ASN D 313 GLN D 442 HIS E 86 GLN E 132 GLN E 188 ASN E 245 GLN F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN F 422 HIS G 51 GLN G 140 GLN G 205 GLN G 388 ASN G 444 HIS G 495 ASN G 571 HIS G 572 HIS G 604 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN H 194 ASN H 235 ASN H 284 GLN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 HIS I 206 GLN P 72 HIS P 79 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN Q 86 ASN Q 109 ASN Q 123 ASN R 70 ASN S 22 HIS S 25 GLN V 50 GLN V 110 ASN W 61 GLN W 105 HIS W 129 HIS ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 99 HIS X 124 GLN Z 8 GLN Z 90 ASN Z 112 HIS Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.119815 restraints weight = 53405.023| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.42 r_work: 0.3439 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35117 Z= 0.208 Angle : 0.965 39.468 47623 Z= 0.419 Chirality : 0.050 0.273 5193 Planarity : 0.007 0.078 6033 Dihedral : 10.123 129.205 4948 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.95 % Allowed : 14.68 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.81 (0.12), residues: 4167 helix: -0.49 (0.12), residues: 1831 sheet: -2.07 (0.24), residues: 355 loop : -1.66 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 135 TYR 0.028 0.002 TYR F 157 PHE 0.031 0.002 PHE S 36 TRP 0.014 0.002 TRP V 114 HIS 0.015 0.002 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00484 (35076) covalent geometry : angle 0.80797 (47531) SS BOND : bond 0.00995 ( 4) SS BOND : angle 1.30007 ( 8) hydrogen bonds : bond 0.05588 ( 1325) hydrogen bonds : angle 5.84259 ( 3771) metal coordination : bond 0.01832 ( 37) metal coordination : angle 12.60007 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 898 time to evaluate : 1.370 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 18 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8521 (mt) REVERT: A 26 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7317 (mm-40) REVERT: A 88 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8241 (ttm) REVERT: B 94 THR cc_start: 0.8395 (p) cc_final: 0.8165 (p) REVERT: C 190 TYR cc_start: 0.8602 (m-80) cc_final: 0.8386 (m-80) REVERT: C 214 GLU cc_start: 0.8272 (tt0) cc_final: 0.8066 (mt-10) REVERT: D 110 ASP cc_start: 0.8029 (t70) cc_final: 0.7792 (t70) REVERT: D 145 MET cc_start: 0.8471 (mtt) cc_final: 0.8047 (mtt) REVERT: D 238 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7213 (mp) REVERT: E 105 GLN cc_start: 0.8450 (mp10) cc_final: 0.8053 (mp10) REVERT: E 194 ASP cc_start: 0.8496 (t0) cc_final: 0.8212 (t0) REVERT: F 44 ASN cc_start: 0.8004 (t0) cc_final: 0.7774 (t0) REVERT: F 53 LEU cc_start: 0.8645 (tp) cc_final: 0.8251 (mt) REVERT: F 75 TRP cc_start: 0.8309 (t60) cc_final: 0.7428 (t60) REVERT: F 80 MET cc_start: 0.8455 (mmm) cc_final: 0.8193 (mmm) REVERT: F 113 LEU cc_start: 0.8349 (tp) cc_final: 0.8141 (tp) REVERT: F 134 ASP cc_start: 0.8186 (t0) cc_final: 0.7810 (t0) REVERT: F 157 TYR cc_start: 0.8308 (t80) cc_final: 0.7965 (t80) REVERT: F 214 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7138 (mt-10) REVERT: F 274 LYS cc_start: 0.7936 (tttm) cc_final: 0.7451 (tptp) REVERT: F 311 TRP cc_start: 0.7022 (t60) cc_final: 0.6709 (t60) REVERT: F 387 GLU cc_start: 0.8041 (mp0) cc_final: 0.7833 (mp0) REVERT: F 396 MET cc_start: 0.8705 (mmm) cc_final: 0.8385 (mmm) REVERT: G 97 MET cc_start: 0.7877 (mtp) cc_final: 0.7674 (mtp) REVERT: G 107 GLU cc_start: 0.8116 (tp30) cc_final: 0.7871 (tp30) REVERT: G 211 GLU cc_start: 0.8172 (pm20) cc_final: 0.7717 (pt0) REVERT: G 271 MET cc_start: 0.8886 (mmp) cc_final: 0.8434 (mmt) REVERT: G 315 THR cc_start: 0.8867 (m) cc_final: 0.8621 (p) REVERT: G 329 MET cc_start: 0.8389 (mmt) cc_final: 0.7830 (mmt) REVERT: G 409 PHE cc_start: 0.8859 (m-10) cc_final: 0.8652 (m-10) REVERT: H 126 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7739 (mmmt) REVERT: H 163 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8409 (tm-30) REVERT: H 193 THR cc_start: 0.9082 (m) cc_final: 0.8871 (p) REVERT: H 261 MET cc_start: 0.8085 (mmt) cc_final: 0.7796 (mmm) REVERT: I 59 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7244 (tmm160) REVERT: I 139 SER cc_start: 0.9330 (t) cc_final: 0.8964 (t) REVERT: I 195 ASP cc_start: 0.8003 (m-30) cc_final: 0.7743 (m-30) REVERT: P 238 GLN cc_start: 0.7579 (mt0) cc_final: 0.7252 (mt0) REVERT: P 283 MET cc_start: 0.8220 (mmm) cc_final: 0.7812 (tpp) REVERT: P 310 PHE cc_start: 0.6867 (m-10) cc_final: 0.6663 (m-10) REVERT: P 313 TRP cc_start: 0.5704 (t60) cc_final: 0.4153 (m-10) REVERT: Q 135 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8870 (mm) REVERT: S 53 ILE cc_start: 0.8779 (mt) cc_final: 0.7930 (mt) REVERT: S 64 LYS cc_start: 0.8442 (mtpt) cc_final: 0.7441 (mtmm) REVERT: S 91 MET cc_start: 0.9009 (tpp) cc_final: 0.8769 (tpp) REVERT: T 82 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8548 (ttm170) REVERT: T 115 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8401 (tm-30) REVERT: T 130 ILE cc_start: 0.8651 (mp) cc_final: 0.8383 (mp) REVERT: T 142 GLN cc_start: 0.8777 (mt0) cc_final: 0.8125 (mt0) REVERT: V 81 ILE cc_start: 0.9258 (mt) cc_final: 0.9042 (mp) REVERT: W 27 ASP cc_start: 0.7565 (t0) cc_final: 0.7345 (t0) REVERT: W 32 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8298 (mttm) REVERT: W 45 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7057 (tm-30) REVERT: W 83 ASP cc_start: 0.8987 (m-30) cc_final: 0.8373 (m-30) REVERT: W 127 MET cc_start: 0.7970 (ptm) cc_final: 0.7315 (ptp) REVERT: X 50 GLU cc_start: 0.7329 (tm-30) cc_final: 0.7033 (tm-30) REVERT: X 83 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8690 (p) REVERT: X 117 TRP cc_start: 0.6916 (m-10) cc_final: 0.6448 (m-90) REVERT: X 125 LEU cc_start: 0.8858 (mt) cc_final: 0.8436 (mp) REVERT: X 135 ARG cc_start: 0.7045 (mtm-85) cc_final: 0.6688 (mtm-85) REVERT: Z 9 ASP cc_start: 0.8086 (t0) cc_final: 0.7500 (t0) REVERT: Z 10 MET cc_start: 0.9075 (mmm) cc_final: 0.8786 (mmm) REVERT: Z 20 ASP cc_start: 0.8225 (t0) cc_final: 0.7799 (p0) REVERT: Z 24 ASN cc_start: 0.8191 (t0) cc_final: 0.7836 (t0) REVERT: Z 80 ASP cc_start: 0.7568 (m-30) cc_final: 0.7293 (m-30) REVERT: Z 129 THR cc_start: 0.6517 (OUTLIER) cc_final: 0.6298 (m) REVERT: a 30 THR cc_start: 0.9000 (m) cc_final: 0.8729 (p) REVERT: b 35 ILE cc_start: 0.9082 (pt) cc_final: 0.8734 (pt) outliers start: 108 outliers final: 54 residues processed: 959 average time/residue: 0.2163 time to fit residues: 332.8015 Evaluate side-chains 795 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 735 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 437 LYS Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 284 HIS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 289 LEU Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 135 ILE Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 48 ASN Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 50 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain Z residue 135 ASN Chi-restraints excluded: chain a residue 41 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 272 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 235 ASN D 83 ASN D 112 HIS D 381 HIS D 442 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN E 188 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 359 ASN G 424 HIS G 517 HIS ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 ASN Q 71 HIS ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN W 51 HIS W 73 ASN X 73 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115558 restraints weight = 53695.464| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.46 r_work: 0.3369 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 35117 Z= 0.217 Angle : 0.880 39.552 47623 Z= 0.370 Chirality : 0.047 0.196 5193 Planarity : 0.006 0.073 6033 Dihedral : 9.869 134.343 4948 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.78 % Rotamer: Outliers : 3.33 % Allowed : 16.37 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4167 helix: -0.08 (0.12), residues: 1837 sheet: -1.93 (0.25), residues: 360 loop : -1.45 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 153 TYR 0.030 0.002 TYR B 170 PHE 0.021 0.002 PHE P 213 TRP 0.015 0.001 TRP b 80 HIS 0.006 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00507 (35076) covalent geometry : angle 0.71258 (47531) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.68026 ( 8) hydrogen bonds : bond 0.04745 ( 1325) hydrogen bonds : angle 5.42522 ( 3771) metal coordination : bond 0.02780 ( 37) metal coordination : angle 12.30356 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 758 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.9115 (tpt) cc_final: 0.8914 (tpp) REVERT: B 150 ASP cc_start: 0.8874 (m-30) cc_final: 0.8661 (m-30) REVERT: B 171 TYR cc_start: 0.8569 (m-80) cc_final: 0.8239 (m-80) REVERT: D 145 MET cc_start: 0.8418 (mtt) cc_final: 0.8128 (mtt) REVERT: D 215 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8573 (pt0) REVERT: D 238 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.7721 (mp) REVERT: E 105 GLN cc_start: 0.8558 (mp10) cc_final: 0.8079 (mp10) REVERT: E 143 ASP cc_start: 0.7974 (m-30) cc_final: 0.7679 (t0) REVERT: E 152 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: E 194 ASP cc_start: 0.8476 (t0) cc_final: 0.8008 (t0) REVERT: F 53 LEU cc_start: 0.8632 (tp) cc_final: 0.8307 (tp) REVERT: F 75 TRP cc_start: 0.8408 (t60) cc_final: 0.6981 (t60) REVERT: F 134 ASP cc_start: 0.8171 (t0) cc_final: 0.7706 (t0) REVERT: F 157 TYR cc_start: 0.8277 (t80) cc_final: 0.7957 (t80) REVERT: F 274 LYS cc_start: 0.8054 (tttm) cc_final: 0.7656 (tptp) REVERT: F 396 MET cc_start: 0.8739 (mmm) cc_final: 0.8392 (mmm) REVERT: G 211 GLU cc_start: 0.8231 (pm20) cc_final: 0.7751 (pt0) REVERT: G 225 ILE cc_start: 0.9046 (tt) cc_final: 0.8838 (mm) REVERT: G 315 THR cc_start: 0.8905 (m) cc_final: 0.8692 (p) REVERT: G 316 TYR cc_start: 0.8532 (m-80) cc_final: 0.8227 (m-80) REVERT: G 362 ASP cc_start: 0.7437 (t70) cc_final: 0.6734 (t0) REVERT: G 409 PHE cc_start: 0.8899 (m-10) cc_final: 0.8685 (m-10) REVERT: G 530 TYR cc_start: 0.9253 (m-80) cc_final: 0.8848 (m-80) REVERT: H 34 ARG cc_start: 0.9164 (ptt-90) cc_final: 0.8641 (ptt90) REVERT: H 126 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7802 (mmpt) REVERT: H 163 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8487 (tm-30) REVERT: H 184 MET cc_start: 0.8839 (mtm) cc_final: 0.8604 (mtm) REVERT: H 193 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8852 (p) REVERT: I 59 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7210 (tmm160) REVERT: I 195 ASP cc_start: 0.8088 (m-30) cc_final: 0.7833 (m-30) REVERT: I 200 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8440 (tp30) REVERT: P 280 ILE cc_start: 0.8804 (mt) cc_final: 0.8560 (mp) REVERT: P 283 MET cc_start: 0.8238 (mmm) cc_final: 0.7848 (tpp) REVERT: P 300 TRP cc_start: 0.7201 (t-100) cc_final: 0.6226 (t60) REVERT: P 310 PHE cc_start: 0.7031 (m-10) cc_final: 0.6748 (m-10) REVERT: P 313 TRP cc_start: 0.5884 (t60) cc_final: 0.3965 (m100) REVERT: Q 105 GLU cc_start: 0.8131 (tt0) cc_final: 0.7859 (tt0) REVERT: S 53 ILE cc_start: 0.8774 (mt) cc_final: 0.8281 (mt) REVERT: S 64 LYS cc_start: 0.8434 (mtpt) cc_final: 0.7491 (mtmm) REVERT: S 89 ARG cc_start: 0.7943 (tpt170) cc_final: 0.7586 (tpt170) REVERT: T 82 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.7940 (ttm170) REVERT: T 103 HIS cc_start: 0.8092 (m-70) cc_final: 0.7680 (m-70) REVERT: T 115 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8519 (tm-30) REVERT: T 126 PHE cc_start: 0.6858 (m-10) cc_final: 0.6275 (m-10) REVERT: V 67 LYS cc_start: 0.8969 (tppt) cc_final: 0.8741 (tppt) REVERT: W 27 ASP cc_start: 0.7641 (t0) cc_final: 0.7216 (t0) REVERT: W 32 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8319 (mttm) REVERT: W 51 HIS cc_start: 0.8303 (t-170) cc_final: 0.8058 (t-170) REVERT: W 127 MET cc_start: 0.8039 (ptm) cc_final: 0.7408 (ptp) REVERT: X 90 ASP cc_start: 0.8256 (p0) cc_final: 0.7984 (p0) REVERT: X 117 TRP cc_start: 0.6767 (m-10) cc_final: 0.6179 (m-10) REVERT: X 125 LEU cc_start: 0.8930 (mt) cc_final: 0.8485 (mp) REVERT: Z 9 ASP cc_start: 0.8140 (t0) cc_final: 0.7733 (t0) REVERT: Z 20 ASP cc_start: 0.8094 (t0) cc_final: 0.7724 (p0) REVERT: Z 24 ASN cc_start: 0.8387 (t0) cc_final: 0.8047 (t0) REVERT: Z 80 ASP cc_start: 0.7525 (m-30) cc_final: 0.7298 (m-30) REVERT: Z 129 THR cc_start: 0.6713 (m) cc_final: 0.6479 (m) REVERT: Z 138 PHE cc_start: 0.8604 (m-80) cc_final: 0.8364 (m-10) REVERT: b 35 ILE cc_start: 0.9049 (pt) cc_final: 0.8708 (pt) REVERT: q 135 HIS cc_start: 0.8036 (m-70) cc_final: 0.7718 (m-70) outliers start: 122 outliers final: 71 residues processed: 828 average time/residue: 0.2083 time to fit residues: 279.0166 Evaluate side-chains 764 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 690 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain b residue 84 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 386 optimal weight: 0.6980 chunk 334 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 333 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN F 44 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS H 169 GLN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN W 61 GLN W 94 GLN Z 112 HIS Z 135 ASN ** a 31 ASN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.151290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112976 restraints weight = 53149.190| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.60 r_work: 0.3269 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 35117 Z= 0.155 Angle : 0.824 39.133 47623 Z= 0.337 Chirality : 0.045 0.199 5193 Planarity : 0.005 0.073 6033 Dihedral : 9.586 139.217 4948 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.44 % Favored : 95.54 % Rotamer: Outliers : 3.38 % Allowed : 17.35 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4167 helix: 0.13 (0.12), residues: 1837 sheet: -1.68 (0.25), residues: 376 loop : -1.38 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 59 TYR 0.026 0.002 TYR B 170 PHE 0.024 0.002 PHE P 213 TRP 0.016 0.001 TRP b 80 HIS 0.007 0.001 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00363 (35076) covalent geometry : angle 0.65152 (47531) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.94483 ( 8) hydrogen bonds : bond 0.04123 ( 1325) hydrogen bonds : angle 5.15258 ( 3771) metal coordination : bond 0.02024 ( 37) metal coordination : angle 12.00899 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 752 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TRP cc_start: 0.7343 (t60) cc_final: 0.6867 (t60) REVERT: B 141 MET cc_start: 0.8927 (tpt) cc_final: 0.8715 (tpp) REVERT: B 171 TYR cc_start: 0.8560 (m-80) cc_final: 0.7871 (m-80) REVERT: C 234 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8228 (pp) REVERT: D 215 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8520 (pt0) REVERT: D 238 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7648 (mm) REVERT: D 282 ASP cc_start: 0.8280 (m-30) cc_final: 0.7892 (m-30) REVERT: E 105 GLN cc_start: 0.8481 (mp10) cc_final: 0.8043 (mp10) REVERT: E 194 ASP cc_start: 0.8368 (t0) cc_final: 0.7934 (t0) REVERT: F 53 LEU cc_start: 0.8596 (tp) cc_final: 0.8188 (tp) REVERT: F 75 TRP cc_start: 0.8400 (t60) cc_final: 0.6893 (t60) REVERT: F 134 ASP cc_start: 0.8294 (t0) cc_final: 0.7857 (t0) REVERT: F 157 TYR cc_start: 0.8117 (t80) cc_final: 0.7840 (t80) REVERT: F 246 GLU cc_start: 0.8166 (tt0) cc_final: 0.7501 (tt0) REVERT: F 255 CYS cc_start: 0.8215 (m) cc_final: 0.7591 (p) REVERT: F 274 LYS cc_start: 0.7972 (tttm) cc_final: 0.7689 (tptp) REVERT: F 396 MET cc_start: 0.8560 (mmm) cc_final: 0.7861 (mmm) REVERT: G 211 GLU cc_start: 0.8190 (pm20) cc_final: 0.7861 (pt0) REVERT: G 223 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8501 (mt) REVERT: G 225 ILE cc_start: 0.9020 (tt) cc_final: 0.8808 (mm) REVERT: G 315 THR cc_start: 0.8832 (m) cc_final: 0.8587 (p) REVERT: G 316 TYR cc_start: 0.8539 (m-80) cc_final: 0.8249 (m-80) REVERT: G 409 PHE cc_start: 0.8867 (m-10) cc_final: 0.8652 (m-10) REVERT: G 530 TYR cc_start: 0.9174 (m-80) cc_final: 0.8717 (m-80) REVERT: H 34 ARG cc_start: 0.9119 (ptt-90) cc_final: 0.8826 (ptt90) REVERT: H 126 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7640 (mmmt) REVERT: H 163 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8200 (tm-30) REVERT: H 184 MET cc_start: 0.8853 (mtm) cc_final: 0.8316 (mtm) REVERT: H 265 LEU cc_start: 0.8872 (mm) cc_final: 0.8336 (tt) REVERT: I 59 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7092 (tmm160) REVERT: I 200 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8252 (tp30) REVERT: P 280 ILE cc_start: 0.8764 (mt) cc_final: 0.8530 (mp) REVERT: P 300 TRP cc_start: 0.7221 (t-100) cc_final: 0.5935 (t60) REVERT: P 311 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7349 (mm-30) REVERT: P 313 TRP cc_start: 0.5885 (t60) cc_final: 0.3912 (m100) REVERT: Q 105 GLU cc_start: 0.8086 (tt0) cc_final: 0.7829 (tt0) REVERT: Q 106 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8250 (ttm170) REVERT: S 53 ILE cc_start: 0.8509 (mt) cc_final: 0.8081 (mp) REVERT: S 64 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7120 (mtmm) REVERT: S 83 SER cc_start: 0.8095 (m) cc_final: 0.7838 (t) REVERT: S 89 ARG cc_start: 0.7965 (tpt170) cc_final: 0.7567 (tpt170) REVERT: S 93 ASN cc_start: 0.8756 (m-40) cc_final: 0.8473 (m110) REVERT: T 104 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: T 115 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8280 (tm-30) REVERT: T 126 PHE cc_start: 0.6733 (m-10) cc_final: 0.6429 (m-10) REVERT: T 142 GLN cc_start: 0.8373 (mt0) cc_final: 0.7646 (mt0) REVERT: T 143 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8326 (mm-30) REVERT: V 11 LEU cc_start: 0.8791 (mt) cc_final: 0.8484 (mt) REVERT: V 32 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8681 (mm) REVERT: W 27 ASP cc_start: 0.7577 (t0) cc_final: 0.7168 (t0) REVERT: W 32 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8065 (mttm) REVERT: W 45 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6779 (tm-30) REVERT: W 60 LYS cc_start: 0.8564 (tppt) cc_final: 0.8299 (tppt) REVERT: W 127 MET cc_start: 0.7910 (ptm) cc_final: 0.7256 (ptp) REVERT: X 90 ASP cc_start: 0.8092 (p0) cc_final: 0.7766 (p0) REVERT: X 117 TRP cc_start: 0.6383 (m-10) cc_final: 0.6011 (m-10) REVERT: Z 9 ASP cc_start: 0.8005 (t0) cc_final: 0.7657 (t0) REVERT: Z 20 ASP cc_start: 0.7987 (t0) cc_final: 0.7665 (p0) REVERT: Z 24 ASN cc_start: 0.8419 (t0) cc_final: 0.8031 (t0) REVERT: Z 50 MET cc_start: 0.7763 (tpp) cc_final: 0.7364 (tpp) REVERT: Z 72 MET cc_start: 0.7910 (mmm) cc_final: 0.7681 (mtt) REVERT: Z 80 ASP cc_start: 0.7430 (m-30) cc_final: 0.7194 (m-30) REVERT: Z 129 THR cc_start: 0.6755 (m) cc_final: 0.6528 (m) REVERT: b 8 PHE cc_start: 0.6703 (t80) cc_final: 0.6438 (t80) REVERT: b 35 ILE cc_start: 0.8976 (pt) cc_final: 0.8652 (pt) REVERT: q 135 HIS cc_start: 0.7785 (m-70) cc_final: 0.7432 (m-70) outliers start: 124 outliers final: 70 residues processed: 819 average time/residue: 0.2122 time to fit residues: 281.2713 Evaluate side-chains 766 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 691 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 311 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 79 ILE Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 261 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 377 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 340 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN P 71 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 HIS W 94 GLN Z 112 HIS Z 135 ASN ** a 31 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.150323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113282 restraints weight = 53478.708| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.37 r_work: 0.3252 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 35117 Z= 0.171 Angle : 0.818 38.718 47623 Z= 0.333 Chirality : 0.045 0.188 5193 Planarity : 0.005 0.076 6033 Dihedral : 9.358 141.096 4948 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 3.71 % Allowed : 17.44 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4167 helix: 0.22 (0.12), residues: 1854 sheet: -1.62 (0.26), residues: 363 loop : -1.31 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 79 TYR 0.023 0.002 TYR H 142 PHE 0.023 0.002 PHE P 213 TRP 0.012 0.001 TRP H 179 HIS 0.022 0.001 HIS G 424 Details of bonding type rmsd covalent geometry : bond 0.00408 (35076) covalent geometry : angle 0.64837 (47531) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.68029 ( 8) hydrogen bonds : bond 0.03941 ( 1325) hydrogen bonds : angle 5.04220 ( 3771) metal coordination : bond 0.02173 ( 37) metal coordination : angle 11.88735 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 714 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8751 (tp) cc_final: 0.8485 (tp) REVERT: A 106 TRP cc_start: 0.7423 (t60) cc_final: 0.6984 (t60) REVERT: B 171 TYR cc_start: 0.8632 (m-80) cc_final: 0.7713 (m-80) REVERT: B 222 TYR cc_start: 0.8710 (t80) cc_final: 0.8216 (t80) REVERT: C 234 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8169 (pp) REVERT: D 215 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8492 (pt0) REVERT: D 238 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7755 (mm) REVERT: D 437 LYS cc_start: 0.8470 (tmtt) cc_final: 0.7938 (mttt) REVERT: E 105 GLN cc_start: 0.8437 (mp10) cc_final: 0.7967 (mp10) REVERT: E 194 ASP cc_start: 0.8313 (t0) cc_final: 0.7884 (t0) REVERT: F 53 LEU cc_start: 0.8571 (tp) cc_final: 0.8247 (tp) REVERT: F 75 TRP cc_start: 0.8433 (t60) cc_final: 0.7053 (t60) REVERT: F 134 ASP cc_start: 0.8452 (t0) cc_final: 0.7951 (t0) REVERT: F 157 TYR cc_start: 0.8173 (t80) cc_final: 0.7885 (t80) REVERT: F 246 GLU cc_start: 0.8094 (tt0) cc_final: 0.7706 (tt0) REVERT: F 255 CYS cc_start: 0.8403 (m) cc_final: 0.7640 (p) REVERT: F 274 LYS cc_start: 0.8112 (tttm) cc_final: 0.7609 (tptp) REVERT: F 290 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: F 396 MET cc_start: 0.8604 (mmm) cc_final: 0.7945 (mmm) REVERT: G 211 GLU cc_start: 0.8125 (pm20) cc_final: 0.7859 (pt0) REVERT: G 223 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8496 (mt) REVERT: G 225 ILE cc_start: 0.9067 (tt) cc_final: 0.8862 (mm) REVERT: G 271 MET cc_start: 0.8481 (mmp) cc_final: 0.8008 (mmt) REVERT: G 315 THR cc_start: 0.8846 (m) cc_final: 0.8644 (p) REVERT: G 316 TYR cc_start: 0.8640 (m-80) cc_final: 0.8174 (m-80) REVERT: G 329 MET cc_start: 0.8406 (mmt) cc_final: 0.7737 (mmt) REVERT: G 409 PHE cc_start: 0.8874 (m-10) cc_final: 0.8652 (m-10) REVERT: H 126 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7743 (mmpt) REVERT: H 163 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8216 (tm-30) REVERT: H 228 TYR cc_start: 0.9144 (m-10) cc_final: 0.8942 (m-80) REVERT: H 265 LEU cc_start: 0.8881 (mm) cc_final: 0.8388 (tt) REVERT: I 68 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8095 (ttt90) REVERT: I 200 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8201 (tp30) REVERT: P 283 MET cc_start: 0.8345 (tpt) cc_final: 0.7961 (tpp) REVERT: P 300 TRP cc_start: 0.7192 (t-100) cc_final: 0.6990 (t-100) REVERT: P 311 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7645 (mm-30) REVERT: P 313 TRP cc_start: 0.5914 (t60) cc_final: 0.3968 (m100) REVERT: Q 159 SER cc_start: 0.9116 (m) cc_final: 0.8631 (p) REVERT: S 53 ILE cc_start: 0.8593 (mt) cc_final: 0.8298 (mp) REVERT: S 64 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7236 (mtmm) REVERT: S 89 ARG cc_start: 0.7964 (tpt170) cc_final: 0.7571 (tpt170) REVERT: S 93 ASN cc_start: 0.8739 (m-40) cc_final: 0.8503 (m110) REVERT: T 103 HIS cc_start: 0.7617 (m170) cc_final: 0.7387 (m-70) REVERT: T 104 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: T 115 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8448 (tm-30) REVERT: T 142 GLN cc_start: 0.8215 (mt0) cc_final: 0.7087 (mt0) REVERT: V 32 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8707 (mm) REVERT: W 19 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7978 (p) REVERT: W 27 ASP cc_start: 0.7585 (t0) cc_final: 0.7226 (t0) REVERT: W 32 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8069 (mttm) REVERT: W 45 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7010 (tm-30) REVERT: W 60 LYS cc_start: 0.8663 (tppt) cc_final: 0.8448 (tppt) REVERT: W 127 MET cc_start: 0.7965 (ptm) cc_final: 0.7411 (ptp) REVERT: Z 9 ASP cc_start: 0.7939 (t0) cc_final: 0.7608 (t0) REVERT: Z 20 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (p0) REVERT: Z 24 ASN cc_start: 0.8483 (t0) cc_final: 0.8093 (t0) REVERT: Z 72 MET cc_start: 0.7975 (mmm) cc_final: 0.7716 (mmm) REVERT: Z 80 ASP cc_start: 0.7501 (m-30) cc_final: 0.7142 (m-30) REVERT: Z 129 THR cc_start: 0.7034 (OUTLIER) cc_final: 0.6815 (m) REVERT: b 10 LYS cc_start: 0.8004 (mtpm) cc_final: 0.7584 (mmmt) REVERT: b 35 ILE cc_start: 0.8995 (pt) cc_final: 0.8663 (pt) REVERT: q 33 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5982 (mt) REVERT: q 135 HIS cc_start: 0.7862 (m-70) cc_final: 0.7516 (m-70) REVERT: s 78 TYR cc_start: 0.7217 (m-80) cc_final: 0.6372 (m-80) outliers start: 136 outliers final: 89 residues processed: 791 average time/residue: 0.2086 time to fit residues: 268.0796 Evaluate side-chains 767 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 668 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 311 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 327 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 79 ILE Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 306 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 409 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 360 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN F 44 ASN F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS I 56 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS W 94 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110993 restraints weight = 53441.133| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.43 r_work: 0.3192 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 35117 Z= 0.218 Angle : 0.852 39.008 47623 Z= 0.345 Chirality : 0.046 0.216 5193 Planarity : 0.005 0.077 6033 Dihedral : 9.300 142.729 4948 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 3.74 % Allowed : 18.20 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4167 helix: 0.30 (0.12), residues: 1853 sheet: -1.57 (0.26), residues: 367 loop : -1.29 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 61 TYR 0.034 0.002 TYR H 142 PHE 0.037 0.002 PHE F 262 TRP 0.012 0.001 TRP F 99 HIS 0.010 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00521 (35076) covalent geometry : angle 0.67642 (47531) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.52746 ( 8) hydrogen bonds : bond 0.04000 ( 1325) hydrogen bonds : angle 5.04085 ( 3771) metal coordination : bond 0.02700 ( 37) metal coordination : angle 12.35063 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 699 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8115 (ttm) REVERT: A 106 TRP cc_start: 0.7510 (t60) cc_final: 0.7089 (t60) REVERT: B 171 TYR cc_start: 0.8866 (m-80) cc_final: 0.8050 (m-80) REVERT: B 222 TYR cc_start: 0.8791 (t80) cc_final: 0.8354 (t80) REVERT: C 234 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8249 (pp) REVERT: D 215 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8507 (pt0) REVERT: D 238 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7694 (mp) REVERT: D 282 ASP cc_start: 0.8427 (m-30) cc_final: 0.8006 (m-30) REVERT: D 437 LYS cc_start: 0.8620 (tmtt) cc_final: 0.7952 (mttt) REVERT: E 105 GLN cc_start: 0.8479 (mp10) cc_final: 0.7968 (mp10) REVERT: E 187 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6897 (tp) REVERT: E 194 ASP cc_start: 0.8406 (t0) cc_final: 0.7996 (t0) REVERT: F 53 LEU cc_start: 0.8580 (tp) cc_final: 0.8243 (tp) REVERT: F 75 TRP cc_start: 0.8427 (t60) cc_final: 0.7010 (t60) REVERT: F 131 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8359 (mpp) REVERT: F 134 ASP cc_start: 0.8537 (t0) cc_final: 0.8008 (t0) REVERT: F 157 TYR cc_start: 0.8201 (t80) cc_final: 0.7962 (t80) REVERT: F 246 GLU cc_start: 0.8097 (tt0) cc_final: 0.7696 (tt0) REVERT: F 255 CYS cc_start: 0.8476 (m) cc_final: 0.7226 (p) REVERT: F 274 LYS cc_start: 0.8303 (tttm) cc_final: 0.7801 (tptp) REVERT: F 337 MET cc_start: 0.8699 (mmm) cc_final: 0.8333 (mtp) REVERT: F 396 MET cc_start: 0.8666 (mmm) cc_final: 0.8417 (mmm) REVERT: G 97 MET cc_start: 0.7827 (mtp) cc_final: 0.7404 (mtp) REVERT: G 211 GLU cc_start: 0.8099 (pm20) cc_final: 0.7881 (pt0) REVERT: G 223 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8526 (mt) REVERT: G 271 MET cc_start: 0.8520 (mmp) cc_final: 0.7849 (mmt) REVERT: G 315 THR cc_start: 0.8874 (m) cc_final: 0.8647 (p) REVERT: G 316 TYR cc_start: 0.8727 (m-80) cc_final: 0.8179 (m-80) REVERT: G 409 PHE cc_start: 0.8940 (m-10) cc_final: 0.8703 (m-10) REVERT: H 126 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7651 (mmpt) REVERT: H 163 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8253 (tm-30) REVERT: H 265 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8431 (tt) REVERT: I 68 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8293 (mtp85) REVERT: I 200 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8432 (tp30) REVERT: P 271 TYR cc_start: 0.7414 (m-80) cc_final: 0.7192 (m-80) REVERT: P 283 MET cc_start: 0.8468 (tpt) cc_final: 0.8091 (tpp) REVERT: P 311 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7691 (mm-30) REVERT: P 346 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7221 (mm-30) REVERT: Q 78 ARG cc_start: 0.8567 (ttt-90) cc_final: 0.8338 (ttt-90) REVERT: Q 105 GLU cc_start: 0.8541 (tt0) cc_final: 0.8189 (tt0) REVERT: Q 159 SER cc_start: 0.9151 (m) cc_final: 0.8690 (p) REVERT: Q 164 PHE cc_start: 0.8419 (m-80) cc_final: 0.8212 (m-10) REVERT: S 53 ILE cc_start: 0.8474 (mt) cc_final: 0.8270 (mp) REVERT: S 64 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7194 (mtmm) REVERT: S 89 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7519 (tpt170) REVERT: S 93 ASN cc_start: 0.8769 (m-40) cc_final: 0.8482 (m-40) REVERT: T 82 ARG cc_start: 0.8558 (ttp-110) cc_final: 0.8166 (ptp-110) REVERT: T 104 PHE cc_start: 0.8416 (m-10) cc_final: 0.8085 (m-80) REVERT: T 115 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8452 (tm-30) REVERT: T 142 GLN cc_start: 0.8257 (mt0) cc_final: 0.7146 (mt0) REVERT: V 32 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8688 (mm) REVERT: W 19 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8025 (p) REVERT: W 27 ASP cc_start: 0.7685 (t0) cc_final: 0.7319 (t0) REVERT: W 32 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8042 (mttm) REVERT: W 60 LYS cc_start: 0.8704 (tppt) cc_final: 0.8471 (tppt) REVERT: W 64 ASP cc_start: 0.7924 (m-30) cc_final: 0.7578 (m-30) REVERT: W 127 MET cc_start: 0.7978 (ptm) cc_final: 0.7409 (ptp) REVERT: X 77 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7288 (t-90) REVERT: Z 9 ASP cc_start: 0.7922 (t0) cc_final: 0.7583 (t0) REVERT: Z 20 ASP cc_start: 0.7992 (t0) cc_final: 0.7753 (p0) REVERT: Z 24 ASN cc_start: 0.8478 (t0) cc_final: 0.7903 (t0) REVERT: Z 72 MET cc_start: 0.7949 (mmm) cc_final: 0.7608 (mmm) REVERT: Z 80 ASP cc_start: 0.7484 (m-30) cc_final: 0.7233 (m-30) REVERT: b 8 PHE cc_start: 0.6845 (t80) cc_final: 0.6574 (t80) REVERT: b 10 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7732 (mmmt) REVERT: b 35 ILE cc_start: 0.8936 (pt) cc_final: 0.8610 (pt) REVERT: q 135 HIS cc_start: 0.7963 (m-70) cc_final: 0.7595 (m-70) REVERT: r 40 LYS cc_start: 0.7756 (tttt) cc_final: 0.7374 (mmtt) REVERT: s 78 TYR cc_start: 0.7219 (m-80) cc_final: 0.6268 (m-80) outliers start: 137 outliers final: 91 residues processed: 780 average time/residue: 0.2132 time to fit residues: 270.6730 Evaluate side-chains 766 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 664 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 163 LYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 311 THR Chi-restraints excluded: chain I residue 62 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 79 ILE Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 16 TYR Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 243 optimal weight: 4.9990 chunk 373 optimal weight: 0.0060 chunk 48 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 304 optimal weight: 0.0040 chunk 196 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 233 optimal weight: 0.8980 chunk 354 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN F 44 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 HIS Z 112 HIS Z 135 ASN a 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.151237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113334 restraints weight = 53375.975| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.56 r_work: 0.3251 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 35117 Z= 0.130 Angle : 0.787 37.426 47623 Z= 0.316 Chirality : 0.043 0.209 5193 Planarity : 0.005 0.071 6033 Dihedral : 9.111 145.558 4948 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 3.14 % Allowed : 19.10 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4167 helix: 0.47 (0.12), residues: 1858 sheet: -1.45 (0.27), residues: 354 loop : -1.21 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 153 TYR 0.027 0.001 TYR H 142 PHE 0.023 0.001 PHE P 213 TRP 0.013 0.001 TRP F 99 HIS 0.011 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00301 (35076) covalent geometry : angle 0.61946 (47531) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.54791 ( 8) hydrogen bonds : bond 0.03572 ( 1325) hydrogen bonds : angle 4.88749 ( 3771) metal coordination : bond 0.01745 ( 37) metal coordination : angle 11.57079 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 726 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8077 (ttm) REVERT: A 106 TRP cc_start: 0.7402 (t60) cc_final: 0.7038 (t60) REVERT: B 171 TYR cc_start: 0.8732 (m-80) cc_final: 0.7984 (m-80) REVERT: B 222 TYR cc_start: 0.8746 (t80) cc_final: 0.8319 (t80) REVERT: C 234 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8156 (pp) REVERT: D 215 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8478 (pt0) REVERT: D 238 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7859 (mm) REVERT: D 282 ASP cc_start: 0.8386 (m-30) cc_final: 0.8001 (m-30) REVERT: D 437 LYS cc_start: 0.8533 (tmtt) cc_final: 0.7808 (mttt) REVERT: E 105 GLN cc_start: 0.8422 (mp10) cc_final: 0.7949 (mp10) REVERT: E 187 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6719 (tp) REVERT: E 194 ASP cc_start: 0.8386 (t0) cc_final: 0.7925 (t0) REVERT: F 53 LEU cc_start: 0.8554 (tp) cc_final: 0.8229 (tp) REVERT: F 75 TRP cc_start: 0.8498 (t60) cc_final: 0.7141 (t60) REVERT: F 131 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8410 (mpp) REVERT: F 134 ASP cc_start: 0.8494 (t0) cc_final: 0.8047 (t0) REVERT: F 289 GLU cc_start: 0.7682 (pm20) cc_final: 0.7267 (tt0) REVERT: F 337 MET cc_start: 0.8662 (mmm) cc_final: 0.8387 (mtp) REVERT: F 396 MET cc_start: 0.8626 (mmm) cc_final: 0.8031 (mmm) REVERT: F 450 MET cc_start: 0.8382 (tpp) cc_final: 0.7830 (mtp) REVERT: G 32 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8434 (pt) REVERT: G 223 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8448 (mt) REVERT: G 271 MET cc_start: 0.8409 (mmp) cc_final: 0.7856 (mmt) REVERT: G 316 TYR cc_start: 0.8756 (m-80) cc_final: 0.8168 (m-80) REVERT: G 409 PHE cc_start: 0.8915 (m-10) cc_final: 0.8656 (m-10) REVERT: G 712 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8695 (tmmt) REVERT: H 34 ARG cc_start: 0.9103 (ptt-90) cc_final: 0.8875 (ptt-90) REVERT: H 126 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7582 (mmpt) REVERT: H 163 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8307 (tm-30) REVERT: H 184 MET cc_start: 0.8845 (mtm) cc_final: 0.8602 (mtm) REVERT: H 261 MET cc_start: 0.8041 (mmm) cc_final: 0.7790 (mtt) REVERT: H 265 LEU cc_start: 0.8816 (mm) cc_final: 0.8410 (tt) REVERT: I 37 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8363 (ttpp) REVERT: I 68 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8330 (ttt90) REVERT: I 200 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8350 (tp30) REVERT: P 154 GLN cc_start: 0.7835 (tp40) cc_final: 0.7599 (tp40) REVERT: P 283 MET cc_start: 0.8385 (tpt) cc_final: 0.7995 (tpp) REVERT: P 311 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7672 (mm-30) REVERT: P 313 TRP cc_start: 0.6052 (t60) cc_final: 0.4173 (m100) REVERT: P 346 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7079 (mm-30) REVERT: P 361 TRP cc_start: 0.7893 (m100) cc_final: 0.7670 (m100) REVERT: Q 105 GLU cc_start: 0.8504 (tt0) cc_final: 0.8157 (tt0) REVERT: Q 159 SER cc_start: 0.9132 (m) cc_final: 0.8617 (p) REVERT: S 53 ILE cc_start: 0.8493 (mt) cc_final: 0.7959 (mp) REVERT: S 89 ARG cc_start: 0.8035 (tpt170) cc_final: 0.7569 (tpt170) REVERT: S 93 ASN cc_start: 0.8731 (m-40) cc_final: 0.8502 (m110) REVERT: T 104 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: T 115 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8506 (tm-30) REVERT: T 142 GLN cc_start: 0.8246 (mt0) cc_final: 0.7734 (mt0) REVERT: V 32 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8831 (mp) REVERT: V 116 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7367 (mt) REVERT: W 19 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8034 (p) REVERT: W 27 ASP cc_start: 0.7602 (t0) cc_final: 0.7201 (t0) REVERT: W 32 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8066 (mttm) REVERT: W 60 LYS cc_start: 0.8620 (tppt) cc_final: 0.8370 (tppt) REVERT: W 127 MET cc_start: 0.7952 (ptm) cc_final: 0.7435 (ptp) REVERT: X 77 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7284 (t-170) REVERT: Z 24 ASN cc_start: 0.8471 (t0) cc_final: 0.7923 (t0) REVERT: Z 80 ASP cc_start: 0.7380 (m-30) cc_final: 0.7105 (m-30) REVERT: Z 120 LEU cc_start: 0.8700 (tp) cc_final: 0.8433 (mm) REVERT: a 31 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8506 (m-40) REVERT: b 8 PHE cc_start: 0.6781 (t80) cc_final: 0.6559 (t80) REVERT: b 10 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7846 (mmmt) REVERT: b 35 ILE cc_start: 0.8900 (pt) cc_final: 0.8593 (pt) REVERT: q 124 TYR cc_start: 0.8141 (t80) cc_final: 0.7010 (t80) REVERT: q 135 HIS cc_start: 0.7863 (m-70) cc_final: 0.7533 (m-70) outliers start: 115 outliers final: 64 residues processed: 797 average time/residue: 0.2076 time to fit residues: 269.2326 Evaluate side-chains 743 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 664 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 401 LYS Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 213 PHE Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 19 LYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 77 HIS Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 328 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 377 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 401 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN X 77 HIS Z 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113646 restraints weight = 53205.847| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.32 r_work: 0.3245 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 35117 Z= 0.156 Angle : 0.815 36.537 47623 Z= 0.326 Chirality : 0.044 0.201 5193 Planarity : 0.005 0.072 6033 Dihedral : 9.061 145.272 4948 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 2.97 % Allowed : 19.78 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4167 helix: 0.54 (0.12), residues: 1854 sheet: -1.40 (0.27), residues: 353 loop : -1.19 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 142 TYR 0.039 0.002 TYR D 135 PHE 0.027 0.001 PHE P 213 TRP 0.015 0.001 TRP F 99 HIS 0.020 0.001 HIS G 424 Details of bonding type rmsd covalent geometry : bond 0.00374 (35076) covalent geometry : angle 0.64326 (47531) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.50024 ( 8) hydrogen bonds : bond 0.03618 ( 1325) hydrogen bonds : angle 4.85370 ( 3771) metal coordination : bond 0.01973 ( 37) metal coordination : angle 11.92146 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 669 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8250 (ttm) REVERT: A 106 TRP cc_start: 0.7589 (t60) cc_final: 0.7184 (t60) REVERT: B 171 TYR cc_start: 0.8907 (m-80) cc_final: 0.8128 (m-80) REVERT: B 222 TYR cc_start: 0.8857 (t80) cc_final: 0.8406 (t80) REVERT: C 234 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8280 (pp) REVERT: D 215 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8631 (pt0) REVERT: D 437 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8061 (mttt) REVERT: E 59 TYR cc_start: 0.8604 (m-80) cc_final: 0.8263 (m-80) REVERT: E 105 GLN cc_start: 0.8517 (mp10) cc_final: 0.8049 (mp10) REVERT: E 187 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6600 (tp) REVERT: E 194 ASP cc_start: 0.8413 (t0) cc_final: 0.7945 (t0) REVERT: F 53 LEU cc_start: 0.8551 (tp) cc_final: 0.8208 (tp) REVERT: F 75 TRP cc_start: 0.8381 (t60) cc_final: 0.7028 (t60) REVERT: F 131 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8499 (mpp) REVERT: F 134 ASP cc_start: 0.8513 (t0) cc_final: 0.8078 (t0) REVERT: F 289 GLU cc_start: 0.7720 (pm20) cc_final: 0.7260 (tt0) REVERT: F 450 MET cc_start: 0.8389 (tpp) cc_final: 0.7784 (mtp) REVERT: G 32 ILE cc_start: 0.8697 (mt) cc_final: 0.8417 (pt) REVERT: G 97 MET cc_start: 0.7887 (mtp) cc_final: 0.7411 (mtp) REVERT: G 223 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8567 (mt) REVERT: G 271 MET cc_start: 0.8653 (mmp) cc_final: 0.7981 (mmt) REVERT: G 316 TYR cc_start: 0.8971 (m-80) cc_final: 0.8276 (m-80) REVERT: G 333 PHE cc_start: 0.8138 (m-80) cc_final: 0.7750 (m-10) REVERT: G 409 PHE cc_start: 0.9009 (m-10) cc_final: 0.8762 (m-10) REVERT: G 712 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8671 (tmmt) REVERT: H 126 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7398 (mmpt) REVERT: H 163 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8437 (tm-30) REVERT: H 261 MET cc_start: 0.8308 (mmm) cc_final: 0.7824 (mtt) REVERT: H 265 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8468 (tt) REVERT: I 37 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8441 (ttpp) REVERT: I 68 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8617 (ttt90) REVERT: I 200 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8480 (tp30) REVERT: P 154 GLN cc_start: 0.7805 (tp40) cc_final: 0.7578 (tp40) REVERT: P 283 MET cc_start: 0.8465 (tpt) cc_final: 0.8124 (tpp) REVERT: P 311 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7622 (mm-30) REVERT: P 313 TRP cc_start: 0.5836 (t60) cc_final: 0.4071 (m100) REVERT: P 346 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7270 (mm-30) REVERT: P 361 TRP cc_start: 0.7942 (m100) cc_final: 0.7737 (m100) REVERT: Q 105 GLU cc_start: 0.8614 (tt0) cc_final: 0.8271 (tt0) REVERT: Q 159 SER cc_start: 0.9195 (m) cc_final: 0.8688 (p) REVERT: Q 164 PHE cc_start: 0.8528 (m-80) cc_final: 0.8285 (m-10) REVERT: S 53 ILE cc_start: 0.8659 (mt) cc_final: 0.8429 (mp) REVERT: S 89 ARG cc_start: 0.8048 (tpt170) cc_final: 0.7554 (tpt170) REVERT: S 92 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8437 (tp40) REVERT: T 104 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: T 115 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8558 (tm-30) REVERT: T 142 GLN cc_start: 0.8263 (mt0) cc_final: 0.7665 (mt0) REVERT: V 32 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8748 (mm) REVERT: V 116 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7682 (mt) REVERT: W 19 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8138 (p) REVERT: W 27 ASP cc_start: 0.7798 (t0) cc_final: 0.7342 (t0) REVERT: W 32 LYS cc_start: 0.8599 (mtpp) cc_final: 0.8120 (mttm) REVERT: W 45 GLU cc_start: 0.7683 (tm-30) cc_final: 0.6947 (tm-30) REVERT: W 54 GLN cc_start: 0.8767 (mm-40) cc_final: 0.7727 (mm-40) REVERT: W 64 ASP cc_start: 0.8028 (m-30) cc_final: 0.7685 (m-30) REVERT: W 127 MET cc_start: 0.8085 (ptm) cc_final: 0.7524 (ptp) REVERT: Z 24 ASN cc_start: 0.8644 (t0) cc_final: 0.8040 (t0) REVERT: Z 80 ASP cc_start: 0.7466 (m-30) cc_final: 0.7178 (m-30) REVERT: Z 120 LEU cc_start: 0.8725 (tp) cc_final: 0.8466 (mm) REVERT: b 8 PHE cc_start: 0.6723 (t80) cc_final: 0.6514 (t80) REVERT: b 10 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7813 (mmmt) REVERT: b 35 ILE cc_start: 0.8862 (pt) cc_final: 0.8555 (pt) REVERT: q 124 TYR cc_start: 0.8262 (t80) cc_final: 0.7145 (t80) REVERT: q 135 HIS cc_start: 0.7967 (m-70) cc_final: 0.7625 (m-70) REVERT: r 40 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7290 (mmtt) REVERT: s 78 TYR cc_start: 0.7172 (m-80) cc_final: 0.6157 (m-80) outliers start: 109 outliers final: 74 residues processed: 739 average time/residue: 0.2058 time to fit residues: 248.7543 Evaluate side-chains 733 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 647 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 72 HIS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 16 GLU Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 93 ASN Chi-restraints excluded: chain Z residue 16 TYR Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 257 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 359 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 305 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 344 optimal weight: 0.6980 chunk 246 optimal weight: 0.7980 chunk 400 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 188 ASN F 44 ASN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 ASN P 166 HIS S 93 ASN V 110 ASN W 94 GLN Z 85 GLN Z 135 ASN a 31 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114731 restraints weight = 53315.999| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.35 r_work: 0.3315 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 35117 Z= 0.137 Angle : 0.803 36.280 47623 Z= 0.322 Chirality : 0.044 0.230 5193 Planarity : 0.005 0.074 6033 Dihedral : 8.965 146.724 4948 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 2.59 % Allowed : 20.33 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4167 helix: 0.61 (0.12), residues: 1850 sheet: -1.36 (0.28), residues: 341 loop : -1.15 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 153 TYR 0.032 0.002 TYR D 135 PHE 0.023 0.001 PHE P 213 TRP 0.014 0.001 TRP A 77 HIS 0.010 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00322 (35076) covalent geometry : angle 0.63864 (47531) SS BOND : bond 0.00123 ( 4) SS BOND : angle 0.46909 ( 8) hydrogen bonds : bond 0.03549 ( 1325) hydrogen bonds : angle 4.79296 ( 3771) metal coordination : bond 0.01786 ( 37) metal coordination : angle 11.60662 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 690 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8246 (ttm) REVERT: A 106 TRP cc_start: 0.7605 (t60) cc_final: 0.7206 (t60) REVERT: B 171 TYR cc_start: 0.8814 (m-80) cc_final: 0.8075 (m-80) REVERT: B 222 TYR cc_start: 0.8877 (t80) cc_final: 0.8508 (t80) REVERT: C 234 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8204 (pp) REVERT: D 215 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8580 (pt0) REVERT: D 437 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8002 (mttt) REVERT: E 59 TYR cc_start: 0.8708 (m-80) cc_final: 0.8423 (m-80) REVERT: E 61 ARG cc_start: 0.8797 (mtt90) cc_final: 0.8586 (mtt90) REVERT: E 88 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: E 105 GLN cc_start: 0.8478 (mp10) cc_final: 0.8004 (mp10) REVERT: E 120 MET cc_start: 0.8882 (mmm) cc_final: 0.8589 (mmm) REVERT: E 152 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7113 (mm-40) REVERT: E 171 ILE cc_start: 0.8976 (pt) cc_final: 0.8569 (pt) REVERT: E 187 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6678 (tp) REVERT: E 194 ASP cc_start: 0.8365 (t0) cc_final: 0.7919 (t0) REVERT: F 53 LEU cc_start: 0.8517 (tp) cc_final: 0.8200 (tp) REVERT: F 75 TRP cc_start: 0.8604 (t60) cc_final: 0.7218 (t60) REVERT: F 131 MET cc_start: 0.8782 (mtm) cc_final: 0.8567 (mpp) REVERT: F 134 ASP cc_start: 0.8474 (t0) cc_final: 0.8050 (t0) REVERT: F 289 GLU cc_start: 0.7630 (pm20) cc_final: 0.7307 (tt0) REVERT: F 445 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: F 450 MET cc_start: 0.8439 (tpp) cc_final: 0.7870 (mtp) REVERT: G 32 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8558 (pt) REVERT: G 97 MET cc_start: 0.7879 (mtp) cc_final: 0.7491 (mtp) REVERT: G 223 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8544 (mt) REVERT: G 271 MET cc_start: 0.8616 (mmp) cc_final: 0.7965 (mmt) REVERT: G 316 TYR cc_start: 0.8951 (m-80) cc_final: 0.8275 (m-80) REVERT: G 333 PHE cc_start: 0.8204 (m-80) cc_final: 0.7817 (m-10) REVERT: G 500 ILE cc_start: 0.9360 (mm) cc_final: 0.9094 (mt) REVERT: G 712 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8700 (tmmt) REVERT: H 114 TYR cc_start: 0.9108 (m-10) cc_final: 0.8507 (m-80) REVERT: H 126 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7414 (mmpt) REVERT: H 163 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8419 (tm-30) REVERT: H 184 MET cc_start: 0.9057 (mtm) cc_final: 0.8803 (mtm) REVERT: H 261 MET cc_start: 0.8339 (mmm) cc_final: 0.8016 (mtt) REVERT: H 265 LEU cc_start: 0.8744 (mm) cc_final: 0.8454 (tt) REVERT: I 200 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8429 (tp30) REVERT: P 154 GLN cc_start: 0.7699 (tp40) cc_final: 0.7493 (tp40) REVERT: P 283 MET cc_start: 0.8523 (tpt) cc_final: 0.8158 (tpp) REVERT: P 310 PHE cc_start: 0.6452 (m-10) cc_final: 0.6205 (m-10) REVERT: P 311 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7717 (mm-30) REVERT: P 313 TRP cc_start: 0.5946 (t60) cc_final: 0.4036 (m100) REVERT: Q 105 GLU cc_start: 0.8577 (tt0) cc_final: 0.8235 (tt0) REVERT: Q 159 SER cc_start: 0.9167 (m) cc_final: 0.8619 (p) REVERT: Q 164 PHE cc_start: 0.8425 (m-80) cc_final: 0.8136 (m-10) REVERT: S 89 ARG cc_start: 0.7943 (tpt170) cc_final: 0.7666 (tpt170) REVERT: T 82 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8179 (ptm160) REVERT: T 115 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8646 (tm-30) REVERT: T 142 GLN cc_start: 0.8272 (mt0) cc_final: 0.7739 (mt0) REVERT: V 32 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8783 (mm) REVERT: V 116 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7571 (mt) REVERT: W 19 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8171 (p) REVERT: W 27 ASP cc_start: 0.7748 (t0) cc_final: 0.7348 (t0) REVERT: W 45 GLU cc_start: 0.7613 (tm-30) cc_final: 0.6918 (tm-30) REVERT: W 54 GLN cc_start: 0.8878 (mm-40) cc_final: 0.7863 (mm-40) REVERT: W 127 MET cc_start: 0.7981 (ptm) cc_final: 0.7554 (ptp) REVERT: Z 24 ASN cc_start: 0.8613 (t0) cc_final: 0.8055 (t0) REVERT: Z 72 MET cc_start: 0.8012 (ttp) cc_final: 0.7779 (mtm) REVERT: Z 79 LYS cc_start: 0.8448 (ttmm) cc_final: 0.7972 (ttpp) REVERT: Z 80 ASP cc_start: 0.7420 (m-30) cc_final: 0.7155 (m-30) REVERT: Z 120 LEU cc_start: 0.8787 (tp) cc_final: 0.8554 (mm) REVERT: b 10 LYS cc_start: 0.8325 (mtpm) cc_final: 0.7858 (mmmt) REVERT: b 35 ILE cc_start: 0.8932 (pt) cc_final: 0.8605 (pt) REVERT: q 124 TYR cc_start: 0.8329 (t80) cc_final: 0.7342 (t80) REVERT: q 135 HIS cc_start: 0.7995 (m-70) cc_final: 0.7705 (m-70) REVERT: r 40 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7354 (mmtt) REVERT: r 101 MET cc_start: 0.8659 (ttp) cc_final: 0.8270 (ttp) REVERT: s 78 TYR cc_start: 0.7194 (m-80) cc_final: 0.6271 (m-80) outliers start: 95 outliers final: 69 residues processed: 748 average time/residue: 0.2011 time to fit residues: 247.8443 Evaluate side-chains 737 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 656 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 72 HIS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 16 TYR Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 131 GLU Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 71 optimal weight: 0.0060 chunk 310 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 255 optimal weight: 0.6980 chunk 319 optimal weight: 2.9990 chunk 394 optimal weight: 7.9990 chunk 163 optimal weight: 0.0980 chunk 276 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN G 424 HIS ** G 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 ASN P 166 HIS T 103 HIS V 53 ASN V 110 ASN W 94 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115829 restraints weight = 53248.561| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.45 r_work: 0.3295 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35117 Z= 0.128 Angle : 0.796 35.734 47623 Z= 0.322 Chirality : 0.043 0.275 5193 Planarity : 0.005 0.077 6033 Dihedral : 8.864 148.229 4948 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.42 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 20.82 % Favored : 76.78 % 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: -0.54 (0.13), residues: 4167 helix: 0.68 (0.12), residues: 1838 sheet: -1.33 (0.28), residues: 343 loop : -1.14 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 34 TYR 0.039 0.002 TYR D 135 PHE 0.023 0.001 PHE T 126 TRP 0.022 0.001 TRP F 99 HIS 0.010 0.001 HIS F 303 Details of bonding type rmsd covalent geometry : bond 0.00297 (35076) covalent geometry : angle 0.63768 (47531) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.56323 ( 8) hydrogen bonds : bond 0.03441 ( 1325) hydrogen bonds : angle 4.79981 ( 3771) metal coordination : bond 0.01573 ( 37) metal coordination : angle 11.37826 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8334 Ramachandran restraints generated. 4167 Oldfield, 0 Emsley, 4167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 681 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: A 106 TRP cc_start: 0.7468 (t60) cc_final: 0.7121 (t60) REVERT: B 171 TYR cc_start: 0.8841 (m-80) cc_final: 0.8101 (m-80) REVERT: B 222 TYR cc_start: 0.8852 (t80) cc_final: 0.8490 (t80) REVERT: C 234 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8243 (pp) REVERT: D 215 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8610 (pt0) REVERT: D 282 ASP cc_start: 0.8646 (m-30) cc_final: 0.8426 (m-30) REVERT: D 323 ARG cc_start: 0.8576 (ttt-90) cc_final: 0.8271 (ttt-90) REVERT: D 437 LYS cc_start: 0.8767 (tmtt) cc_final: 0.7944 (mttt) REVERT: E 59 TYR cc_start: 0.8796 (m-80) cc_final: 0.8506 (m-80) REVERT: E 105 GLN cc_start: 0.8395 (mp10) cc_final: 0.7915 (mp10) REVERT: E 120 MET cc_start: 0.8861 (mmm) cc_final: 0.8537 (mmm) REVERT: E 187 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6452 (tp) REVERT: E 194 ASP cc_start: 0.8334 (t0) cc_final: 0.7900 (t0) REVERT: F 53 LEU cc_start: 0.8499 (tp) cc_final: 0.8168 (tp) REVERT: F 75 TRP cc_start: 0.8592 (t60) cc_final: 0.7267 (t60) REVERT: F 131 MET cc_start: 0.8693 (mtm) cc_final: 0.8460 (mpp) REVERT: F 134 ASP cc_start: 0.8481 (t0) cc_final: 0.8050 (t0) REVERT: F 289 GLU cc_start: 0.7689 (pm20) cc_final: 0.7230 (tt0) REVERT: F 445 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: F 450 MET cc_start: 0.8354 (tpp) cc_final: 0.7741 (mtp) REVERT: G 32 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8462 (pt) REVERT: G 97 MET cc_start: 0.7969 (mtp) cc_final: 0.7520 (mtp) REVERT: G 223 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8500 (mt) REVERT: G 271 MET cc_start: 0.8631 (mmp) cc_final: 0.8015 (mmt) REVERT: G 316 TYR cc_start: 0.8977 (m-80) cc_final: 0.8240 (m-80) REVERT: G 333 PHE cc_start: 0.8110 (m-80) cc_final: 0.7696 (m-10) REVERT: G 500 ILE cc_start: 0.9299 (mm) cc_final: 0.9034 (mt) REVERT: G 712 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8656 (tmmt) REVERT: H 114 TYR cc_start: 0.9114 (m-10) cc_final: 0.8399 (m-80) REVERT: H 126 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7374 (mmpt) REVERT: H 163 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8414 (tm-30) REVERT: H 184 MET cc_start: 0.8961 (mtm) cc_final: 0.8625 (mtm) REVERT: H 261 MET cc_start: 0.8172 (mmm) cc_final: 0.7940 (mtt) REVERT: H 265 LEU cc_start: 0.8739 (mm) cc_final: 0.8455 (tt) REVERT: I 200 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8422 (tp30) REVERT: I 211 TYR cc_start: 0.8253 (m-80) cc_final: 0.8036 (m-80) REVERT: P 283 MET cc_start: 0.8475 (tpt) cc_final: 0.8097 (tpp) REVERT: P 311 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7539 (mm-30) REVERT: P 313 TRP cc_start: 0.5937 (t60) cc_final: 0.4010 (m100) REVERT: Q 105 GLU cc_start: 0.8579 (tt0) cc_final: 0.8207 (tt0) REVERT: Q 159 SER cc_start: 0.9137 (m) cc_final: 0.8560 (p) REVERT: S 43 GLU cc_start: 0.8275 (mp0) cc_final: 0.8046 (pm20) REVERT: S 89 ARG cc_start: 0.7879 (tpt170) cc_final: 0.7667 (tpt170) REVERT: T 82 ARG cc_start: 0.8502 (ttp-110) cc_final: 0.8005 (ptm160) REVERT: T 103 HIS cc_start: 0.7317 (m170) cc_final: 0.7036 (m-70) REVERT: T 115 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8494 (tm-30) REVERT: T 142 GLN cc_start: 0.8306 (mt0) cc_final: 0.7967 (mt0) REVERT: T 143 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7538 (tp30) REVERT: V 34 ILE cc_start: 0.8846 (tp) cc_final: 0.8369 (tp) REVERT: W 19 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8226 (p) REVERT: W 27 ASP cc_start: 0.7669 (t0) cc_final: 0.7255 (t0) REVERT: W 45 GLU cc_start: 0.7633 (tm-30) cc_final: 0.6926 (tm-30) REVERT: W 54 GLN cc_start: 0.8744 (mm-40) cc_final: 0.7777 (mm-40) REVERT: W 127 MET cc_start: 0.7956 (ptm) cc_final: 0.7503 (ptp) REVERT: Z 24 ASN cc_start: 0.8614 (t0) cc_final: 0.8089 (t0) REVERT: Z 51 MET cc_start: 0.8248 (ttp) cc_final: 0.7974 (ttp) REVERT: Z 79 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7880 (ttpp) REVERT: Z 80 ASP cc_start: 0.7334 (m-30) cc_final: 0.7090 (m-30) REVERT: Z 120 LEU cc_start: 0.8693 (tp) cc_final: 0.8481 (mm) REVERT: b 10 LYS cc_start: 0.8315 (mtpm) cc_final: 0.7831 (mmmt) REVERT: b 35 ILE cc_start: 0.8853 (pt) cc_final: 0.8536 (pt) REVERT: q 124 TYR cc_start: 0.8263 (t80) cc_final: 0.7156 (t80) REVERT: q 135 HIS cc_start: 0.7923 (m-70) cc_final: 0.7606 (m-70) REVERT: r 40 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7298 (mmtt) REVERT: r 101 MET cc_start: 0.8579 (ttp) cc_final: 0.8269 (ttp) REVERT: s 78 TYR cc_start: 0.7118 (m-80) cc_final: 0.6153 (m-80) outliers start: 88 outliers final: 63 residues processed: 730 average time/residue: 0.2056 time to fit residues: 247.5369 Evaluate side-chains 735 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 663 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 445 GLU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 111 LYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 662 THR Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 126 LYS Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 72 HIS Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain W residue 19 SER Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 16 TYR Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 105 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 370 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 222 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 ASN ** G 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 128 ASN P 166 HIS V 53 ASN V 110 ASN W 111 HIS Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 18 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115533 restraints weight = 53032.297| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.42 r_work: 0.3291 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 35117 Z= 0.227 Angle : 0.920 59.197 47623 Z= 0.456 Chirality : 0.047 0.784 5193 Planarity : 0.006 0.209 6033 Dihedral : 8.873 148.209 4948 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 2.26 % Allowed : 21.28 % Favored : 76.45 % Cbeta Deviations : 0.05 % 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: -0.54 (0.13), residues: 4167 helix: 0.68 (0.12), residues: 1838 sheet: -1.32 (0.28), residues: 343 loop : -1.15 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 68 TYR 0.064 0.002 TYR H 317 PHE 0.060 0.001 PHE F 265 TRP 0.026 0.001 TRP A 77 HIS 0.353 0.003 HIS G 424 Details of bonding type rmsd covalent geometry : bond 0.00440 (35076) covalent geometry : angle 0.78777 (47531) SS BOND : bond 0.00115 ( 4) SS BOND : angle 0.56194 ( 8) hydrogen bonds : bond 0.03509 ( 1325) hydrogen bonds : angle 4.80057 ( 3771) metal coordination : bond 0.01644 ( 37) metal coordination : angle 11.35228 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10700.46 seconds wall clock time: 183 minutes 12.48 seconds (10992.48 seconds total)