Starting phenix.real_space_refine on Mon Jul 6 07:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibe_35341/07_2026/8ibe_35341_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibe_35341/07_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_35341/07_2026/8ibe_35341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibe_35341/07_2026/8ibe_35341.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibe_35341/07_2026/8ibe_35341_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibe_35341/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.91, per 1000 atoms: 0.20 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: 3.15 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: 0.84 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: 7.14 Time building geometry restraints manager: 4.14 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=" N PRO q 143 " pdb=" CD PRO q 143 " ideal model delta sigma weight residual 1.473 1.326 0.147 1.40e-02 5.10e+03 1.11e+02 ... (remaining 35071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 46567 6.18 - 12.35: 749 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: 20541 27.97 - 55.93: 597 55.93 - 83.90: 57 83.90 - 111.86: 8 111.86 - 139.83: 5 Dihedral angle restraints: 21208 sinusoidal: 8949 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 21205 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: 3.770 Set stop_for_unknowns flag: 0.010 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.310 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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= 1.042 Angle : 2.266 56.972 47623 Z= 1.498 Chirality : 0.128 0.952 5193 Planarity : 0.010 0.290 6033 Dihedral : 13.001 139.825 13292 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/Z covalent geometry : bond 0.01520 / 0.96 (35076) covalent geometry : angle 2.16148 / 1.50 (47531) SS BOND : bond 0.00814 / 0.41 ( 4) SS BOND : angle 1.32585 / 0.65 ( 8) hydrogen bonds : bond 0.25022 / 16.15 ( 1325) hydrogen bonds : angle 9.67443 / 6.96 ( 3771) metal coordination : bond 0.46129 / 30.52 ( 37) metal coordination : angle 16.38195 / 12.21 ( 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 : 1.147 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: 0.2314 time to fit residues: 491.0676 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 : 1.291 ------------------------------------------------------------------------------- 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... B 106 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN C 102 HIS C 130 ASN C 235 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 171 HIS 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 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: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119222 restraints weight = 53434.364| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.49 r_work: 0.3366 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 35117 Z= 0.214 Angle : 0.958 39.986 47623 Z= 0.420 Chirality : 0.049 0.246 5193 Planarity : 0.007 0.078 6033 Dihedral : 9.761 130.319 4964 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 2.70 % Allowed : 14.82 % Favored : 82.48 % 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: -1.79 (0.12), residues: 4167 helix: -0.46 (0.12), residues: 1824 sheet: -2.05 (0.25), residues: 350 loop : -1.67 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 135 TYR 0.027 0.002 TYR F 157 PHE 0.031 0.002 PHE S 36 TRP 0.015 0.002 TRP b 80 HIS 0.014 0.002 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (35076) covalent geometry : angle 0.80358 / 0.42 (47531) SS BOND : bond 0.02337 / 1.21 ( 4) SS BOND : angle 1.30686 / 0.58 ( 8) hydrogen bonds : bond 0.05619 / 3.66 ( 1325) hydrogen bonds : angle 5.83426 / 4.18 ( 3771) metal coordination : bond 0.02261 / 1.55 ( 37) metal coordination : angle 12.42828 / 9.38 ( 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 1000 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 901 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 26 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7348 (mm-40) REVERT: A 88 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8273 (ttm) REVERT: B 94 THR cc_start: 0.8449 (p) cc_final: 0.8217 (p) REVERT: C 190 TYR cc_start: 0.8654 (m-80) cc_final: 0.8431 (m-80) REVERT: C 214 GLU cc_start: 0.8359 (tt0) cc_final: 0.8085 (mt-10) REVERT: D 110 ASP cc_start: 0.8109 (t70) cc_final: 0.7851 (t70) REVERT: D 145 MET cc_start: 0.8564 (mtt) cc_final: 0.8148 (mtt) REVERT: D 238 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7272 (mp) REVERT: E 105 GLN cc_start: 0.8471 (mp10) cc_final: 0.8072 (mp10) REVERT: E 146 SER cc_start: 0.9375 (t) cc_final: 0.9170 (p) REVERT: E 188 ASN cc_start: 0.8139 (m110) cc_final: 0.7901 (m-40) REVERT: E 194 ASP cc_start: 0.8484 (t0) cc_final: 0.8196 (t0) REVERT: F 44 ASN cc_start: 0.8039 (t0) cc_final: 0.7770 (t0) REVERT: F 53 LEU cc_start: 0.8572 (tp) cc_final: 0.8116 (tp) REVERT: F 75 TRP cc_start: 0.8236 (t60) cc_final: 0.6879 (t60) REVERT: F 113 LEU cc_start: 0.8316 (tp) cc_final: 0.8111 (tp) REVERT: F 134 ASP cc_start: 0.8102 (t0) cc_final: 0.7721 (t0) REVERT: F 157 TYR cc_start: 0.8326 (t80) cc_final: 0.8003 (t80) REVERT: F 214 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7176 (mt-10) REVERT: F 274 LYS cc_start: 0.7938 (tttm) cc_final: 0.7410 (tptp) REVERT: F 311 TRP cc_start: 0.6967 (t60) cc_final: 0.6661 (t60) REVERT: F 387 GLU cc_start: 0.8105 (mp0) cc_final: 0.7667 (mp0) REVERT: F 396 MET cc_start: 0.8711 (mmm) cc_final: 0.8388 (mmm) REVERT: G 107 GLU cc_start: 0.8184 (tp30) cc_final: 0.7909 (tp30) REVERT: G 211 GLU cc_start: 0.8175 (pm20) cc_final: 0.7705 (pt0) REVERT: G 271 MET cc_start: 0.8906 (mmp) cc_final: 0.8423 (mmt) REVERT: G 315 THR cc_start: 0.8828 (m) cc_final: 0.8528 (p) REVERT: G 329 MET cc_start: 0.8343 (mmt) cc_final: 0.7758 (mmt) REVERT: G 409 PHE cc_start: 0.8911 (m-10) cc_final: 0.8667 (m-10) REVERT: G 518 ARG cc_start: 0.8896 (ptt90) cc_final: 0.8673 (ptt-90) REVERT: H 126 LYS cc_start: 0.8213 (mmtt) cc_final: 0.7676 (mmmt) REVERT: H 163 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8393 (tm-30) REVERT: H 192 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: H 193 THR cc_start: 0.9122 (m) cc_final: 0.8888 (p) REVERT: H 261 MET cc_start: 0.8098 (mmt) cc_final: 0.7751 (mmm) REVERT: I 59 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7225 (tmm160) REVERT: I 139 SER cc_start: 0.9378 (t) cc_final: 0.8990 (t) REVERT: I 195 ASP cc_start: 0.8040 (m-30) cc_final: 0.7769 (m-30) REVERT: P 238 GLN cc_start: 0.7489 (mt0) cc_final: 0.7163 (mt0) REVERT: P 283 MET cc_start: 0.8247 (mmm) cc_final: 0.7831 (tpp) REVERT: P 300 TRP cc_start: 0.7193 (t-100) cc_final: 0.6323 (t60) REVERT: P 310 PHE cc_start: 0.6899 (m-10) cc_final: 0.6683 (m-10) REVERT: P 313 TRP cc_start: 0.5803 (t60) cc_final: 0.4109 (m-10) REVERT: Q 78 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8262 (ttt-90) REVERT: Q 135 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8862 (mm) REVERT: S 53 ILE cc_start: 0.8695 (mt) cc_final: 0.7834 (mt) REVERT: S 57 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7738 (mm-30) REVERT: S 64 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7350 (mtmm) REVERT: S 91 MET cc_start: 0.9057 (tpp) cc_final: 0.8812 (tpp) REVERT: T 82 ARG cc_start: 0.8816 (mtp-110) cc_final: 0.8038 (ttm170) REVERT: T 115 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8352 (tm-30) REVERT: T 142 GLN cc_start: 0.8663 (mt0) cc_final: 0.7969 (mt0) REVERT: V 81 ILE cc_start: 0.9257 (mt) cc_final: 0.9028 (mp) REVERT: W 27 ASP cc_start: 0.7583 (t0) cc_final: 0.7346 (t0) REVERT: W 32 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8278 (mttm) REVERT: W 45 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7108 (tm-30) REVERT: W 83 ASP cc_start: 0.9055 (m-30) cc_final: 0.8423 (m-30) REVERT: W 127 MET cc_start: 0.7972 (ptm) cc_final: 0.7275 (ptp) REVERT: X 50 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6969 (tm-30) REVERT: X 83 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8634 (p) REVERT: X 117 TRP cc_start: 0.6978 (m-10) cc_final: 0.6450 (m-90) REVERT: X 125 LEU cc_start: 0.8877 (mt) cc_final: 0.8439 (mp) REVERT: Z 9 ASP cc_start: 0.8136 (t0) cc_final: 0.7533 (t0) REVERT: Z 10 MET cc_start: 0.9063 (mmm) cc_final: 0.8735 (mmm) REVERT: Z 20 ASP cc_start: 0.8292 (t0) cc_final: 0.7807 (p0) REVERT: Z 24 ASN cc_start: 0.8217 (t0) cc_final: 0.7834 (t0) REVERT: Z 80 ASP cc_start: 0.7567 (m-30) cc_final: 0.7279 (m-30) REVERT: Z 129 THR cc_start: 0.6452 (OUTLIER) cc_final: 0.6237 (m) REVERT: a 30 THR cc_start: 0.9036 (m) cc_final: 0.8720 (p) REVERT: b 35 ILE cc_start: 0.9069 (pt) cc_final: 0.8719 (pt) REVERT: r 11 LEU cc_start: 0.7359 (mt) cc_final: 0.7149 (mt) outliers start: 99 outliers final: 53 residues processed: 958 average time/residue: 0.2360 time to fit residues: 363.7536 Evaluate side-chains 789 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 729 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 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 284 HIS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 160 VAL 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 192 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 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 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 Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 272 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 363 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS 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 ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN 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 ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116444 restraints weight = 53565.457| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.41 r_work: 0.3333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4191 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= 0.201 Angle : 0.869 39.995 47623 Z= 0.364 Chirality : 0.046 0.185 5193 Planarity : 0.006 0.071 6033 Dihedral : 9.537 135.273 4964 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 3.41 % Allowed : 16.73 % Favored : 79.86 % 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: -1.32 (0.13), residues: 4167 helix: -0.03 (0.12), residues: 1837 sheet: -1.92 (0.25), residues: 360 loop : -1.45 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 153 TYR 0.030 0.002 TYR B 170 PHE 0.025 0.002 PHE T 126 TRP 0.015 0.001 TRP b 80 HIS 0.007 0.001 HIS G 444 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (35076) covalent geometry : angle 0.70103 / 0.36 (47531) SS BOND : bond 0.00260 / 0.13 ( 4) SS BOND : angle 1.83770 / 1.06 ( 8) hydrogen bonds : bond 0.04646 / 3.02 ( 1325) hydrogen bonds : angle 5.39016 / 3.87 ( 3771) metal coordination : bond 0.02705 / 1.89 ( 37) metal coordination : angle 12.23670 / 9.09 ( 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 890 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 765 time to evaluate : 1.610 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: 0.9109 (tpt) cc_final: 0.8891 (tpp) REVERT: B 171 TYR cc_start: 0.8608 (m-80) cc_final: 0.8253 (m-80) REVERT: D 145 MET cc_start: 0.8499 (mtt) cc_final: 0.8172 (mtt) REVERT: D 215 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8704 (pt0) REVERT: D 238 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7667 (mp) REVERT: D 282 ASP cc_start: 0.8623 (m-30) cc_final: 0.8328 (m-30) REVERT: E 105 GLN cc_start: 0.8550 (mp10) cc_final: 0.8086 (mp10) REVERT: E 143 ASP cc_start: 0.8110 (m-30) cc_final: 0.7643 (t0) REVERT: E 146 SER cc_start: 0.9234 (t) cc_final: 0.8733 (p) REVERT: E 188 ASN cc_start: 0.8270 (m110) cc_final: 0.8055 (m-40) REVERT: E 194 ASP cc_start: 0.8467 (t0) cc_final: 0.8046 (t0) REVERT: F 51 TRP cc_start: 0.7690 (p-90) cc_final: 0.7225 (p-90) REVERT: F 53 LEU cc_start: 0.8622 (tp) cc_final: 0.8285 (tp) REVERT: F 75 TRP cc_start: 0.8040 (t60) cc_final: 0.6927 (t60) REVERT: F 134 ASP cc_start: 0.8167 (t0) cc_final: 0.7675 (t0) REVERT: F 157 TYR cc_start: 0.8263 (t80) cc_final: 0.7929 (t80) REVERT: F 255 CYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7522 (p) REVERT: F 274 LYS cc_start: 0.8035 (tttm) cc_final: 0.7616 (tptp) REVERT: F 396 MET cc_start: 0.8724 (mmm) cc_final: 0.8362 (mmm) REVERT: G 211 GLU cc_start: 0.8219 (pm20) cc_final: 0.7812 (pt0) REVERT: G 225 ILE cc_start: 0.9065 (tt) cc_final: 0.8831 (mm) REVERT: G 315 THR cc_start: 0.8906 (m) cc_final: 0.8622 (p) REVERT: G 316 TYR cc_start: 0.8559 (m-80) cc_final: 0.8227 (m-80) REVERT: G 329 MET cc_start: 0.8387 (mmt) cc_final: 0.7719 (mmt) REVERT: G 362 ASP cc_start: 0.7407 (t70) cc_final: 0.6751 (t0) REVERT: G 409 PHE cc_start: 0.8916 (m-10) cc_final: 0.8692 (m-10) REVERT: G 530 TYR cc_start: 0.9252 (m-80) cc_final: 0.8846 (m-80) REVERT: H 34 ARG cc_start: 0.9160 (ptt-90) cc_final: 0.8900 (ptt90) REVERT: H 49 PHE cc_start: 0.8088 (m-10) cc_final: 0.7861 (m-10) REVERT: H 126 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7718 (mmpt) REVERT: H 163 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8453 (tm-30) REVERT: H 184 MET cc_start: 0.8914 (mtm) cc_final: 0.8663 (mtm) REVERT: H 192 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: H 261 MET cc_start: 0.8114 (mmt) cc_final: 0.7905 (mmm) REVERT: I 59 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7228 (tmm160) REVERT: I 200 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8475 (tp30) REVERT: P 280 ILE cc_start: 0.8801 (mt) cc_final: 0.8560 (mp) REVERT: P 283 MET cc_start: 0.8225 (mmm) cc_final: 0.7838 (tpp) REVERT: P 300 TRP cc_start: 0.7216 (t-100) cc_final: 0.6280 (t60) REVERT: P 310 PHE cc_start: 0.7028 (m-10) cc_final: 0.6737 (m-10) REVERT: P 313 TRP cc_start: 0.5853 (t60) cc_final: 0.3943 (m100) REVERT: Q 105 GLU cc_start: 0.8117 (tt0) cc_final: 0.7820 (tt0) REVERT: Q 106 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8302 (ttm170) REVERT: S 53 ILE cc_start: 0.8712 (mt) cc_final: 0.8192 (mt) REVERT: S 57 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7655 (mt-10) REVERT: S 64 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7318 (mtmm) REVERT: S 89 ARG cc_start: 0.8025 (tpt170) cc_final: 0.7650 (tpt170) REVERT: T 82 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8431 (ttp-110) REVERT: T 103 HIS cc_start: 0.8114 (m-70) cc_final: 0.7692 (m-70) REVERT: T 115 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8514 (tm-30) REVERT: T 126 PHE cc_start: 0.6799 (m-10) cc_final: 0.6411 (m-10) REVERT: V 67 LYS cc_start: 0.8939 (tppt) cc_final: 0.8690 (tppt) REVERT: V 81 ILE cc_start: 0.9275 (mt) cc_final: 0.9058 (mp) REVERT: W 27 ASP cc_start: 0.7630 (t0) cc_final: 0.7167 (t0) REVERT: W 32 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8247 (mttm) REVERT: W 51 HIS cc_start: 0.8306 (t-170) cc_final: 0.8049 (t-170) REVERT: W 127 MET cc_start: 0.8043 (ptm) cc_final: 0.7402 (ptp) REVERT: X 117 TRP cc_start: 0.6736 (m-10) cc_final: 0.6097 (m-10) REVERT: X 125 LEU cc_start: 0.8928 (mt) cc_final: 0.8466 (mp) REVERT: Z 9 ASP cc_start: 0.8100 (t0) cc_final: 0.7696 (t0) REVERT: Z 24 ASN cc_start: 0.8451 (t0) cc_final: 0.8064 (t0) REVERT: Z 80 ASP cc_start: 0.7500 (m-30) cc_final: 0.7276 (m-30) REVERT: Z 129 THR cc_start: 0.6688 (m) cc_final: 0.6450 (m) REVERT: Z 138 PHE cc_start: 0.8578 (m-80) cc_final: 0.8353 (m-10) REVERT: a 30 THR cc_start: 0.9000 (m) cc_final: 0.8781 (p) REVERT: b 35 ILE cc_start: 0.9023 (pt) cc_final: 0.8684 (pt) REVERT: q 135 HIS cc_start: 0.7971 (m-70) cc_final: 0.7645 (m-70) REVERT: r 11 LEU cc_start: 0.7402 (mt) cc_final: 0.7090 (mt) outliers start: 125 outliers final: 71 residues processed: 834 average time/residue: 0.2229 time to fit residues: 299.7900 Evaluate side-chains 766 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 692 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 99 CYS 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 180 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET 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 627 SER 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 192 GLU 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 349 SER 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 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 19 SER Chi-restraints excluded: chain W residue 49 THR 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 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 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: 3.9990 chunk 334 optimal weight: 0.7980 chunk 170 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 333 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 442 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 112 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112752 restraints weight = 53399.944| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.73 r_work: 0.3267 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 35117 Z= 0.155 Angle : 0.816 39.633 47623 Z= 0.332 Chirality : 0.044 0.195 5193 Planarity : 0.005 0.073 6033 Dihedral : 9.371 139.464 4964 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.46 % Favored : 95.51 % Rotamer: Outliers : 3.38 % Allowed : 17.57 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4167 helix: 0.17 (0.12), residues: 1842 sheet: -1.74 (0.26), residues: 366 loop : -1.34 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 153 TYR 0.024 0.002 TYR B 170 PHE 0.029 0.002 PHE P 213 TRP 0.012 0.001 TRP b 80 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (35076) covalent geometry : angle 0.64263 / 0.33 (47531) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.97174 / 0.55 ( 8) hydrogen bonds : bond 0.04079 / 2.66 ( 1325) hydrogen bonds : angle 5.12998 / 3.68 ( 3771) metal coordination : bond 0.01963 / 1.44 ( 37) metal coordination : angle 11.99805 / 8.81 ( 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 873 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 749 time to evaluate : 1.339 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: A 53 MET cc_start: 0.7897 (tpt) cc_final: 0.7689 (tpt) REVERT: A 106 TRP cc_start: 0.7326 (t60) cc_final: 0.6836 (t60) REVERT: B 141 MET cc_start: 0.8928 (tpt) cc_final: 0.8718 (tpp) REVERT: B 171 TYR cc_start: 0.8549 (m-80) cc_final: 0.7869 (m-80) REVERT: B 222 TYR cc_start: 0.8660 (t80) cc_final: 0.8155 (t80) REVERT: C 234 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8237 (pp) REVERT: D 185 MET cc_start: 0.8780 (tpt) cc_final: 0.7909 (tpt) REVERT: D 215 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8575 (pt0) REVERT: D 238 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7667 (mm) REVERT: D 355 GLU cc_start: 0.8570 (pm20) cc_final: 0.8365 (pt0) REVERT: E 105 GLN cc_start: 0.8396 (mp10) cc_final: 0.7967 (mp10) REVERT: E 194 ASP cc_start: 0.8293 (t0) cc_final: 0.7861 (t0) REVERT: F 44 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7521 (t0) REVERT: F 53 LEU cc_start: 0.8618 (tp) cc_final: 0.8285 (tp) REVERT: F 75 TRP cc_start: 0.8188 (t60) cc_final: 0.7004 (t60) REVERT: F 134 ASP cc_start: 0.8299 (t0) cc_final: 0.7833 (t0) REVERT: F 157 TYR cc_start: 0.8085 (t80) cc_final: 0.7787 (t80) REVERT: F 246 GLU cc_start: 0.8186 (tt0) cc_final: 0.7504 (tt0) REVERT: F 255 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7307 (p) REVERT: F 274 LYS cc_start: 0.7963 (tttm) cc_final: 0.7668 (tptp) REVERT: F 396 MET cc_start: 0.8532 (mmm) cc_final: 0.7794 (mmm) REVERT: G 211 GLU cc_start: 0.8260 (pm20) cc_final: 0.7923 (pt0) REVERT: G 223 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8494 (mt) REVERT: G 225 ILE cc_start: 0.9016 (tt) cc_final: 0.8805 (mm) REVERT: G 271 MET cc_start: 0.8537 (mmp) cc_final: 0.8115 (mmt) REVERT: G 315 THR cc_start: 0.8845 (m) cc_final: 0.8569 (p) REVERT: G 316 TYR cc_start: 0.8610 (m-80) cc_final: 0.8196 (m-80) REVERT: G 409 PHE cc_start: 0.8854 (m-10) cc_final: 0.8615 (m-10) REVERT: G 530 TYR cc_start: 0.9170 (m-80) cc_final: 0.8719 (m-80) REVERT: H 34 ARG cc_start: 0.9109 (ptt-90) cc_final: 0.8857 (ptt90) REVERT: H 49 PHE cc_start: 0.8068 (m-10) cc_final: 0.7866 (m-10) REVERT: H 126 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7660 (mmmt) REVERT: H 163 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8192 (tm-30) REVERT: H 184 MET cc_start: 0.8825 (mtm) cc_final: 0.8225 (mtm) REVERT: H 192 GLU cc_start: 0.7469 (tt0) cc_final: 0.7258 (tm-30) REVERT: H 199 ASP cc_start: 0.7585 (m-30) cc_final: 0.7319 (m-30) REVERT: H 265 LEU cc_start: 0.8881 (mm) cc_final: 0.8356 (tt) REVERT: I 59 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7418 (tmm160) REVERT: I 139 SER cc_start: 0.9290 (t) cc_final: 0.9086 (p) REVERT: I 200 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8286 (tp30) REVERT: P 280 ILE cc_start: 0.8746 (mt) cc_final: 0.8526 (mp) REVERT: P 283 MET cc_start: 0.8208 (mmm) cc_final: 0.7825 (tpp) REVERT: P 300 TRP cc_start: 0.7260 (t-100) cc_final: 0.6235 (t60) REVERT: P 311 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7530 (mm-30) REVERT: P 313 TRP cc_start: 0.5841 (t60) cc_final: 0.3890 (m100) REVERT: Q 78 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7820 (ttm170) REVERT: Q 106 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8251 (ttm170) REVERT: Q 144 SER cc_start: 0.8400 (t) cc_final: 0.8194 (t) REVERT: R 75 ARG cc_start: 0.7321 (mmp-170) cc_final: 0.7107 (mmp-170) REVERT: S 53 ILE cc_start: 0.8496 (mt) cc_final: 0.8209 (mp) REVERT: S 64 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7093 (mtmm) REVERT: S 89 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7592 (tpt170) REVERT: S 93 ASN cc_start: 0.8765 (m-40) cc_final: 0.8437 (m-40) REVERT: T 79 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6904 (pt) REVERT: T 104 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7584 (m-10) REVERT: T 115 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8257 (tm-30) REVERT: T 142 GLN cc_start: 0.8103 (mt0) cc_final: 0.7051 (mt0) REVERT: V 32 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8688 (mm) REVERT: W 27 ASP cc_start: 0.7527 (t0) cc_final: 0.7121 (t0) REVERT: W 45 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6795 (tm-30) REVERT: W 60 LYS cc_start: 0.8558 (tppt) cc_final: 0.8292 (tppt) REVERT: W 127 MET cc_start: 0.7961 (ptm) cc_final: 0.7293 (ptp) REVERT: X 117 TRP cc_start: 0.6320 (m-10) cc_final: 0.5938 (m-10) REVERT: Z 9 ASP cc_start: 0.8045 (t0) cc_final: 0.7756 (t0) REVERT: Z 24 ASN cc_start: 0.8437 (t0) cc_final: 0.8005 (t0) REVERT: Z 50 MET cc_start: 0.7763 (tpp) cc_final: 0.7377 (tpp) REVERT: Z 72 MET cc_start: 0.7907 (mmm) cc_final: 0.7669 (mtt) REVERT: Z 80 ASP cc_start: 0.7394 (m-30) cc_final: 0.7158 (m-30) REVERT: Z 129 THR cc_start: 0.6717 (OUTLIER) cc_final: 0.6506 (m) REVERT: a 30 THR cc_start: 0.9048 (m) cc_final: 0.8845 (p) REVERT: b 8 PHE cc_start: 0.6711 (t80) cc_final: 0.6483 (t80) REVERT: b 35 ILE cc_start: 0.8976 (pt) cc_final: 0.8649 (pt) REVERT: q 135 HIS cc_start: 0.7768 (m-70) cc_final: 0.7427 (m-70) REVERT: r 11 LEU cc_start: 0.6691 (mt) cc_final: 0.6362 (mt) outliers start: 124 outliers final: 74 residues processed: 815 average time/residue: 0.2198 time to fit residues: 291.2149 Evaluate side-chains 773 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 690 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 99 CYS 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 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 396 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 450 ILE 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 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 44 ASN Chi-restraints excluded: chain F residue 255 CYS 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 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 223 ILE Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 424 HIS Chi-restraints excluded: chain G residue 479 SER Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 10 LEU 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 Z residue 129 THR Chi-restraints excluded: chain a residue 47 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 261 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 377 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 328 optimal weight: 0.1980 chunk 236 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 340 optimal weight: 0.9990 chunk 255 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN C 76 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 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 G 605 GLN H 99 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 GLN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS T 103 HIS Z 85 GLN Z 112 HIS a 31 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.113497 restraints weight = 53464.626| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.70 r_work: 0.3287 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 35117 Z= 0.137 Angle : 0.791 39.160 47623 Z= 0.321 Chirality : 0.044 0.227 5193 Planarity : 0.005 0.078 6033 Dihedral : 9.195 141.482 4964 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 3.57 % Allowed : 17.41 % Favored : 79.02 % 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: -0.92 (0.13), residues: 4167 helix: 0.30 (0.12), residues: 1840 sheet: -1.57 (0.26), residues: 362 loop : -1.27 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 79 TYR 0.040 0.002 TYR E 192 PHE 0.025 0.001 PHE P 213 TRP 0.012 0.001 TRP H 179 HIS 0.016 0.001 HIS G 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (35076) covalent geometry : angle 0.62441 / 0.32 (47531) SS BOND : bond 0.00187 / 0.10 ( 4) SS BOND : angle 0.70880 / 0.40 ( 8) hydrogen bonds : bond 0.03806 / 2.49 ( 1325) hydrogen bonds : angle 4.98089 / 3.57 ( 3771) metal coordination : bond 0.01751 / 1.30 ( 37) metal coordination : angle 11.57303 / 8.64 ( 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 854 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 723 time to evaluate : 1.691 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: A 49 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6266 (tp) REVERT: A 53 MET cc_start: 0.7974 (tpt) cc_final: 0.7708 (tpt) REVERT: A 106 TRP cc_start: 0.7307 (t60) cc_final: 0.6831 (t60) REVERT: B 141 MET cc_start: 0.8938 (tpt) cc_final: 0.8725 (tpp) REVERT: B 171 TYR cc_start: 0.8519 (m-80) cc_final: 0.7697 (m-80) REVERT: B 222 TYR cc_start: 0.8652 (t80) cc_final: 0.8158 (t80) REVERT: C 234 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8141 (pp) REVERT: D 215 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8541 (pt0) REVERT: D 238 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7687 (mm) REVERT: D 282 ASP cc_start: 0.8372 (m-30) cc_final: 0.8016 (m-30) REVERT: D 437 LYS cc_start: 0.8435 (tmtt) cc_final: 0.7892 (mttp) REVERT: E 105 GLN cc_start: 0.8432 (mp10) cc_final: 0.7936 (mp10) REVERT: E 194 ASP cc_start: 0.8327 (t0) cc_final: 0.7905 (t0) REVERT: F 51 TRP cc_start: 0.7608 (p-90) cc_final: 0.7050 (p-90) REVERT: F 53 LEU cc_start: 0.8601 (tp) cc_final: 0.8179 (tp) REVERT: F 75 TRP cc_start: 0.8232 (t60) cc_final: 0.6916 (t60) REVERT: F 134 ASP cc_start: 0.8392 (t0) cc_final: 0.7949 (t0) REVERT: F 157 TYR cc_start: 0.8104 (t80) cc_final: 0.7794 (t80) REVERT: F 246 GLU cc_start: 0.8133 (tt0) cc_final: 0.7708 (tt0) REVERT: F 255 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7308 (p) REVERT: F 274 LYS cc_start: 0.7982 (tttm) cc_final: 0.7485 (tptp) REVERT: G 211 GLU cc_start: 0.8175 (pm20) cc_final: 0.7923 (pt0) REVERT: G 271 MET cc_start: 0.8425 (mmp) cc_final: 0.7939 (mmt) REVERT: G 315 THR cc_start: 0.8821 (m) cc_final: 0.8595 (p) REVERT: G 316 TYR cc_start: 0.8625 (m-80) cc_final: 0.8183 (m-80) REVERT: G 329 MET cc_start: 0.8283 (mmt) cc_final: 0.7580 (mmt) REVERT: G 409 PHE cc_start: 0.8850 (m-10) cc_final: 0.8599 (m-10) REVERT: G 581 ASP cc_start: 0.8158 (m-30) cc_final: 0.7833 (m-30) REVERT: G 663 ASN cc_start: 0.7200 (p0) cc_final: 0.6945 (p0) REVERT: H 49 PHE cc_start: 0.8103 (m-10) cc_final: 0.7892 (m-10) REVERT: H 126 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7713 (mmpt) REVERT: H 163 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8360 (tm-30) REVERT: H 184 MET cc_start: 0.8826 (mtm) cc_final: 0.8185 (mtm) REVERT: H 199 ASP cc_start: 0.7553 (m-30) cc_final: 0.7234 (m-30) REVERT: H 228 TYR cc_start: 0.9102 (m-10) cc_final: 0.8901 (m-80) REVERT: H 265 LEU cc_start: 0.8846 (mm) cc_final: 0.8383 (tt) REVERT: H 277 TYR cc_start: 0.9027 (m-80) cc_final: 0.8805 (m-80) REVERT: I 59 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7213 (tmm160) REVERT: I 68 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8175 (mtp85) REVERT: I 139 SER cc_start: 0.9253 (t) cc_final: 0.9040 (p) REVERT: I 200 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8217 (tp30) REVERT: P 280 ILE cc_start: 0.8758 (mt) cc_final: 0.8546 (mp) REVERT: P 283 MET cc_start: 0.8234 (mmm) cc_final: 0.7913 (tpp) REVERT: P 300 TRP cc_start: 0.7255 (t-100) cc_final: 0.6054 (t60) REVERT: P 311 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7636 (mm-30) REVERT: P 313 TRP cc_start: 0.5927 (t60) cc_final: 0.3925 (m100) REVERT: Q 106 ARG cc_start: 0.8522 (mtm-85) cc_final: 0.8210 (ttm170) REVERT: Q 164 PHE cc_start: 0.8490 (m-80) cc_final: 0.8144 (m-80) REVERT: S 53 ILE cc_start: 0.8449 (mt) cc_final: 0.7896 (mp) REVERT: S 64 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7159 (mtmm) REVERT: S 89 ARG cc_start: 0.7992 (tpt170) cc_final: 0.7527 (tpt170) REVERT: S 93 ASN cc_start: 0.8730 (m-40) cc_final: 0.8431 (m-40) REVERT: T 97 LYS cc_start: 0.7836 (tttt) cc_final: 0.7184 (ptpp) REVERT: T 104 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: T 115 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8358 (tm-30) REVERT: T 142 GLN cc_start: 0.8153 (mt0) cc_final: 0.7583 (mt0) REVERT: V 32 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8699 (mm) REVERT: W 19 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8040 (p) REVERT: W 27 ASP cc_start: 0.7566 (t0) cc_final: 0.7171 (t0) REVERT: W 32 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8034 (mttm) REVERT: W 45 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6963 (tm-30) REVERT: W 127 MET cc_start: 0.7903 (ptm) cc_final: 0.7387 (ptp) REVERT: X 91 TYR cc_start: 0.8090 (t80) cc_final: 0.7857 (t80) REVERT: Z 9 ASP cc_start: 0.7929 (t0) cc_final: 0.7682 (t0) REVERT: Z 24 ASN cc_start: 0.8469 (t0) cc_final: 0.8043 (t0) REVERT: Z 72 MET cc_start: 0.7926 (mmm) cc_final: 0.7705 (mtt) REVERT: Z 80 ASP cc_start: 0.7445 (m-30) cc_final: 0.7085 (m-30) REVERT: Z 94 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: Z 129 THR cc_start: 0.6899 (OUTLIER) cc_final: 0.6693 (m) REVERT: a 30 THR cc_start: 0.9015 (m) cc_final: 0.8811 (p) REVERT: a 31 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: a 34 LYS cc_start: 0.8306 (mtmm) cc_final: 0.8099 (mtmt) REVERT: b 8 PHE cc_start: 0.6757 (t80) cc_final: 0.6530 (t80) REVERT: b 10 LYS cc_start: 0.7904 (mtpm) cc_final: 0.7416 (mmmt) REVERT: b 35 ILE cc_start: 0.8961 (pt) cc_final: 0.8636 (pt) REVERT: q 81 MET cc_start: 0.7668 (mmm) cc_final: 0.7091 (mmt) REVERT: q 135 HIS cc_start: 0.7778 (m-70) cc_final: 0.7460 (m-70) REVERT: r 11 LEU cc_start: 0.6628 (mt) cc_final: 0.6276 (mt) outliers start: 131 outliers final: 78 residues processed: 799 average time/residue: 0.2258 time to fit residues: 292.5497 Evaluate side-chains 752 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 663 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 B residue 78 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 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 447 VAL Chi-restraints excluded: chain D residue 450 ILE 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 F residue 41 ILE Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 346 GLN 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 215 MET Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 283 GLU 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 632 ILE Chi-restraints excluded: chain G residue 646 LEU Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 10 LEU 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 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 64 THR 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 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 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 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 22 LYS Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 129 THR 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 47 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 201 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 409 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 188 ASN F 44 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN G 424 HIS G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS R 52 GLN T 103 HIS W 51 HIS Z 85 GLN a 31 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107633 restraints weight = 53678.477| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.43 r_work: 0.3158 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 35117 Z= 0.325 Angle : 0.934 40.635 47623 Z= 0.384 Chirality : 0.050 0.232 5193 Planarity : 0.006 0.073 6033 Dihedral : 9.421 141.619 4964 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 3.74 % Allowed : 18.06 % Favored : 78.20 % 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: -1.04 (0.13), residues: 4167 helix: 0.18 (0.12), residues: 1851 sheet: -1.58 (0.26), residues: 375 loop : -1.31 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 62 TYR 0.034 0.002 TYR H 142 PHE 0.031 0.002 PHE F 262 TRP 0.015 0.002 TRP V 114 HIS 0.011 0.002 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.32 (35076) covalent geometry : angle 0.74989 / 0.38 (47531) SS BOND : bond 0.00290 / 0.15 ( 4) SS BOND : angle 0.68239 / 0.38 ( 8) hydrogen bonds : bond 0.04463 / 2.93 ( 1325) hydrogen bonds : angle 5.17562 / 3.72 ( 3771) metal coordination : bond 0.03553 / 2.42 ( 37) metal coordination : angle 13.26732 / 9.67 ( 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 818 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 681 time to evaluate : 1.401 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: A 49 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6488 (tp) REVERT: A 53 MET cc_start: 0.8209 (tpt) cc_final: 0.7922 (tpt) REVERT: A 88 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8331 (ttm) REVERT: A 106 TRP cc_start: 0.7708 (t60) cc_final: 0.7180 (t60) REVERT: B 171 TYR cc_start: 0.8979 (m-80) cc_final: 0.8146 (m-80) REVERT: B 222 TYR cc_start: 0.8971 (t80) cc_final: 0.8528 (t80) REVERT: C 234 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8509 (pp) REVERT: D 215 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8690 (pt0) REVERT: D 238 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.7893 (mp) REVERT: D 282 ASP cc_start: 0.8788 (m-30) cc_final: 0.8455 (m-30) REVERT: D 437 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8078 (mttp) REVERT: E 105 GLN cc_start: 0.8629 (mp10) cc_final: 0.8153 (mp10) REVERT: E 153 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7825 (tmm160) REVERT: E 194 ASP cc_start: 0.8431 (t0) cc_final: 0.8019 (t0) REVERT: F 53 LEU cc_start: 0.8586 (tp) cc_final: 0.8218 (tp) REVERT: F 131 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8362 (mpp) REVERT: F 134 ASP cc_start: 0.8424 (t0) cc_final: 0.7921 (t0) REVERT: F 157 TYR cc_start: 0.8328 (t80) cc_final: 0.8105 (t80) REVERT: F 255 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7072 (p) REVERT: F 337 MET cc_start: 0.8705 (mmm) cc_final: 0.8349 (mtp) REVERT: G 211 GLU cc_start: 0.8169 (pm20) cc_final: 0.7902 (pt0) REVERT: G 223 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8704 (mt) REVERT: G 271 MET cc_start: 0.8834 (mmp) cc_final: 0.8177 (mmt) REVERT: G 315 THR cc_start: 0.8968 (m) cc_final: 0.8726 (p) REVERT: G 316 TYR cc_start: 0.8871 (m-80) cc_final: 0.8347 (m-80) REVERT: G 409 PHE cc_start: 0.9034 (m-10) cc_final: 0.8820 (m-10) REVERT: G 581 ASP cc_start: 0.8550 (m-30) cc_final: 0.8263 (m-30) REVERT: G 663 ASN cc_start: 0.7476 (p0) cc_final: 0.7100 (p0) REVERT: H 71 PHE cc_start: 0.9052 (t80) cc_final: 0.8817 (t80) REVERT: H 126 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7790 (mmpt) REVERT: H 163 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8552 (tm-30) REVERT: H 199 ASP cc_start: 0.7792 (m-30) cc_final: 0.7467 (m-30) REVERT: H 261 MET cc_start: 0.8460 (mmm) cc_final: 0.8258 (tpp) REVERT: H 265 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8482 (tt) REVERT: I 59 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7330 (tmm160) REVERT: I 139 SER cc_start: 0.9357 (t) cc_final: 0.9097 (p) REVERT: I 200 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8617 (tp30) REVERT: P 271 TYR cc_start: 0.7531 (m-80) cc_final: 0.7307 (m-80) REVERT: P 300 TRP cc_start: 0.7286 (t-100) cc_final: 0.6091 (t60) REVERT: P 311 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8019 (mt-10) REVERT: P 346 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7335 (mm-30) REVERT: Q 78 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8016 (ttm170) REVERT: Q 105 GLU cc_start: 0.8690 (tt0) cc_final: 0.8352 (tt0) REVERT: Q 159 SER cc_start: 0.9274 (m) cc_final: 0.8829 (p) REVERT: S 53 ILE cc_start: 0.8697 (mt) cc_final: 0.7960 (mp) REVERT: S 64 LYS cc_start: 0.8428 (mtpt) cc_final: 0.7445 (mtmm) REVERT: S 93 ASN cc_start: 0.8844 (m-40) cc_final: 0.8571 (m110) REVERT: T 104 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: T 115 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8505 (tm-30) REVERT: T 142 GLN cc_start: 0.8264 (mt0) cc_final: 0.7622 (mt0) REVERT: V 32 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8778 (mm) REVERT: V 34 ILE cc_start: 0.8909 (tp) cc_final: 0.8434 (tp) REVERT: W 27 ASP cc_start: 0.7867 (t0) cc_final: 0.7496 (t0) REVERT: W 45 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7667 (tm-30) REVERT: W 127 MET cc_start: 0.8035 (ptm) cc_final: 0.7425 (ptp) REVERT: X 77 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7339 (t-90) REVERT: Z 9 ASP cc_start: 0.8124 (t0) cc_final: 0.7648 (t0) REVERT: Z 20 ASP cc_start: 0.8260 (t0) cc_final: 0.7864 (p0) REVERT: Z 24 ASN cc_start: 0.8654 (t0) cc_final: 0.8123 (t0) REVERT: Z 72 MET cc_start: 0.8292 (mmm) cc_final: 0.8022 (mmm) REVERT: Z 80 ASP cc_start: 0.7585 (m-30) cc_final: 0.7344 (m-30) REVERT: a 34 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8293 (mtmt) REVERT: a 52 ARG cc_start: 0.8745 (ttp-170) cc_final: 0.8538 (ttt-90) REVERT: b 10 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7714 (mmmt) REVERT: b 35 ILE cc_start: 0.8869 (pt) cc_final: 0.8513 (pt) REVERT: q 135 HIS cc_start: 0.8156 (m-70) cc_final: 0.7763 (m-70) REVERT: r 11 LEU cc_start: 0.6562 (mt) cc_final: 0.6337 (mt) REVERT: r 40 LYS cc_start: 0.7838 (tttt) cc_final: 0.7387 (mmtt) outliers start: 137 outliers final: 88 residues processed: 763 average time/residue: 0.2231 time to fit residues: 277.3024 Evaluate side-chains 742 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 642 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 88 MET Chi-restraints excluded: chain B residue 89 SER 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 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 285 ASN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 447 VAL 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 145 ASP 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 255 CYS Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 445 GLU 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 283 GLU 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 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 126 LYS 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 100 LEU Chi-restraints excluded: chain P residue 106 LEU Chi-restraints excluded: chain P residue 349 SER Chi-restraints excluded: chain P residue 374 THR 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 9 THR 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 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 77 HIS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 16 TYR 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 84 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain q residue 142 THR 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: 2.9990 chunk 373 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 304 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 354 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** E 47 ASN ** 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS S 92 GLN T 103 HIS Z 112 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112266 restraints weight = 53308.392| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.43 r_work: 0.3269 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 35117 Z= 0.160 Angle : 0.830 39.260 47623 Z= 0.332 Chirality : 0.045 0.252 5193 Planarity : 0.005 0.071 6033 Dihedral : 9.264 145.435 4964 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 3.22 % Allowed : 19.32 % Favored : 77.46 % 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: -0.85 (0.13), residues: 4167 helix: 0.38 (0.12), residues: 1848 sheet: -1.53 (0.26), residues: 369 loop : -1.25 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 142 TYR 0.030 0.002 TYR H 142 PHE 0.024 0.001 PHE P 213 TRP 0.011 0.001 TRP H 179 HIS 0.008 0.001 HIS F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (35076) covalent geometry : angle 0.65089 / 0.33 (47531) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 0.59107 / 0.33 ( 8) hydrogen bonds : bond 0.03850 / 2.53 ( 1325) hydrogen bonds : angle 4.99240 / 3.57 ( 3771) metal coordination : bond 0.02162 / 1.60 ( 37) metal coordination : angle 12.26617 / 9.13 ( 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 811 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 693 time to evaluate : 1.404 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: A 3 LEU cc_start: 0.8796 (tp) cc_final: 0.8583 (tp) REVERT: A 53 MET cc_start: 0.8152 (tpt) cc_final: 0.7844 (tpt) REVERT: A 88 MET cc_start: 0.8479 (mtm) cc_final: 0.8261 (ttm) REVERT: A 106 TRP cc_start: 0.7683 (t60) cc_final: 0.7325 (t60) REVERT: B 171 TYR cc_start: 0.8880 (m-80) cc_final: 0.8087 (m-80) REVERT: B 222 TYR cc_start: 0.8882 (t80) cc_final: 0.8453 (t80) REVERT: C 168 GLU cc_start: 0.8795 (tt0) cc_final: 0.8511 (tt0) REVERT: C 234 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (pp) REVERT: D 215 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8626 (pt0) REVERT: D 238 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8057 (mm) REVERT: D 437 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8004 (mttp) REVERT: E 87 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8168 (mtt-85) REVERT: E 105 GLN cc_start: 0.8590 (mp10) cc_final: 0.8149 (mp10) REVERT: E 194 ASP cc_start: 0.8439 (t0) cc_final: 0.8074 (t0) REVERT: F 53 LEU cc_start: 0.8566 (tp) cc_final: 0.8217 (tp) REVERT: F 131 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8445 (mpp) REVERT: F 134 ASP cc_start: 0.8538 (t0) cc_final: 0.8045 (t0) REVERT: F 157 TYR cc_start: 0.8248 (t80) cc_final: 0.7986 (t80) REVERT: F 246 GLU cc_start: 0.8491 (tt0) cc_final: 0.8246 (mt-10) REVERT: F 255 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.6987 (p) REVERT: F 337 MET cc_start: 0.8692 (mmm) cc_final: 0.8372 (mtp) REVERT: G 223 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8613 (mt) REVERT: G 271 MET cc_start: 0.8610 (mmp) cc_final: 0.8114 (mmt) REVERT: G 282 ASN cc_start: 0.8158 (p0) cc_final: 0.7914 (p0) REVERT: G 316 TYR cc_start: 0.8895 (m-80) cc_final: 0.8286 (m-80) REVERT: G 409 PHE cc_start: 0.8980 (m-10) cc_final: 0.8762 (m-10) REVERT: G 663 ASN cc_start: 0.7288 (p0) cc_final: 0.6921 (p0) REVERT: G 712 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8725 (tmmt) REVERT: H 22 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8900 (tp) REVERT: H 126 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7635 (mmpt) REVERT: H 163 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8589 (tm-30) REVERT: H 184 MET cc_start: 0.9015 (mtm) cc_final: 0.8803 (mtm) REVERT: H 199 ASP cc_start: 0.7710 (m-30) cc_final: 0.7319 (m-30) REVERT: H 261 MET cc_start: 0.8485 (mmm) cc_final: 0.8235 (tpp) REVERT: I 59 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7166 (tmm160) REVERT: I 139 SER cc_start: 0.9310 (t) cc_final: 0.9105 (p) REVERT: I 200 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8511 (tp30) REVERT: P 271 TYR cc_start: 0.7466 (m-80) cc_final: 0.7261 (m-80) REVERT: P 300 TRP cc_start: 0.7230 (t-100) cc_final: 0.6049 (t60) REVERT: P 311 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7817 (mm-30) REVERT: P 313 TRP cc_start: 0.6061 (t60) cc_final: 0.4166 (m100) REVERT: P 346 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7257 (mm-30) REVERT: Q 78 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7964 (ttm170) REVERT: Q 105 GLU cc_start: 0.8591 (tt0) cc_final: 0.8287 (tt0) REVERT: Q 148 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7941 (mt-10) REVERT: Q 159 SER cc_start: 0.9210 (m) cc_final: 0.8779 (p) REVERT: S 64 LYS cc_start: 0.8496 (mtpt) cc_final: 0.7542 (mtmm) REVERT: T 115 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8554 (tm-30) REVERT: T 142 GLN cc_start: 0.8288 (mt0) cc_final: 0.7699 (mt0) REVERT: V 32 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8756 (mm) REVERT: V 116 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7727 (mt) REVERT: W 27 ASP cc_start: 0.7812 (t0) cc_final: 0.7458 (t0) REVERT: W 45 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7080 (tm-30) REVERT: W 64 ASP cc_start: 0.7994 (m-30) cc_final: 0.7713 (m-30) REVERT: W 127 MET cc_start: 0.8041 (ptm) cc_final: 0.7505 (ptp) REVERT: X 77 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7397 (t-90) REVERT: Z 9 ASP cc_start: 0.7806 (t0) cc_final: 0.7478 (t0) REVERT: Z 20 ASP cc_start: 0.8179 (t0) cc_final: 0.7881 (p0) REVERT: Z 24 ASN cc_start: 0.8655 (t0) cc_final: 0.8094 (t0) REVERT: Z 80 ASP cc_start: 0.7483 (m-30) cc_final: 0.7272 (m-30) REVERT: Z 94 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: a 52 ARG cc_start: 0.8667 (ttp-170) cc_final: 0.8445 (ttt-90) REVERT: b 8 PHE cc_start: 0.6724 (t80) cc_final: 0.6441 (t80) REVERT: b 10 LYS cc_start: 0.8266 (mtpm) cc_final: 0.7857 (mmmt) REVERT: b 35 ILE cc_start: 0.8966 (pt) cc_final: 0.8639 (pt) REVERT: b 58 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6087 (ttm-80) REVERT: q 124 TYR cc_start: 0.8321 (t80) cc_final: 0.7187 (t80) REVERT: q 135 HIS cc_start: 0.8116 (m-70) cc_final: 0.7799 (m-70) REVERT: r 40 LYS cc_start: 0.7788 (tttt) cc_final: 0.7351 (mmtt) outliers start: 118 outliers final: 74 residues processed: 757 average time/residue: 0.2258 time to fit residues: 278.0611 Evaluate side-chains 732 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 647 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 79 ILE 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 124 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 118 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 320 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 443 MET 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 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 255 CYS 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 G residue 111 LYS Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 223 ILE 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 424 HIS Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 593 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 10 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 231 ILE 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 I residue 62 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 116 CYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain P residue 106 LEU 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 79 ILE Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain V residue 9 THR 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 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 77 HIS Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain Z residue 40 ILE Chi-restraints excluded: chain Z residue 94 GLU 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 Z residue 131 GLU 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 b residue 84 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: 0.9980 chunk 377 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 401 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 265 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 241 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 188 ASN F 44 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** 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 72 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 ASN T 103 HIS V 110 ASN W 94 GLN X 35 GLN X 77 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112927 restraints weight = 53211.911| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.39 r_work: 0.3237 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 35117 Z= 0.139 Angle : 0.802 36.394 47623 Z= 0.323 Chirality : 0.044 0.224 5193 Planarity : 0.005 0.072 6033 Dihedral : 9.133 146.490 4964 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 2.73 % Allowed : 20.11 % Favored : 77.16 % 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: 0.50 (0.12), residues: 1852 sheet: -1.45 (0.27), residues: 369 loop : -1.23 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 61 TYR 0.027 0.002 TYR D 135 PHE 0.021 0.001 PHE P 213 TRP 0.013 0.001 TRP F 99 HIS 0.028 0.001 HIS G 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (35076) covalent geometry : angle 0.63466 / 0.32 (47531) SS BOND : bond 0.00139 / 0.07 ( 4) SS BOND : angle 0.48098 / 0.27 ( 8) hydrogen bonds : bond 0.03684 / 2.43 ( 1325) hydrogen bonds : angle 4.89029 / 3.49 ( 3771) metal coordination : bond 0.01839 / 1.36 ( 37) metal coordination : angle 11.70047 / 8.78 ( 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 779 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 679 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8752 (tp) cc_final: 0.8551 (tp) REVERT: A 53 MET cc_start: 0.8178 (tpt) cc_final: 0.7859 (tpt) REVERT: A 88 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (ttm) REVERT: A 106 TRP cc_start: 0.7632 (t60) cc_final: 0.7234 (t60) REVERT: B 171 TYR cc_start: 0.8921 (m-80) cc_final: 0.8198 (m-80) REVERT: B 222 TYR cc_start: 0.8875 (t80) cc_final: 0.8439 (t80) REVERT: C 168 GLU cc_start: 0.8875 (tt0) cc_final: 0.8407 (tt0) REVERT: C 234 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8265 (pp) REVERT: D 215 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8650 (pt0) REVERT: D 238 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8108 (mm) REVERT: D 282 ASP cc_start: 0.8756 (m-30) cc_final: 0.8368 (m-30) REVERT: D 437 LYS cc_start: 0.8710 (tmtt) cc_final: 0.7938 (mttp) REVERT: D 443 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: E 105 GLN cc_start: 0.8519 (mp10) cc_final: 0.8065 (mp10) REVERT: E 152 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6945 (mm-40) REVERT: E 194 ASP cc_start: 0.8411 (t0) cc_final: 0.8018 (t0) REVERT: F 53 LEU cc_start: 0.8564 (tp) cc_final: 0.8209 (tp) REVERT: F 131 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8390 (mpp) REVERT: F 134 ASP cc_start: 0.8522 (t0) cc_final: 0.8086 (t0) REVERT: F 157 TYR cc_start: 0.8184 (t80) cc_final: 0.7882 (t80) REVERT: G 223 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8564 (mt) REVERT: G 271 MET cc_start: 0.8621 (mmp) cc_final: 0.8114 (mmt) REVERT: G 316 TYR cc_start: 0.8858 (m-80) cc_final: 0.8203 (m-80) REVERT: G 333 PHE cc_start: 0.8148 (m-80) cc_final: 0.7749 (m-10) REVERT: G 409 PHE cc_start: 0.9009 (m-10) cc_final: 0.8755 (m-10) REVERT: G 712 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8692 (tmmt) REVERT: H 126 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7447 (mmpt) REVERT: H 163 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8496 (tm-30) REVERT: H 199 ASP cc_start: 0.7626 (m-30) cc_final: 0.7275 (m-30) REVERT: I 59 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7042 (tmm160) REVERT: I 139 SER cc_start: 0.9261 (t) cc_final: 0.9016 (p) REVERT: I 200 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8543 (tp30) REVERT: P 300 TRP cc_start: 0.7242 (t-100) cc_final: 0.6047 (t60) REVERT: P 311 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7625 (mm-30) REVERT: P 313 TRP cc_start: 0.5863 (t60) cc_final: 0.4052 (m100) REVERT: P 346 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7238 (mm-30) REVERT: Q 78 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7989 (ttm170) REVERT: Q 105 GLU cc_start: 0.8616 (tt0) cc_final: 0.8292 (tt0) REVERT: Q 124 MET cc_start: 0.8419 (tpt) cc_final: 0.8132 (tpt) REVERT: Q 148 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8044 (mt-10) REVERT: Q 159 SER cc_start: 0.9198 (m) cc_final: 0.8700 (p) REVERT: S 64 LYS cc_start: 0.8420 (mtpt) cc_final: 0.7492 (mtmm) REVERT: S 93 ASN cc_start: 0.8642 (m-40) cc_final: 0.8417 (m110) REVERT: T 115 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8513 (tm-30) REVERT: T 128 PHE cc_start: 0.7891 (t80) cc_final: 0.7654 (t80) REVERT: T 142 GLN cc_start: 0.8219 (mt0) cc_final: 0.7639 (mt0) REVERT: V 32 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8929 (mp) REVERT: V 116 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7746 (mt) REVERT: W 19 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.8135 (p) REVERT: W 27 ASP cc_start: 0.7784 (t0) cc_final: 0.7363 (t0) REVERT: W 45 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7115 (tm-30) REVERT: W 127 MET cc_start: 0.8059 (ptm) cc_final: 0.7502 (ptp) REVERT: Z 20 ASP cc_start: 0.8217 (t0) cc_final: 0.7879 (p0) REVERT: Z 24 ASN cc_start: 0.8655 (t0) cc_final: 0.8186 (t0) REVERT: Z 80 ASP cc_start: 0.7426 (m-30) cc_final: 0.7165 (m-30) REVERT: Z 120 LEU cc_start: 0.8722 (tp) cc_final: 0.8449 (mm) REVERT: a 52 ARG cc_start: 0.8679 (ttp-170) cc_final: 0.8426 (ttt-90) REVERT: b 8 PHE cc_start: 0.6730 (t80) cc_final: 0.6465 (t80) REVERT: b 10 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7804 (mmmt) REVERT: b 35 ILE cc_start: 0.8855 (pt) cc_final: 0.8551 (pt) REVERT: q 124 TYR cc_start: 0.8249 (t80) cc_final: 0.7129 (t80) REVERT: q 135 HIS cc_start: 0.7984 (m-70) cc_final: 0.7633 (m-70) REVERT: r 40 LYS cc_start: 0.7714 (tttt) cc_final: 0.7255 (mmtt) REVERT: r 101 MET cc_start: 0.8684 (ttp) cc_final: 0.8263 (ttp) outliers start: 100 outliers final: 70 residues processed: 733 average time/residue: 0.2123 time to fit residues: 253.2390 Evaluate side-chains 729 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 649 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 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 118 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 438 MET Chi-restraints excluded: chain D residue 443 MET 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 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 G residue 111 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 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 632 ILE Chi-restraints excluded: chain G residue 679 VAL Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER 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 72 HIS Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 106 LEU 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 79 ILE 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 35 GLN Chi-restraints excluded: chain X residue 69 ASN 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 a residue 41 VAL Chi-restraints excluded: chain a residue 47 LEU Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 84 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: 0.9990 chunk 333 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 246 optimal weight: 0.8980 chunk 400 optimal weight: 0.0970 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** 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 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN P 71 ASN ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 HIS ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN W 94 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113454 restraints weight = 53370.361| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.47 r_work: 0.3252 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 35117 Z= 0.143 Angle : 0.815 35.357 47623 Z= 0.326 Chirality : 0.044 0.225 5193 Planarity : 0.005 0.072 6033 Dihedral : 9.025 147.852 4964 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 2.65 % Allowed : 20.27 % 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: -0.63 (0.13), residues: 4167 helix: 0.58 (0.12), residues: 1848 sheet: -1.34 (0.28), residues: 343 loop : -1.18 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 153 TYR 0.041 0.002 TYR D 135 PHE 0.022 0.001 PHE P 213 TRP 0.017 0.001 TRP G 510 HIS 0.009 0.001 HIS X 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (35076) covalent geometry : angle 0.64359 / 0.32 (47531) SS BOND : bond 0.00154 / 0.08 ( 4) SS BOND : angle 0.46089 / 0.26 ( 8) hydrogen bonds : bond 0.03600 / 2.37 ( 1325) hydrogen bonds : angle 4.84941 / 3.46 ( 3771) metal coordination : bond 0.01862 / 1.36 ( 37) metal coordination : angle 11.92092 / 8.80 ( 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 770 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 673 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8053 (tpt) cc_final: 0.7719 (tpt) REVERT: A 88 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8119 (ttm) REVERT: A 106 TRP cc_start: 0.7502 (t60) cc_final: 0.7086 (t60) REVERT: B 141 MET cc_start: 0.9064 (tpt) cc_final: 0.8788 (tpp) REVERT: B 171 TYR cc_start: 0.8818 (m-80) cc_final: 0.8135 (m-80) REVERT: B 222 TYR cc_start: 0.8816 (t80) cc_final: 0.8408 (t80) REVERT: C 234 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8167 (pp) REVERT: D 144 MET cc_start: 0.8497 (mpp) cc_final: 0.7967 (mpp) REVERT: D 215 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8471 (pt0) REVERT: D 282 ASP cc_start: 0.8442 (m-30) cc_final: 0.8038 (m-30) REVERT: D 437 LYS cc_start: 0.8534 (tmtt) cc_final: 0.7971 (mttt) REVERT: D 443 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: E 105 GLN cc_start: 0.8453 (mp10) cc_final: 0.7998 (mp10) REVERT: E 194 ASP cc_start: 0.8387 (t0) cc_final: 0.7981 (t0) REVERT: F 53 LEU cc_start: 0.8544 (tp) cc_final: 0.8218 (tp) REVERT: F 131 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: F 134 ASP cc_start: 0.8462 (t0) cc_final: 0.8008 (t0) REVERT: G 223 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8471 (mt) REVERT: G 271 MET cc_start: 0.8360 (mmp) cc_final: 0.7898 (mmt) REVERT: G 316 TYR cc_start: 0.8654 (m-80) cc_final: 0.8009 (m-80) REVERT: G 333 PHE cc_start: 0.8130 (m-80) cc_final: 0.7745 (m-10) REVERT: G 409 PHE cc_start: 0.8944 (m-10) cc_final: 0.8714 (m-10) REVERT: G 712 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8686 (tmmt) REVERT: H 114 TYR cc_start: 0.9018 (m-10) cc_final: 0.8336 (m-80) REVERT: H 126 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7526 (mmpt) REVERT: H 163 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8320 (tm-30) REVERT: H 184 MET cc_start: 0.8805 (mtm) cc_final: 0.8514 (mtm) REVERT: H 199 ASP cc_start: 0.7580 (m-30) cc_final: 0.7257 (m-30) REVERT: H 261 MET cc_start: 0.8528 (tpp) cc_final: 0.8207 (mtt) REVERT: H 265 LEU cc_start: 0.8738 (mm) cc_final: 0.8418 (tt) REVERT: I 59 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7054 (tmm160) REVERT: I 139 SER cc_start: 0.9231 (t) cc_final: 0.8637 (m) REVERT: I 200 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8372 (tp30) REVERT: P 154 GLN cc_start: 0.7730 (tp40) cc_final: 0.7516 (tp40) REVERT: P 300 TRP cc_start: 0.7195 (t-100) cc_final: 0.6011 (t60) REVERT: P 311 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7621 (mm-30) REVERT: P 313 TRP cc_start: 0.6007 (t60) cc_final: 0.4035 (m100) REVERT: Q 105 GLU cc_start: 0.8531 (tt0) cc_final: 0.8197 (tt0) REVERT: Q 124 MET cc_start: 0.8229 (tpt) cc_final: 0.7943 (tpt) REVERT: Q 159 SER cc_start: 0.9094 (m) cc_final: 0.8609 (p) REVERT: S 53 ILE cc_start: 0.8434 (mt) cc_final: 0.8050 (mp) REVERT: S 64 LYS cc_start: 0.8318 (mtpt) cc_final: 0.7339 (mtmm) REVERT: T 115 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8486 (tm-30) REVERT: T 142 GLN cc_start: 0.8318 (mt0) cc_final: 0.7778 (mt0) REVERT: V 32 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8920 (mp) REVERT: V 34 ILE cc_start: 0.8827 (tp) cc_final: 0.8357 (tp) REVERT: V 58 MET cc_start: 0.8090 (mtp) cc_final: 0.7872 (mtp) REVERT: V 116 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7422 (mt) REVERT: W 19 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8111 (p) REVERT: W 27 ASP cc_start: 0.7605 (t0) cc_final: 0.7251 (t0) REVERT: W 45 GLU cc_start: 0.7451 (tm-30) cc_final: 0.6933 (tm-30) REVERT: W 127 MET cc_start: 0.7840 (ptm) cc_final: 0.7421 (ptp) REVERT: Z 24 ASN cc_start: 0.8509 (t0) cc_final: 0.8051 (t0) REVERT: Z 79 LYS cc_start: 0.8444 (ttmm) cc_final: 0.7903 (ttpp) REVERT: Z 80 ASP cc_start: 0.7361 (m-30) cc_final: 0.7110 (m-30) REVERT: Z 120 LEU cc_start: 0.8713 (tp) cc_final: 0.8469 (mm) REVERT: a 52 ARG cc_start: 0.8568 (ttp-170) cc_final: 0.8296 (ttt-90) REVERT: b 8 PHE cc_start: 0.6673 (t80) cc_final: 0.6439 (t80) REVERT: b 10 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7828 (mmmt) REVERT: b 35 ILE cc_start: 0.8923 (pt) cc_final: 0.8595 (pt) REVERT: q 124 TYR cc_start: 0.8225 (t80) cc_final: 0.7270 (t80) REVERT: q 135 HIS cc_start: 0.7876 (m-70) cc_final: 0.7558 (m-70) REVERT: r 40 LYS cc_start: 0.7754 (tttt) cc_final: 0.7400 (mmtt) REVERT: r 101 MET cc_start: 0.8548 (ttp) cc_final: 0.8183 (ttp) outliers start: 97 outliers final: 62 residues processed: 727 average time/residue: 0.2044 time to fit residues: 244.0011 Evaluate side-chains 721 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 649 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 124 SER 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 234 LEU Chi-restraints excluded: chain D residue 94 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 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 187 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 111 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 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 632 ILE 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 172 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER 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 88 VAL Chi-restraints excluded: chain P residue 106 LEU 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 79 ILE 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 110 VAL Chi-restraints excluded: chain Z residue 129 THR 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 62 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain b residue 84 LEU 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: 0.0000 chunk 310 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 394 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 321 optimal weight: 10.0000 chunk 373 optimal weight: 0.0370 overall best weight: 0.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 HIS ** 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 F 44 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 ASN V 110 ASN W 94 GLN X 35 GLN Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.151665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114602 restraints weight = 53396.045| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.55 r_work: 0.3261 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 35117 Z= 0.132 Angle : 0.801 35.227 47623 Z= 0.323 Chirality : 0.044 0.219 5193 Planarity : 0.005 0.073 6033 Dihedral : 8.924 149.737 4964 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 2.16 % Allowed : 20.95 % Favored : 76.89 % 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: -0.58 (0.13), residues: 4167 helix: 0.66 (0.12), residues: 1848 sheet: -1.37 (0.29), residues: 344 loop : -1.18 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 68 TYR 0.032 0.002 TYR Z 143 PHE 0.020 0.001 PHE P 213 TRP 0.019 0.001 TRP G 510 HIS 0.008 0.001 HIS F 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (35076) covalent geometry : angle 0.64047 / 0.32 (47531) SS BOND : bond 0.00168 / 0.09 ( 4) SS BOND : angle 0.55510 / 0.31 ( 8) hydrogen bonds : bond 0.03529 / 2.33 ( 1325) hydrogen bonds : angle 4.82159 / 3.45 ( 3771) metal coordination : bond 0.01781 / 1.37 ( 37) metal coordination : angle 11.47299 / 8.72 ( 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 775 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 696 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8103 (ttm) REVERT: A 106 TRP cc_start: 0.7420 (t60) cc_final: 0.7004 (t60) REVERT: B 141 MET cc_start: 0.9063 (tpt) cc_final: 0.8812 (tpt) REVERT: B 171 TYR cc_start: 0.8847 (m-80) cc_final: 0.8121 (m-80) REVERT: B 222 TYR cc_start: 0.8796 (t80) cc_final: 0.8378 (t80) REVERT: C 234 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8158 (pp) REVERT: D 144 MET cc_start: 0.8478 (mpp) cc_final: 0.7948 (mpp) REVERT: D 185 MET cc_start: 0.8884 (tpt) cc_final: 0.7926 (tpt) REVERT: D 215 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8471 (pt0) REVERT: D 282 ASP cc_start: 0.8466 (m-30) cc_final: 0.8078 (m-30) REVERT: D 323 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8213 (ttt180) REVERT: D 437 LYS cc_start: 0.8599 (tmtt) cc_final: 0.7993 (mptt) REVERT: D 443 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7520 (mtp) REVERT: E 105 GLN cc_start: 0.8400 (mp10) cc_final: 0.7944 (mp10) REVERT: E 120 MET cc_start: 0.8829 (mmm) cc_final: 0.8495 (mmm) REVERT: E 171 ILE cc_start: 0.8891 (pt) cc_final: 0.8491 (pt) REVERT: E 194 ASP cc_start: 0.8335 (t0) cc_final: 0.7920 (t0) REVERT: F 53 LEU cc_start: 0.8542 (tp) cc_final: 0.8215 (tp) REVERT: F 131 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8383 (mpp) REVERT: F 134 ASP cc_start: 0.8442 (t0) cc_final: 0.8024 (t0) REVERT: F 289 GLU cc_start: 0.7565 (pm20) cc_final: 0.6046 (tm-30) REVERT: G 223 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8410 (mt) REVERT: G 271 MET cc_start: 0.8342 (mmp) cc_final: 0.7723 (mmt) REVERT: G 316 TYR cc_start: 0.8790 (m-80) cc_final: 0.8169 (m-80) REVERT: G 333 PHE cc_start: 0.8100 (m-80) cc_final: 0.7699 (m-10) REVERT: G 380 ASP cc_start: 0.8311 (t0) cc_final: 0.8086 (t0) REVERT: G 581 ASP cc_start: 0.8053 (m-30) cc_final: 0.7727 (m-30) REVERT: G 712 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8669 (tmmt) REVERT: H 114 TYR cc_start: 0.9012 (m-10) cc_final: 0.8270 (m-80) REVERT: H 126 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7404 (mmpt) REVERT: H 163 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8253 (tm-30) REVERT: H 184 MET cc_start: 0.8799 (mtm) cc_final: 0.8463 (mtm) REVERT: H 199 ASP cc_start: 0.7609 (m-30) cc_final: 0.7263 (m-30) REVERT: H 261 MET cc_start: 0.8610 (tpp) cc_final: 0.8308 (mtt) REVERT: H 265 LEU cc_start: 0.8735 (mm) cc_final: 0.8323 (tt) REVERT: H 311 THR cc_start: 0.8650 (m) cc_final: 0.8442 (m) REVERT: I 59 ARG cc_start: 0.7479 (ttp80) cc_final: 0.6980 (tmm160) REVERT: I 90 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8676 (mttp) REVERT: I 139 SER cc_start: 0.9215 (t) cc_final: 0.8674 (m) REVERT: I 200 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8355 (tp30) REVERT: P 154 GLN cc_start: 0.7719 (tp40) cc_final: 0.7498 (tp40) REVERT: P 300 TRP cc_start: 0.7298 (t-100) cc_final: 0.6032 (t60) REVERT: P 311 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7607 (mm-30) REVERT: P 313 TRP cc_start: 0.5965 (t60) cc_final: 0.3999 (m100) REVERT: Q 105 GLU cc_start: 0.8506 (tt0) cc_final: 0.8166 (tt0) REVERT: Q 124 MET cc_start: 0.8148 (tpt) cc_final: 0.7878 (tpt) REVERT: Q 159 SER cc_start: 0.9076 (m) cc_final: 0.8570 (p) REVERT: S 53 ILE cc_start: 0.8221 (mt) cc_final: 0.7811 (mp) REVERT: S 64 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7241 (mtmm) REVERT: T 115 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8491 (tm-30) REVERT: T 142 GLN cc_start: 0.8327 (mt0) cc_final: 0.7837 (mt0) REVERT: V 34 ILE cc_start: 0.8810 (tp) cc_final: 0.8346 (tp) REVERT: V 58 MET cc_start: 0.8218 (mtp) cc_final: 0.7976 (mtp) REVERT: W 19 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8183 (p) REVERT: W 27 ASP cc_start: 0.7574 (t0) cc_final: 0.7195 (t0) REVERT: W 45 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6897 (tm-30) REVERT: W 127 MET cc_start: 0.7847 (ptm) cc_final: 0.7411 (ptp) REVERT: Z 24 ASN cc_start: 0.8538 (t0) cc_final: 0.8052 (t0) REVERT: Z 79 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7866 (ttpp) REVERT: Z 80 ASP cc_start: 0.7339 (m-30) cc_final: 0.7122 (m-30) REVERT: Z 120 LEU cc_start: 0.8685 (tp) cc_final: 0.8460 (mm) REVERT: a 12 MET cc_start: 0.8368 (tpp) cc_final: 0.7980 (mmm) REVERT: a 52 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8323 (ttt-90) REVERT: b 8 PHE cc_start: 0.6808 (t80) cc_final: 0.6596 (t80) REVERT: b 10 LYS cc_start: 0.8313 (mtpm) cc_final: 0.7836 (mmmt) REVERT: b 35 ILE cc_start: 0.8875 (pt) cc_final: 0.8539 (pt) REVERT: q 124 TYR cc_start: 0.8185 (t80) cc_final: 0.7103 (t80) REVERT: q 135 HIS cc_start: 0.7856 (m-70) cc_final: 0.7556 (m-70) REVERT: r 40 LYS cc_start: 0.7834 (tttt) cc_final: 0.7448 (mmtt) REVERT: r 101 MET cc_start: 0.8535 (ttp) cc_final: 0.8184 (ttp) outliers start: 79 outliers final: 55 residues processed: 737 average time/residue: 0.2057 time to fit residues: 247.4078 Evaluate side-chains 728 residues out of total 3665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 665 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 124 SER 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 234 LEU Chi-restraints excluded: chain D residue 94 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 E residue 94 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 146 SER 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 111 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 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 632 ILE 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 172 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 306 SER 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 88 VAL Chi-restraints excluded: chain P residue 106 LEU 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 W residue 19 SER Chi-restraints excluded: chain X residue 15 VAL Chi-restraints excluded: chain X residue 69 ASN Chi-restraints excluded: chain Z residue 16 TYR 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 74 LEU 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 105 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 370 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 265 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN F 44 ASN F 303 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 HIS ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 72 HIS ** P 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3955 r_free = 0.3955 target = 0.151582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114653 restraints weight = 53025.214| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.41 r_work: 0.3274 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 35117 Z= 0.139 Angle : 0.808 34.888 47623 Z= 0.326 Chirality : 0.044 0.312 5193 Planarity : 0.005 0.073 6033 Dihedral : 8.878 151.024 4964 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.05 % Allowed : 21.04 % Favored : 76.92 % 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: -0.53 (0.13), residues: 4167 helix: 0.70 (0.12), residues: 1850 sheet: -1.32 (0.29), residues: 346 loop : -1.16 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 153 TYR 0.046 0.002 TYR D 135 PHE 0.028 0.001 PHE F 265 TRP 0.029 0.001 TRP A 77 HIS 0.014 0.001 HIS G 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (35076) covalent geometry : angle 0.64488 / 0.32 (47531) SS BOND : bond 0.00141 / 0.07 ( 4) SS BOND : angle 0.55994 / 0.31 ( 8) hydrogen bonds : bond 0.03505 / 2.31 ( 1325) hydrogen bonds : angle 4.81627 / 3.44 ( 3771) metal coordination : bond 0.01855 / 1.40 ( 37) metal coordination : angle 11.62104 / 8.71 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10573.92 seconds wall clock time: 181 minutes 21.03 seconds (10881.03 seconds total)