Starting phenix.real_space_refine on Mon Jul 6 08:40:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314.map" model { file = "/net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iap_35314/07_2026/8iap_35314_neut.cif" } resolution = 3.2 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= 0.002 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 246 5.16 5 C 22106 2.51 5 N 5873 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34534 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2532 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "s" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 189 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UQ1': 1} Classifications: {'undetermined': 1} 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: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "q" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1017 SG CYS B 99 82.131 58.442 105.242 1.00 29.52 S ATOM 1750 SG CYS B 194 85.043 55.269 108.864 1.00 29.28 S ATOM 1023 SG CYS B 100 80.431 54.072 103.965 1.00 30.11 S ATOM 1520 SG CYS B 164 79.435 54.835 110.001 1.00 28.96 S ATOM 7530 SG CYS E 134 142.316 50.320 150.972 1.00 56.01 S ATOM 7564 SG CYS E 139 145.290 51.862 150.000 1.00 56.50 S ATOM 7848 SG CYS E 175 140.238 54.000 153.439 1.00 54.42 S ATOM 7871 SG CYS E 179 143.126 55.704 154.201 1.00 57.95 S ATOM 11401 SG CYS F 425 123.763 59.806 153.663 1.00 45.60 S ATOM 11079 SG CYS F 385 123.724 57.270 147.896 1.00 39.95 S ATOM 11059 SG CYS F 382 119.488 58.458 150.208 1.00 40.29 S ATOM 11040 SG CYS F 379 121.486 54.421 153.087 1.00 43.09 S ATOM 12449 SG CYS G 131 103.289 47.086 137.112 1.00 31.31 S ATOM 12428 SG CYS G 128 105.242 50.847 132.425 1.00 30.26 S ATOM 12489 SG CYS G 137 102.966 53.014 138.435 1.00 33.13 S ATOM 13174 SG CYS G 226 104.920 47.245 145.680 1.00 34.31 S ATOM 12845 SG CYS G 182 108.133 45.674 151.425 1.00 36.31 S ATOM 12821 SG CYS G 179 107.477 51.208 148.794 1.00 35.62 S ATOM 12798 SG CYS G 176 110.897 46.902 146.360 1.00 34.05 S ATOM 11935 SG CYS G 64 108.900 57.283 150.687 1.00 35.53 S ATOM 12021 SG CYS G 75 109.605 59.297 148.978 1.00 36.47 S ATOM 12046 SG CYS G 78 108.717 63.551 150.845 1.00 36.76 S ATOM 12147 SG CYS G 92 107.936 61.579 154.101 1.00 39.04 S ATOM 20202 SG CYS I 123 88.744 49.977 118.438 1.00 27.30 S ATOM 20428 SG CYS I 152 88.407 48.721 113.352 1.00 27.39 S ATOM 20475 SG CYS I 158 94.101 48.878 115.364 1.00 26.60 S ATOM 20454 SG CYS I 155 91.022 53.313 115.015 1.00 27.04 S ATOM 20151 SG CYS I 116 98.679 45.990 125.734 1.00 29.24 S ATOM 20174 SG CYS I 119 94.255 45.635 122.456 1.00 28.85 S ATOM 20132 SG CYS I 113 97.442 40.804 122.580 1.00 28.61 S ATOM 20504 SG CYS I 162 100.333 45.348 120.350 1.00 28.07 S ATOM 25003 SG CYS R 79 113.814 38.804 124.424 1.00 32.60 S ATOM 25179 SG CYS R 104 111.127 39.321 127.013 1.00 32.49 S ATOM 25201 SG CYS R 107 110.863 38.034 122.869 1.00 30.78 S Time building chain proxies: 7.48, per 1000 atoms: 0.22 Number of scatterers: 34534 At special positions: 0 Unit cell: (170.5, 126.5, 201.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 246 16.00 P 12 15.00 O 6268 8.00 N 5873 7.00 C 22106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.02 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.4 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 175 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " 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 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 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=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " Number of angles added : 3 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7970 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 32 sheets defined 49.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.312A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.638A pdb=" N ASP B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.016A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.711A pdb=" N LYS B 147 " --> pdb=" O PRO B 143 " (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: 4.014A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 129 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.513A pdb=" N ALA D 150 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.830A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.178A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.469A 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: 3.924A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.708A 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: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.952A 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 removed outlier: 3.680A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 4.162A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.554A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.922A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.514A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.602A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.533A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.562A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 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: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.645A 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: 3.518A 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: 3.725A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.818A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.670A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.026A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.638A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 629 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.522A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.301A 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 Proline residue: H 12 - end of helix removed outlier: 3.509A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.574A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.740A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.688A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.753A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET H 146 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.538A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.528A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.866A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.144A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.670A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.195A 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 112 through 122 removed outlier: 4.106A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.598A 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 removed outlier: 3.625A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.754A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.080A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.881A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER P 308 " --> pdb=" O LEU P 304 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 358 through 363 removed outlier: 4.675A pdb=" N SER P 363 " --> pdb=" O TYR P 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.414A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 165 Processing helix chain 'R' and resid 44 through 49 removed outlier: 3.727A pdb=" N PHE R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 67 removed outlier: 4.039A pdb=" N ALA R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 5.952A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 126 Processing helix chain 'T' and resid 131 through 138 removed outlier: 3.678A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.586A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.616A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 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 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.510A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.427A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA X 34 " --> pdb=" O HIS X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 3.575A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.944A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 111 Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.992A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 99 removed outlier: 3.534A pdb=" N GLY Z 39 " --> pdb=" O MET Z 35 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.633A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.556A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 55 through 58 Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.126A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.628A 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 53 through 57 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.954A pdb=" N GLU r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 's' and resid 43 through 54 removed outlier: 4.202A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.136A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.506A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.890A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.148A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.562A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.601A pdb=" N LEU D 97 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA8, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.587A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 194 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: 6.228A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 291 removed outlier: 3.515A pdb=" N GLU F 290 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.547A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 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=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.203A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.360A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.120A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 70 through 71 removed outlier: 5.820A pdb=" N ASN R 70 " --> pdb=" O LYS R 112 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 76 through 79 removed outlier: 3.588A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 53 through 58 removed outlier: 3.576A pdb=" N LYS S 64 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'q' and resid 37 through 41 removed outlier: 6.595A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'q' and resid 67 through 68 1468 hydrogen bonds defined for protein. 4209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.96 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.36: 11212 1.36 - 1.57: 23670 1.57 - 1.79: 181 1.79 - 2.01: 223 2.01 - 2.23: 80 Bond restraints: 35366 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=" C GLU H 214 " pdb=" N TYR H 215 " ideal model delta sigma weight residual 1.330 1.556 -0.226 1.46e-02 4.69e+03 2.41e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.286 0.187 1.40e-02 5.10e+03 1.79e+02 bond pdb=" N PRO G 532 " pdb=" CD PRO G 532 " ideal model delta sigma weight residual 1.473 1.298 0.175 1.40e-02 5.10e+03 1.57e+02 bond pdb=" N PRO q 102 " pdb=" CD PRO q 102 " ideal model delta sigma weight residual 1.473 1.316 0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 35361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 47075 6.18 - 12.36: 654 12.36 - 18.53: 187 18.53 - 24.71: 8 24.71 - 30.89: 3 Bond angle restraints: 47927 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.39 89.04 25.35 1.45e+00 4.76e-01 3.06e+02 angle pdb=" N CYS F 332 " pdb=" CA CYS F 332 " pdb=" C CYS F 332 " ideal model delta sigma weight residual 111.02 130.05 -19.03 1.22e+00 6.72e-01 2.43e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.60 16.73 1.14e+00 7.69e-01 2.15e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.43 16.90 1.20e+00 6.94e-01 1.98e+02 angle pdb=" N ILE G 632 " pdb=" CA ILE G 632 " pdb=" C ILE G 632 " ideal model delta sigma weight residual 107.80 88.01 19.79 1.45e+00 4.76e-01 1.86e+02 ... (remaining 47922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 20844 30.72 - 61.43: 495 61.43 - 92.15: 40 92.15 - 122.86: 1 122.86 - 153.58: 7 Dihedral angle restraints: 21387 sinusoidal: 9025 harmonic: 12362 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" N LEU H 98 " pdb=" C LEU H 98 " pdb=" CA LEU H 98 " pdb=" CB LEU H 98 " ideal model delta harmonic sigma weight residual 122.80 104.01 18.79 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" C TYR D 214 " pdb=" N TYR D 214 " pdb=" CA TYR D 214 " pdb=" CB TYR D 214 " ideal model delta harmonic sigma weight residual -122.60 -104.90 -17.70 0 2.50e+00 1.60e-01 5.01e+01 ... (remaining 21384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4680 0.182 - 0.363: 480 0.363 - 0.545: 40 0.545 - 0.727: 8 0.727 - 0.909: 24 Chirality restraints: 5232 Sorted by residual: chirality pdb="FE3 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.91 2.00e-01 2.50e+01 2.05e+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 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5229 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 UQ9 H 401 " 0.337 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C23 UQ9 H 401 " -0.500 2.00e-02 2.50e+03 pdb=" C24 UQ9 H 401 " -0.105 2.00e-02 2.50e+03 pdb=" C25 UQ9 H 401 " 0.162 2.00e-02 2.50e+03 pdb=" C26 UQ9 H 401 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 D 501 " 0.165 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C11 UQ1 D 501 " 0.069 2.00e-02 2.50e+03 pdb=" C7 UQ1 D 501 " 0.305 2.00e-02 2.50e+03 pdb=" C8 UQ1 D 501 " -0.462 2.00e-02 2.50e+03 pdb=" C9 UQ1 D 501 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 401 " -0.187 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" C18 UQ9 H 401 " 0.257 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 401 " 0.057 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 401 " 0.011 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 401 " -0.138 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 83 2.38 - 3.01: 23550 3.01 - 3.64: 54624 3.64 - 4.27: 86788 4.27 - 4.90: 140194 Nonbonded interactions: 305239 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.969 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.008 3.400 nonbonded pdb=" OG1 THR V 48 " pdb=" OE2 GLU V 87 " model vdw 2.011 3.040 nonbonded pdb=" O SER B 89 " pdb=" CD LYS H 54 " model vdw 2.058 3.440 ... (remaining 305234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 41.080 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.022 1.048 35406 Z= 1.025 Angle : 2.196 48.493 48017 Z= 1.455 Chirality : 0.126 0.909 5232 Planarity : 0.009 0.287 6088 Dihedral : 13.069 153.577 13408 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 42.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 0.32 % Allowed : 7.39 % Favored : 92.29 % Cbeta Deviations : 1.56 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.12), residues: 4209 helix: -0.56 (0.12), residues: 1801 sheet: -0.97 (0.28), residues: 346 loop : -1.96 (0.12), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.033 0.002 TYR D 214 PHE 0.030 0.002 PHE D 200 TRP 0.031 0.002 TRP V 114 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.01447 / 0.93 (35366) covalent geometry : angle 2.07416 / 1.45 (47927) SS BOND : bond 0.00979 / 0.50 ( 3) SS BOND : angle 2.44852 / 1.22 ( 6) hydrogen bonds : bond 0.23508 / 15.57 ( 1468) hydrogen bonds : angle 8.98263 / 6.38 ( 4209) metal coordination : bond 0.49973 / 32.75 ( 37) metal coordination : angle 17.37726 / 13.24 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1460 time to evaluate : 1.325 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 126 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7537 (mmt90) REVERT: C 211 TYR cc_start: 0.8717 (t80) cc_final: 0.8451 (t80) REVERT: D 84 PHE cc_start: 0.7106 (t80) cc_final: 0.6817 (t80) REVERT: E 40 HIS cc_start: 0.7440 (t-90) cc_final: 0.7210 (t-90) REVERT: E 143 ASP cc_start: 0.8169 (t0) cc_final: 0.7529 (t70) REVERT: E 146 SER cc_start: 0.8571 (t) cc_final: 0.8037 (m) REVERT: E 242 PHE cc_start: 0.8053 (t80) cc_final: 0.7775 (t80) REVERT: G 145 MET cc_start: 0.8372 (mmt) cc_final: 0.8130 (mmt) REVERT: G 284 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6962 (mt-10) REVERT: G 544 MET cc_start: 0.8397 (ttt) cc_final: 0.8132 (ttt) REVERT: H 317 TYR cc_start: 0.6607 (t80) cc_final: 0.6120 (t80) REVERT: I 80 GLU cc_start: 0.7947 (tt0) cc_final: 0.7723 (tt0) REVERT: I 128 ILE cc_start: 0.8863 (mt) cc_final: 0.8645 (mt) REVERT: P 269 ASN cc_start: 0.7568 (p0) cc_final: 0.7193 (p0) REVERT: Q 168 LYS cc_start: 0.5057 (mttt) cc_final: 0.3716 (tptt) REVERT: R 41 LYS cc_start: 0.7560 (mmmt) cc_final: 0.6336 (tptt) REVERT: S 64 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7392 (mtmt) REVERT: S 92 GLN cc_start: 0.7918 (tp40) cc_final: 0.7556 (tp-100) REVERT: T 80 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8456 (ttpt) REVERT: T 108 LEU cc_start: 0.7209 (tt) cc_final: 0.6683 (tp) REVERT: T 119 ILE cc_start: 0.9157 (mm) cc_final: 0.8885 (tt) REVERT: Z 8 GLN cc_start: 0.7786 (tt0) cc_final: 0.7497 (tt0) REVERT: a 58 ASN cc_start: 0.7725 (m-40) cc_final: 0.7327 (m-40) REVERT: q 24 LEU cc_start: 0.9042 (mt) cc_final: 0.8824 (mt) REVERT: q 48 TYR cc_start: 0.8400 (m-80) cc_final: 0.7502 (m-80) REVERT: r 46 SER cc_start: 0.8244 (m) cc_final: 0.7841 (p) REVERT: s 44 THR cc_start: 0.8732 (m) cc_final: 0.8205 (m) REVERT: s 57 LEU cc_start: 0.8627 (tt) cc_final: 0.8142 (tp) outliers start: 12 outliers final: 1 residues processed: 1465 average time/residue: 0.2416 time to fit residues: 555.1834 Evaluate side-chains 918 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 917 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 172 HIS B 209 GLN C 73 GLN C 88 HIS C 123 ASN C 180 HIS C 195 HIS D 83 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 381 HIS ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 122 ASN E 181 ASN E 245 GLN F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 376 HIS F 393 ASN F 418 GLN G 74 ASN G 123 ASN G 140 GLN G 142 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN G 444 HIS G 460 HIS G 495 ASN G 571 HIS G 605 GLN H 5 ASN H 47 GLN H 258 ASN ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS I 85 ASN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 102 GLN P 138 ASN P 251 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 341 GLN P 376 ASN Q 88 GLN R 33 HIS R 113 GLN S 25 GLN V 21 HIS W 54 GLN W 94 GLN ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 HIS X 104 GLN X 143 HIS Z 135 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 83 ASN q 52 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 HIS r 21 GLN r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108579 restraints weight = 55096.123| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.76 r_work: 0.3257 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35406 Z= 0.192 Angle : 0.926 57.071 48017 Z= 0.399 Chirality : 0.048 0.246 5232 Planarity : 0.006 0.073 6088 Dihedral : 9.912 158.610 5007 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.46 % Allowed : 15.02 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.12), residues: 4209 helix: 0.36 (0.12), residues: 1872 sheet: -0.95 (0.26), residues: 368 loop : -1.28 (0.13), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 61 TYR 0.030 0.002 TYR P 271 PHE 0.034 0.002 PHE H 223 TRP 0.018 0.002 TRP V 114 HIS 0.007 0.002 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (35366) covalent geometry : angle 0.76020 / 0.40 (47927) SS BOND : bond 0.00410 / 0.20 ( 3) SS BOND : angle 1.45188 / 0.70 ( 6) hydrogen bonds : bond 0.05574 / 3.63 ( 1468) hydrogen bonds : angle 5.83775 / 4.08 ( 4209) metal coordination : bond 0.02431 / 1.56 ( 37) metal coordination : angle 12.67225 / 8.13 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 958 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8550 (mm) cc_final: 0.8271 (mt) REVERT: A 90 MET cc_start: 0.8730 (mmm) cc_final: 0.8183 (mmt) REVERT: C 74 GLN cc_start: 0.8594 (mt0) cc_final: 0.8111 (pt0) REVERT: D 84 PHE cc_start: 0.7678 (t80) cc_final: 0.7086 (t80) REVERT: D 212 GLU cc_start: 0.8293 (tt0) cc_final: 0.8085 (mt-10) REVERT: D 443 MET cc_start: 0.7993 (mmm) cc_final: 0.7657 (mmt) REVERT: D 446 ASP cc_start: 0.8574 (m-30) cc_final: 0.8211 (m-30) REVERT: D 457 VAL cc_start: 0.9313 (t) cc_final: 0.8969 (t) REVERT: E 69 TYR cc_start: 0.8642 (m-80) cc_final: 0.8274 (m-80) REVERT: E 143 ASP cc_start: 0.8761 (t0) cc_final: 0.8094 (t70) REVERT: E 146 SER cc_start: 0.8901 (t) cc_final: 0.8340 (m) REVERT: E 152 GLN cc_start: 0.8007 (tt0) cc_final: 0.7450 (mt0) REVERT: E 176 LEU cc_start: 0.8372 (mt) cc_final: 0.8163 (mt) REVERT: E 194 ASP cc_start: 0.8235 (t70) cc_final: 0.7915 (t70) REVERT: F 149 MET cc_start: 0.8795 (mtm) cc_final: 0.8528 (mtm) REVERT: F 152 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8003 (ttm-80) REVERT: F 244 ASN cc_start: 0.8551 (t0) cc_final: 0.8226 (t0) REVERT: F 405 ARG cc_start: 0.8175 (ptp90) cc_final: 0.7896 (mmp80) REVERT: F 406 PRO cc_start: 0.8803 (Cg_endo) cc_final: 0.8475 (Cg_exo) REVERT: F 450 MET cc_start: 0.8505 (mmt) cc_final: 0.7548 (mmt) REVERT: G 117 MET cc_start: 0.8633 (mmt) cc_final: 0.8246 (mmt) REVERT: G 513 MET cc_start: 0.9128 (tpp) cc_final: 0.8715 (tpp) REVERT: H 17 MET cc_start: 0.9081 (tmm) cc_final: 0.8794 (ttp) REVERT: H 148 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9071 (mp) REVERT: H 200 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7455 (pp) REVERT: H 317 TYR cc_start: 0.7024 (t80) cc_final: 0.6102 (t80) REVERT: I 40 ASN cc_start: 0.9075 (t0) cc_final: 0.8795 (t0) REVERT: P 78 SER cc_start: 0.8990 (m) cc_final: 0.8728 (p) REVERT: P 121 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7172 (tp40) REVERT: P 147 ASN cc_start: 0.8364 (m-40) cc_final: 0.8039 (m110) REVERT: P 211 ASP cc_start: 0.7980 (p0) cc_final: 0.7664 (p0) REVERT: P 247 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7835 (tppt) REVERT: P 355 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6488 (mmt90) REVERT: Q 166 TRP cc_start: 0.6263 (t60) cc_final: 0.6048 (t60) REVERT: R 41 LYS cc_start: 0.7571 (mmmt) cc_final: 0.5820 (tptt) REVERT: S 39 GLN cc_start: 0.8577 (mt0) cc_final: 0.8293 (mp10) REVERT: S 53 ILE cc_start: 0.8679 (tp) cc_final: 0.8378 (tp) REVERT: S 64 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7346 (mtmt) REVERT: S 88 THR cc_start: 0.8136 (m) cc_final: 0.7922 (p) REVERT: S 92 GLN cc_start: 0.8372 (tp40) cc_final: 0.7942 (tp-100) REVERT: T 80 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8373 (ttpt) REVERT: T 91 ASP cc_start: 0.8895 (m-30) cc_final: 0.8571 (p0) REVERT: T 117 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8334 (mt-10) REVERT: T 119 ILE cc_start: 0.9010 (mm) cc_final: 0.8688 (tt) REVERT: V 33 ASP cc_start: 0.8829 (t0) cc_final: 0.8539 (m-30) REVERT: W 58 THR cc_start: 0.8036 (m) cc_final: 0.7793 (p) REVERT: W 69 MET cc_start: 0.8997 (mmp) cc_final: 0.8759 (mmt) REVERT: X 36 CYS cc_start: 0.8116 (m) cc_final: 0.7587 (m) REVERT: X 102 GLN cc_start: 0.6718 (tm-30) cc_final: 0.6509 (tm-30) REVERT: X 107 PHE cc_start: 0.8052 (t80) cc_final: 0.7338 (t80) REVERT: Z 98 MET cc_start: 0.5414 (mmp) cc_final: 0.4920 (tpp) REVERT: Z 101 VAL cc_start: 0.7393 (t) cc_final: 0.6982 (p) REVERT: Z 129 THR cc_start: 0.7999 (m) cc_final: 0.7791 (p) REVERT: a 26 ILE cc_start: 0.8958 (mm) cc_final: 0.8607 (mt) REVERT: a 29 PHE cc_start: 0.8018 (t80) cc_final: 0.7716 (t80) REVERT: q 27 PHE cc_start: 0.7923 (t80) cc_final: 0.7554 (t80) REVERT: q 47 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8550 (mttm) REVERT: q 68 MET cc_start: 0.9023 (ttt) cc_final: 0.8576 (ttt) REVERT: r 19 ASP cc_start: 0.8175 (t0) cc_final: 0.7926 (t0) REVERT: s 57 LEU cc_start: 0.8291 (tt) cc_final: 0.7850 (tp) outliers start: 128 outliers final: 59 residues processed: 1016 average time/residue: 0.2305 time to fit residues: 375.8409 Evaluate side-chains 854 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 792 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain P residue 175 LYS Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 164 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 128 VAL Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 133 MET Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 49 GLU Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 136 GLU Chi-restraints excluded: chain r residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 24 optimal weight: 0.0070 chunk 48 optimal weight: 0.6980 chunk 294 optimal weight: 0.0020 chunk 29 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 379 optimal weight: 2.9990 chunk 265 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 207 GLN C 56 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 ASN G 123 ASN G 202 ASN G 260 ASN G 336 ASN G 460 HIS G 604 GLN H 258 ASN I 126 GLN P 71 ASN P 138 ASN P 251 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN V 21 HIS W 105 HIS ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 71 GLN q 17 HIS ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 HIS q 91 HIS q 101 ASN q 123 GLN r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108251 restraints weight = 54853.168| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.78 r_work: 0.3258 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 35406 Z= 0.139 Angle : 0.804 61.293 48017 Z= 0.328 Chirality : 0.043 0.294 5232 Planarity : 0.005 0.060 6088 Dihedral : 9.504 168.722 5007 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.41 % Allowed : 16.37 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4209 helix: 0.72 (0.12), residues: 1895 sheet: -0.90 (0.26), residues: 378 loop : -1.02 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 199 TYR 0.023 0.002 TYR a 61 PHE 0.019 0.002 PHE F 442 TRP 0.018 0.001 TRP b 26 HIS 0.007 0.001 HIS F 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (35366) covalent geometry : angle 0.63328 / 0.32 (47927) SS BOND : bond 0.00548 / 0.27 ( 3) SS BOND : angle 1.28806 / 0.56 ( 6) hydrogen bonds : bond 0.04560 / 2.97 ( 1468) hydrogen bonds : angle 5.29642 / 3.71 ( 4209) metal coordination : bond 0.02164 / 1.40 ( 37) metal coordination : angle 11.85518 / 7.39 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 884 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8104 (m-40) cc_final: 0.7711 (m-40) REVERT: A 19 LEU cc_start: 0.8095 (tt) cc_final: 0.7681 (mp) REVERT: A 89 ILE cc_start: 0.8468 (mm) cc_final: 0.8234 (mt) REVERT: A 90 MET cc_start: 0.8601 (mmm) cc_final: 0.8153 (mmt) REVERT: B 77 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8300 (mmmm) REVERT: C 74 GLN cc_start: 0.8552 (mt0) cc_final: 0.8076 (pt0) REVERT: C 229 PHE cc_start: 0.8810 (t80) cc_final: 0.8602 (t80) REVERT: D 84 PHE cc_start: 0.7752 (t80) cc_final: 0.7299 (t80) REVERT: D 107 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7837 (mmt-90) REVERT: D 212 GLU cc_start: 0.8304 (tt0) cc_final: 0.8064 (mt-10) REVERT: D 359 ASP cc_start: 0.7143 (t0) cc_final: 0.6839 (t0) REVERT: D 443 MET cc_start: 0.8060 (mmm) cc_final: 0.7758 (mmt) REVERT: D 446 ASP cc_start: 0.8493 (m-30) cc_final: 0.8194 (m-30) REVERT: E 41 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6942 (mtm-85) REVERT: E 143 ASP cc_start: 0.8675 (t0) cc_final: 0.8005 (t70) REVERT: E 146 SER cc_start: 0.8881 (t) cc_final: 0.8310 (m) REVERT: E 154 LYS cc_start: 0.7011 (mmtm) cc_final: 0.6583 (mmmt) REVERT: E 176 LEU cc_start: 0.8426 (mt) cc_final: 0.8123 (mt) REVERT: E 221 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7485 (ttp80) REVERT: F 159 ARG cc_start: 0.7589 (ttp-110) cc_final: 0.7346 (ttp-110) REVERT: F 170 GLN cc_start: 0.8903 (mt0) cc_final: 0.8537 (mt0) REVERT: F 392 MET cc_start: 0.8792 (mtp) cc_final: 0.8454 (mtt) REVERT: F 405 ARG cc_start: 0.8071 (ptp90) cc_final: 0.7851 (mmp80) REVERT: F 406 PRO cc_start: 0.8884 (Cg_endo) cc_final: 0.8480 (Cg_exo) REVERT: F 450 MET cc_start: 0.8587 (mmt) cc_final: 0.7597 (mmt) REVERT: G 117 MET cc_start: 0.8733 (mmt) cc_final: 0.8413 (mmt) REVERT: G 674 LEU cc_start: 0.8485 (mt) cc_final: 0.8279 (mp) REVERT: H 148 ILE cc_start: 0.9303 (mt) cc_final: 0.9039 (mp) REVERT: H 261 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7350 (mpp) REVERT: P 78 SER cc_start: 0.8828 (m) cc_final: 0.8626 (p) REVERT: P 211 ASP cc_start: 0.7899 (p0) cc_final: 0.7670 (p0) REVERT: P 247 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7805 (tppt) REVERT: P 355 ARG cc_start: 0.7163 (ptp-170) cc_final: 0.6500 (mmt90) REVERT: Q 99 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9146 (ptm) REVERT: R 45 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8141 (mtp-110) REVERT: S 64 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7308 (mtmt) REVERT: S 88 THR cc_start: 0.8126 (m) cc_final: 0.7873 (p) REVERT: S 92 GLN cc_start: 0.8599 (tp40) cc_final: 0.8188 (tp-100) REVERT: T 80 LYS cc_start: 0.8982 (ttmt) cc_final: 0.8378 (ttpt) REVERT: T 119 ILE cc_start: 0.8978 (mm) cc_final: 0.8650 (tt) REVERT: V 33 ASP cc_start: 0.8874 (t0) cc_final: 0.8547 (m-30) REVERT: W 69 MET cc_start: 0.8889 (mmp) cc_final: 0.8675 (mmt) REVERT: X 36 CYS cc_start: 0.8093 (m) cc_final: 0.7518 (m) REVERT: X 40 ASN cc_start: 0.7590 (m-40) cc_final: 0.7324 (m110) REVERT: X 56 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7220 (m) REVERT: X 102 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6517 (tm-30) REVERT: X 107 PHE cc_start: 0.8079 (t80) cc_final: 0.7537 (t80) REVERT: X 113 ASP cc_start: 0.7423 (m-30) cc_final: 0.7170 (m-30) REVERT: Z 35 MET cc_start: 0.8572 (ttm) cc_final: 0.8329 (mtp) REVERT: Z 79 LYS cc_start: 0.8875 (tttt) cc_final: 0.8543 (tttm) REVERT: Z 98 MET cc_start: 0.5364 (mmp) cc_final: 0.4915 (tpp) REVERT: Z 106 VAL cc_start: 0.7331 (t) cc_final: 0.7087 (p) REVERT: Z 129 THR cc_start: 0.7815 (m) cc_final: 0.7603 (p) REVERT: a 26 ILE cc_start: 0.8962 (mm) cc_final: 0.8745 (mt) REVERT: a 51 ASP cc_start: 0.8046 (m-30) cc_final: 0.7839 (m-30) REVERT: q 27 PHE cc_start: 0.8078 (t80) cc_final: 0.7814 (t80) REVERT: q 47 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8442 (mttm) REVERT: q 68 MET cc_start: 0.8980 (ttt) cc_final: 0.8537 (ttt) REVERT: r 30 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: r 70 MET cc_start: 0.6363 (mmt) cc_final: 0.6074 (mmt) REVERT: s 57 LEU cc_start: 0.7757 (tt) cc_final: 0.7375 (tp) outliers start: 126 outliers final: 69 residues processed: 954 average time/residue: 0.2222 time to fit residues: 342.1387 Evaluate side-chains 837 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 763 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 133 MET Chi-restraints excluded: chain a residue 49 GLU Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 113 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain r residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 391 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 390 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN D 87 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN E 40 HIS ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN G 522 GLN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 ASN P 138 ASN ** P 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 86 ASN X 95 GLN b 71 GLN b 83 ASN q 12 GLN q 17 HIS ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 ASN ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.096985 restraints weight = 55657.247| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.76 r_work: 0.3082 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 35406 Z= 0.291 Angle : 0.920 61.749 48017 Z= 0.377 Chirality : 0.049 0.222 5232 Planarity : 0.006 0.059 6088 Dihedral : 9.558 164.915 5007 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.65 % Allowed : 17.07 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4209 helix: 0.64 (0.12), residues: 1886 sheet: -1.04 (0.27), residues: 365 loop : -0.93 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 135 TYR 0.034 0.002 TYR D 385 PHE 0.027 0.002 PHE D 174 TRP 0.022 0.002 TRP b 26 HIS 0.010 0.002 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.29 (35366) covalent geometry : angle 0.73470 / 0.37 (47927) SS BOND : bond 0.00906 / 0.45 ( 3) SS BOND : angle 1.22789 / 0.58 ( 6) hydrogen bonds : bond 0.04832 / 3.16 ( 1468) hydrogen bonds : angle 5.33035 / 3.72 ( 4209) metal coordination : bond 0.03554 / 2.32 ( 37) metal coordination : angle 13.24017 / 8.39 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 821 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8496 (mm) cc_final: 0.8258 (mt) REVERT: A 90 MET cc_start: 0.8579 (mmm) cc_final: 0.8111 (mmt) REVERT: C 74 GLN cc_start: 0.8882 (mt0) cc_final: 0.8132 (pt0) REVERT: D 84 PHE cc_start: 0.7817 (t80) cc_final: 0.7449 (t80) REVERT: D 107 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8318 (mmt180) REVERT: D 212 GLU cc_start: 0.8385 (tt0) cc_final: 0.8051 (mt-10) REVERT: D 229 PRO cc_start: 0.8354 (Cg_endo) cc_final: 0.8056 (Cg_exo) REVERT: D 443 MET cc_start: 0.8217 (mmm) cc_final: 0.8001 (mmt) REVERT: E 41 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7239 (mtm-85) REVERT: E 143 ASP cc_start: 0.8749 (t0) cc_final: 0.8065 (t70) REVERT: E 146 SER cc_start: 0.8891 (t) cc_final: 0.8300 (m) REVERT: E 154 LYS cc_start: 0.6752 (mmtm) cc_final: 0.6136 (mmmt) REVERT: E 221 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7604 (ttp80) REVERT: F 97 LEU cc_start: 0.8769 (mt) cc_final: 0.8564 (tp) REVERT: F 131 MET cc_start: 0.8567 (mmm) cc_final: 0.8333 (mmm) REVERT: F 357 MET cc_start: 0.8870 (mtm) cc_final: 0.8492 (mtt) REVERT: F 403 ASP cc_start: 0.7852 (m-30) cc_final: 0.7562 (t0) REVERT: F 405 ARG cc_start: 0.8174 (ptp90) cc_final: 0.7828 (mmp80) REVERT: F 450 MET cc_start: 0.8643 (mmt) cc_final: 0.7754 (mmt) REVERT: G 484 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8106 (p0) REVERT: G 516 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8674 (tp) REVERT: G 657 ASP cc_start: 0.7945 (t0) cc_final: 0.7577 (t0) REVERT: H 7 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8368 (mp) REVERT: H 35 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8270 (mtmt) REVERT: H 181 MET cc_start: 0.8549 (mtm) cc_final: 0.8246 (mtm) REVERT: H 215 TYR cc_start: 0.8512 (m-80) cc_final: 0.7986 (m-80) REVERT: H 261 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7784 (mtp) REVERT: I 40 ASN cc_start: 0.9208 (t0) cc_final: 0.8910 (t0) REVERT: I 98 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7708 (mtt-85) REVERT: P 134 TRP cc_start: 0.9020 (p90) cc_final: 0.8685 (p90) REVERT: P 247 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8041 (tppt) REVERT: P 355 ARG cc_start: 0.7285 (ptp-170) cc_final: 0.6565 (mmt180) REVERT: Q 94 THR cc_start: 0.8969 (m) cc_final: 0.8600 (p) REVERT: Q 99 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9117 (ptp) REVERT: R 45 ARG cc_start: 0.8915 (mtm110) cc_final: 0.8489 (mtp180) REVERT: S 64 LYS cc_start: 0.8626 (mtpp) cc_final: 0.7657 (mtmt) REVERT: S 88 THR cc_start: 0.8146 (m) cc_final: 0.7893 (p) REVERT: S 92 GLN cc_start: 0.8685 (tp40) cc_final: 0.8294 (tp-100) REVERT: T 80 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8363 (ttpt) REVERT: T 119 ILE cc_start: 0.9046 (mm) cc_final: 0.8715 (tt) REVERT: T 123 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7625 (mt-10) REVERT: V 33 ASP cc_start: 0.8928 (t0) cc_final: 0.8617 (m-30) REVERT: W 117 ARG cc_start: 0.6833 (mtp-110) cc_final: 0.6573 (mtp180) REVERT: W 119 LYS cc_start: 0.8961 (mttm) cc_final: 0.8703 (mmtp) REVERT: X 36 CYS cc_start: 0.8323 (m) cc_final: 0.7837 (m) REVERT: X 56 CYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7230 (m) REVERT: X 102 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6767 (tm-30) REVERT: X 104 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8272 (tm-30) REVERT: X 107 PHE cc_start: 0.8120 (t80) cc_final: 0.7641 (t80) REVERT: X 135 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7349 (mmm-85) REVERT: Z 79 LYS cc_start: 0.9002 (tttt) cc_final: 0.8654 (tttm) REVERT: Z 129 THR cc_start: 0.7886 (m) cc_final: 0.7668 (p) REVERT: Z 143 TYR cc_start: 0.8022 (p90) cc_final: 0.7556 (p90) REVERT: a 29 PHE cc_start: 0.8218 (t80) cc_final: 0.7864 (t80) REVERT: a 47 LEU cc_start: 0.9138 (mp) cc_final: 0.8869 (mt) REVERT: a 51 ASP cc_start: 0.8081 (m-30) cc_final: 0.7800 (m-30) REVERT: q 47 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8884 (mtpp) REVERT: q 68 MET cc_start: 0.8965 (ttt) cc_final: 0.8674 (ttt) REVERT: q 122 GLU cc_start: 0.8162 (mp0) cc_final: 0.7906 (mp0) REVERT: r 19 ASP cc_start: 0.8563 (t0) cc_final: 0.8239 (t0) REVERT: r 30 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: r 103 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8239 (mtm-85) REVERT: s 53 SER cc_start: 0.8635 (t) cc_final: 0.8432 (p) outliers start: 172 outliers final: 101 residues processed: 920 average time/residue: 0.2260 time to fit residues: 336.3035 Evaluate side-chains 840 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 730 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 253 THR Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 163 ASN Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain X residue 142 TYR Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 49 GLU Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 120 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 64 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 261 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 409 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 352 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN D 112 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS H 258 ASN P 166 HIS ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 ASN R 52 GLN W 73 ASN X 95 GLN Z 76 GLN b 71 GLN q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101502 restraints weight = 55107.007| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.78 r_work: 0.3138 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 35406 Z= 0.139 Angle : 0.802 64.581 48017 Z= 0.314 Chirality : 0.043 0.235 5232 Planarity : 0.005 0.056 6088 Dihedral : 9.316 177.324 5007 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.73 % Allowed : 18.83 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4209 helix: 0.90 (0.12), residues: 1873 sheet: -1.15 (0.27), residues: 364 loop : -0.78 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 37 TYR 0.020 0.002 TYR T 147 PHE 0.030 0.002 PHE P 213 TRP 0.015 0.001 TRP G 243 HIS 0.006 0.001 HIS F 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (35366) covalent geometry : angle 0.61273 / 0.31 (47927) SS BOND : bond 0.00299 / 0.15 ( 3) SS BOND : angle 0.89480 / 0.37 ( 6) hydrogen bonds : bond 0.03998 / 2.59 ( 1468) hydrogen bonds : angle 5.00585 / 3.51 ( 4209) metal coordination : bond 0.01811 / 1.28 ( 37) metal coordination : angle 12.38880 / 7.65 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 787 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8097 (tt) cc_final: 0.7784 (mp) REVERT: A 90 MET cc_start: 0.8521 (mmm) cc_final: 0.8034 (mmt) REVERT: C 74 GLN cc_start: 0.8800 (mt0) cc_final: 0.8151 (pt0) REVERT: D 84 PHE cc_start: 0.7656 (t80) cc_final: 0.6922 (t80) REVERT: D 212 GLU cc_start: 0.8334 (tt0) cc_final: 0.8045 (mt-10) REVERT: D 261 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8684 (tpp) REVERT: D 443 MET cc_start: 0.8172 (mmm) cc_final: 0.7928 (mmt) REVERT: E 41 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7065 (mtm-85) REVERT: E 143 ASP cc_start: 0.8699 (t0) cc_final: 0.7988 (t70) REVERT: E 146 SER cc_start: 0.8863 (t) cc_final: 0.8241 (m) REVERT: E 176 LEU cc_start: 0.8519 (mt) cc_final: 0.8242 (mt) REVERT: E 194 ASP cc_start: 0.8583 (t70) cc_final: 0.8193 (t70) REVERT: E 221 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7846 (ttp80) REVERT: F 147 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8500 (tpt170) REVERT: F 405 ARG cc_start: 0.8125 (ptp90) cc_final: 0.7852 (mmp80) REVERT: F 450 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7764 (mmt) REVERT: G 145 MET cc_start: 0.9277 (mmt) cc_final: 0.8927 (mmt) REVERT: G 447 ASP cc_start: 0.7128 (p0) cc_final: 0.6722 (p0) REVERT: G 484 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8116 (p0) REVERT: H 181 MET cc_start: 0.8438 (mtm) cc_final: 0.8211 (mtm) REVERT: H 261 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7714 (mtp) REVERT: I 40 ASN cc_start: 0.9129 (t0) cc_final: 0.8840 (t0) REVERT: P 134 TRP cc_start: 0.8941 (p90) cc_final: 0.8627 (p90) REVERT: P 247 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8115 (tppt) REVERT: P 355 ARG cc_start: 0.7283 (ptp-170) cc_final: 0.6426 (mmt-90) REVERT: Q 89 SER cc_start: 0.9355 (m) cc_final: 0.9142 (p) REVERT: Q 103 THR cc_start: 0.9180 (p) cc_final: 0.8976 (p) REVERT: Q 146 ASP cc_start: 0.8476 (p0) cc_final: 0.8184 (p0) REVERT: R 45 ARG cc_start: 0.8902 (mtm110) cc_final: 0.8393 (mtp180) REVERT: R 52 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: R 92 TYR cc_start: 0.9166 (m-80) cc_final: 0.8961 (m-80) REVERT: S 64 LYS cc_start: 0.8589 (mtpp) cc_final: 0.7724 (mtmt) REVERT: S 83 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8226 (p) REVERT: S 88 THR cc_start: 0.8023 (m) cc_final: 0.7793 (p) REVERT: S 92 GLN cc_start: 0.8723 (tp40) cc_final: 0.8279 (tp-100) REVERT: T 80 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8347 (ttpt) REVERT: T 104 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7546 (p90) REVERT: T 123 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7654 (mt-10) REVERT: V 33 ASP cc_start: 0.8896 (t0) cc_final: 0.8611 (m-30) REVERT: W 58 THR cc_start: 0.8204 (m) cc_final: 0.7869 (p) REVERT: W 69 MET cc_start: 0.9066 (mmt) cc_final: 0.8827 (mmt) REVERT: X 36 CYS cc_start: 0.8329 (m) cc_final: 0.7844 (m) REVERT: X 56 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7225 (m) REVERT: X 102 GLN cc_start: 0.7153 (tm-30) cc_final: 0.6729 (tm-30) REVERT: X 107 PHE cc_start: 0.8060 (t80) cc_final: 0.7625 (t80) REVERT: Z 35 MET cc_start: 0.8729 (ttm) cc_final: 0.8515 (mtp) REVERT: Z 79 LYS cc_start: 0.8966 (tttt) cc_final: 0.8613 (tttm) REVERT: Z 129 THR cc_start: 0.7899 (m) cc_final: 0.7674 (p) REVERT: a 29 PHE cc_start: 0.8201 (t80) cc_final: 0.7861 (t80) REVERT: a 47 LEU cc_start: 0.9158 (mp) cc_final: 0.8838 (mt) REVERT: a 51 ASP cc_start: 0.8045 (m-30) cc_final: 0.7741 (m-30) REVERT: q 47 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8939 (mtmm) REVERT: q 68 MET cc_start: 0.8950 (ttt) cc_final: 0.8622 (ttt) REVERT: r 30 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8126 (pm20) REVERT: r 103 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8173 (mtm-85) outliers start: 138 outliers final: 83 residues processed: 866 average time/residue: 0.2060 time to fit residues: 288.8846 Evaluate side-chains 814 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 720 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 77 ASP Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 120 MET Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 95 GLN Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 49 GLU Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 113 HIS Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 51 ASP Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 chunk 386 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN E 40 HIS E 74 GLN E 152 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 GLN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN q 17 HIS ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN r 36 GLN ** r 52 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 = 0.3590 r_free = 0.3590 target = 0.125440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099570 restraints weight = 54969.203| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.78 r_work: 0.3109 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 35406 Z= 0.170 Angle : 0.817 65.660 48017 Z= 0.318 Chirality : 0.044 0.234 5232 Planarity : 0.005 0.055 6088 Dihedral : 9.244 179.815 5007 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.19 % Allowed : 18.80 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4209 helix: 0.94 (0.12), residues: 1888 sheet: -1.27 (0.26), residues: 376 loop : -0.73 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 159 TYR 0.019 0.002 TYR a 61 PHE 0.022 0.002 PHE E 242 TRP 0.012 0.001 TRP G 243 HIS 0.005 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (35366) covalent geometry : angle 0.62349 / 0.32 (47927) SS BOND : bond 0.00915 / 0.46 ( 3) SS BOND : angle 0.94674 / 0.44 ( 6) hydrogen bonds : bond 0.04025 / 2.60 ( 1468) hydrogen bonds : angle 4.94201 / 3.46 ( 4209) metal coordination : bond 0.02184 / 1.51 ( 37) metal coordination : angle 12.64961 / 7.81 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 757 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8058 (tt) cc_final: 0.7770 (mp) REVERT: C 74 GLN cc_start: 0.8835 (mt0) cc_final: 0.8122 (pt0) REVERT: D 84 PHE cc_start: 0.7778 (t80) cc_final: 0.7486 (t80) REVERT: D 212 GLU cc_start: 0.8362 (tt0) cc_final: 0.8045 (mt-10) REVERT: D 356 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8867 (pp) REVERT: D 360 ASP cc_start: 0.8374 (m-30) cc_final: 0.8118 (t0) REVERT: D 443 MET cc_start: 0.8230 (mmm) cc_final: 0.8012 (mmt) REVERT: E 41 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7059 (mtm-85) REVERT: E 124 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7276 (mtpp) REVERT: E 143 ASP cc_start: 0.8697 (t0) cc_final: 0.8023 (t70) REVERT: E 146 SER cc_start: 0.8890 (t) cc_final: 0.8301 (m) REVERT: E 194 ASP cc_start: 0.8616 (t70) cc_final: 0.8298 (t70) REVERT: E 221 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7740 (ttp80) REVERT: F 119 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7946 (mm-30) REVERT: F 147 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8554 (tpt170) REVERT: F 405 ARG cc_start: 0.8161 (ptp90) cc_final: 0.7840 (mmp80) REVERT: F 450 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7759 (mmt) REVERT: G 145 MET cc_start: 0.9288 (mmt) cc_final: 0.8832 (mmt) REVERT: G 484 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8159 (p0) REVERT: H 69 SER cc_start: 0.8785 (m) cc_final: 0.8390 (t) REVERT: H 181 MET cc_start: 0.8351 (mtm) cc_final: 0.8141 (mtm) REVERT: H 215 TYR cc_start: 0.8373 (m-80) cc_final: 0.7847 (m-80) REVERT: H 261 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7731 (mtp) REVERT: H 282 TYR cc_start: 0.8262 (t80) cc_final: 0.7995 (t80) REVERT: I 40 ASN cc_start: 0.9152 (t0) cc_final: 0.8824 (t0) REVERT: I 98 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7617 (mtt-85) REVERT: P 134 TRP cc_start: 0.9007 (p90) cc_final: 0.8723 (p90) REVERT: P 205 ASP cc_start: 0.7225 (p0) cc_final: 0.6577 (m-30) REVERT: P 233 PHE cc_start: 0.8264 (m-80) cc_final: 0.7959 (m-80) REVERT: P 247 LYS cc_start: 0.8377 (mtpt) cc_final: 0.8037 (tppt) REVERT: P 355 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.6446 (mmt-90) REVERT: Q 94 THR cc_start: 0.8955 (m) cc_final: 0.8662 (p) REVERT: Q 146 ASP cc_start: 0.8492 (p0) cc_final: 0.8176 (p0) REVERT: R 45 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8391 (mtp180) REVERT: S 64 LYS cc_start: 0.8731 (mtpp) cc_final: 0.7794 (mtmt) REVERT: S 88 THR cc_start: 0.8125 (m) cc_final: 0.7853 (p) REVERT: S 92 GLN cc_start: 0.8737 (tp40) cc_final: 0.8296 (tp-100) REVERT: T 80 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8301 (ttpt) REVERT: T 94 ASP cc_start: 0.7059 (t0) cc_final: 0.6739 (t0) REVERT: T 104 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7436 (p90) REVERT: T 108 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6637 (tt) REVERT: T 123 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7685 (mt-10) REVERT: V 33 ASP cc_start: 0.8902 (t0) cc_final: 0.8589 (m-30) REVERT: W 58 THR cc_start: 0.8303 (m) cc_final: 0.8006 (p) REVERT: X 36 CYS cc_start: 0.8218 (m) cc_final: 0.7771 (m) REVERT: X 56 CYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7198 (m) REVERT: X 102 GLN cc_start: 0.7214 (tm-30) cc_final: 0.6753 (tm-30) REVERT: X 104 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8213 (tm-30) REVERT: X 107 PHE cc_start: 0.8125 (t80) cc_final: 0.7646 (t80) REVERT: Z 35 MET cc_start: 0.8776 (ttm) cc_final: 0.8551 (mtp) REVERT: Z 79 LYS cc_start: 0.8991 (tttt) cc_final: 0.8618 (tttm) REVERT: Z 98 MET cc_start: 0.4796 (mmp) cc_final: 0.4490 (tpp) REVERT: Z 129 THR cc_start: 0.7933 (m) cc_final: 0.7704 (p) REVERT: a 29 PHE cc_start: 0.8206 (t80) cc_final: 0.7883 (t80) REVERT: a 47 LEU cc_start: 0.9194 (mp) cc_final: 0.8866 (mt) REVERT: a 51 ASP cc_start: 0.8051 (m-30) cc_final: 0.7701 (m-30) REVERT: q 41 GLU cc_start: 0.8390 (tt0) cc_final: 0.8147 (tt0) REVERT: q 47 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8548 (mtpp) REVERT: q 68 MET cc_start: 0.8899 (ttt) cc_final: 0.8693 (ttt) REVERT: q 122 GLU cc_start: 0.7944 (mp0) cc_final: 0.7665 (mp0) REVERT: r 30 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: r 103 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8154 (mtm-85) outliers start: 155 outliers final: 105 residues processed: 851 average time/residue: 0.2091 time to fit residues: 290.0210 Evaluate side-chains 839 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 722 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 212 LYS Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 266 THR Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 54 THR Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain Q residue 164 PHE Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 77 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 76 ASP Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 19 optimal weight: 2.9990 chunk 397 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 381 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 chunk 404 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 152 GLN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 GLN S 62 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 ASN b 71 GLN q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101532 restraints weight = 55270.447| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.75 r_work: 0.3141 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35406 Z= 0.141 Angle : 0.805 65.807 48017 Z= 0.307 Chirality : 0.043 0.267 5232 Planarity : 0.005 0.053 6088 Dihedral : 9.047 174.209 5007 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.76 % Allowed : 19.59 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 4209 helix: 1.04 (0.12), residues: 1889 sheet: -1.26 (0.26), residues: 378 loop : -0.67 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 37 TYR 0.020 0.001 TYR C 211 PHE 0.023 0.001 PHE E 242 TRP 0.012 0.001 TRP G 243 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (35366) covalent geometry : angle 0.60128 / 0.30 (47927) SS BOND : bond 0.00501 / 0.25 ( 3) SS BOND : angle 0.97912 / 0.44 ( 6) hydrogen bonds : bond 0.03810 / 2.45 ( 1468) hydrogen bonds : angle 4.82961 / 3.38 ( 4209) metal coordination : bond 0.01834 / 1.31 ( 37) metal coordination : angle 12.81530 / 7.84 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 782 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8105 (tt) cc_final: 0.7818 (mp) REVERT: A 90 MET cc_start: 0.8340 (mmm) cc_final: 0.7877 (mmt) REVERT: C 74 GLN cc_start: 0.8795 (mt0) cc_final: 0.8144 (pt0) REVERT: D 84 PHE cc_start: 0.7675 (t80) cc_final: 0.7302 (t80) REVERT: D 212 GLU cc_start: 0.8264 (tt0) cc_final: 0.7988 (mt-10) REVERT: D 229 PRO cc_start: 0.8524 (Cg_endo) cc_final: 0.8281 (Cg_exo) REVERT: D 356 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8861 (pp) REVERT: D 360 ASP cc_start: 0.8440 (m-30) cc_final: 0.8187 (t0) REVERT: E 41 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6962 (mtm-85) REVERT: E 124 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7305 (mtpp) REVERT: E 143 ASP cc_start: 0.8636 (t0) cc_final: 0.7929 (t70) REVERT: E 146 SER cc_start: 0.8858 (t) cc_final: 0.8256 (m) REVERT: E 194 ASP cc_start: 0.8609 (t70) cc_final: 0.8284 (t70) REVERT: F 119 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 147 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (tpt170) REVERT: F 405 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7892 (mmp80) REVERT: F 450 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7693 (mmt) REVERT: G 145 MET cc_start: 0.9260 (mmt) cc_final: 0.8823 (mmt) REVERT: G 484 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (p0) REVERT: H 68 MET cc_start: 0.7039 (tpt) cc_final: 0.5166 (ttp) REVERT: H 69 SER cc_start: 0.8766 (m) cc_final: 0.8350 (t) REVERT: H 181 MET cc_start: 0.8294 (mtm) cc_final: 0.8087 (mtm) REVERT: H 261 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7891 (mtp) REVERT: H 271 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9054 (mt) REVERT: H 302 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8107 (mtp) REVERT: I 40 ASN cc_start: 0.9086 (t0) cc_final: 0.8834 (t0) REVERT: I 98 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7630 (mtt-85) REVERT: P 92 MET cc_start: 0.8969 (mmt) cc_final: 0.8525 (mmm) REVERT: P 134 TRP cc_start: 0.8992 (p90) cc_final: 0.8724 (p90) REVERT: P 205 ASP cc_start: 0.7291 (p0) cc_final: 0.6576 (m-30) REVERT: P 233 PHE cc_start: 0.8267 (m-80) cc_final: 0.7980 (m-80) REVERT: P 355 ARG cc_start: 0.7357 (ptp-170) cc_final: 0.6457 (mmt-90) REVERT: Q 78 ARG cc_start: 0.8635 (ttp80) cc_final: 0.7789 (ttp80) REVERT: Q 94 THR cc_start: 0.8898 (m) cc_final: 0.8572 (p) REVERT: Q 146 ASP cc_start: 0.8424 (p0) cc_final: 0.8081 (p0) REVERT: R 45 ARG cc_start: 0.8923 (mtm110) cc_final: 0.8417 (mtp180) REVERT: R 77 ILE cc_start: 0.8899 (tp) cc_final: 0.8619 (tt) REVERT: S 64 LYS cc_start: 0.8815 (mtpp) cc_final: 0.7813 (mtmt) REVERT: S 88 THR cc_start: 0.8067 (m) cc_final: 0.7789 (p) REVERT: S 92 GLN cc_start: 0.8689 (tp40) cc_final: 0.8207 (tp-100) REVERT: T 80 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8387 (ttpt) REVERT: T 104 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7181 (p90) REVERT: T 123 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7885 (mt-10) REVERT: V 33 ASP cc_start: 0.8850 (t0) cc_final: 0.8562 (m-30) REVERT: W 58 THR cc_start: 0.8279 (m) cc_final: 0.7999 (p) REVERT: X 36 CYS cc_start: 0.8164 (m) cc_final: 0.7747 (m) REVERT: X 44 MET cc_start: 0.8234 (tpp) cc_final: 0.7982 (mtt) REVERT: X 56 CYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7178 (m) REVERT: X 102 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6718 (tm-30) REVERT: X 107 PHE cc_start: 0.8125 (t80) cc_final: 0.7678 (t80) REVERT: Z 35 MET cc_start: 0.8775 (ttm) cc_final: 0.8550 (mtp) REVERT: Z 76 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8541 (tp-100) REVERT: Z 79 LYS cc_start: 0.8977 (tttt) cc_final: 0.8607 (tttm) REVERT: Z 98 MET cc_start: 0.4889 (mmp) cc_final: 0.4630 (mtt) REVERT: Z 129 THR cc_start: 0.7953 (m) cc_final: 0.7708 (p) REVERT: a 47 LEU cc_start: 0.9199 (mp) cc_final: 0.8886 (mt) REVERT: a 51 ASP cc_start: 0.7966 (m-30) cc_final: 0.7662 (m-30) REVERT: q 41 GLU cc_start: 0.8248 (tt0) cc_final: 0.7999 (tt0) REVERT: q 42 ASP cc_start: 0.8144 (p0) cc_final: 0.7931 (p0) REVERT: q 47 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8557 (mtpp) REVERT: q 68 MET cc_start: 0.8884 (ttt) cc_final: 0.8595 (ttt) REVERT: q 136 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8571 (mp0) REVERT: r 30 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8129 (pm20) outliers start: 139 outliers final: 90 residues processed: 864 average time/residue: 0.2063 time to fit residues: 289.6399 Evaluate side-chains 826 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 723 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 152 GLN Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 258 ASN Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 76 ASP Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 148 optimal weight: 0.9980 chunk 367 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 chunk 334 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 374 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 122 ASN E 152 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 GLN ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099924 restraints weight = 55343.433| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.82 r_work: 0.3123 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 35406 Z= 0.167 Angle : 0.822 66.567 48017 Z= 0.317 Chirality : 0.043 0.212 5232 Planarity : 0.005 0.070 6088 Dihedral : 9.005 174.196 5007 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.60 % Allowed : 19.94 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.13), residues: 4209 helix: 1.09 (0.12), residues: 1888 sheet: -1.30 (0.26), residues: 386 loop : -0.66 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 159 TYR 0.030 0.002 TYR I 76 PHE 0.025 0.002 PHE E 242 TRP 0.010 0.001 TRP G 243 HIS 0.006 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (35366) covalent geometry : angle 0.62148 / 0.31 (47927) SS BOND : bond 0.00688 / 0.34 ( 3) SS BOND : angle 1.02904 / 0.46 ( 6) hydrogen bonds : bond 0.03873 / 2.48 ( 1468) hydrogen bonds : angle 4.84681 / 3.39 ( 4209) metal coordination : bond 0.02118 / 1.49 ( 37) metal coordination : angle 12.88664 / 7.86 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 737 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8070 (tt) cc_final: 0.7780 (mp) REVERT: A 90 MET cc_start: 0.8331 (mmm) cc_final: 0.7869 (mmt) REVERT: B 219 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8331 (ttpp) REVERT: C 74 GLN cc_start: 0.8823 (mt0) cc_final: 0.8134 (pt0) REVERT: D 84 PHE cc_start: 0.7664 (t80) cc_final: 0.7282 (t80) REVERT: D 105 MET cc_start: 0.5897 (ttm) cc_final: 0.5671 (tpp) REVERT: D 107 ARG cc_start: 0.8493 (mmt180) cc_final: 0.7929 (mmt-90) REVERT: D 212 GLU cc_start: 0.8325 (tt0) cc_final: 0.8001 (mt-10) REVERT: D 229 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8377 (Cg_exo) REVERT: D 356 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8887 (pp) REVERT: D 360 ASP cc_start: 0.8435 (m-30) cc_final: 0.8143 (t0) REVERT: E 41 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6941 (mtm-85) REVERT: E 124 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7281 (mtpp) REVERT: E 143 ASP cc_start: 0.8680 (t0) cc_final: 0.7955 (t70) REVERT: E 146 SER cc_start: 0.8851 (t) cc_final: 0.8232 (m) REVERT: E 221 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7737 (ttp80) REVERT: F 147 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8648 (tpt170) REVERT: F 351 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9131 (t) REVERT: F 450 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7692 (mmt) REVERT: G 145 MET cc_start: 0.9286 (mmt) cc_final: 0.8893 (mmt) REVERT: G 329 MET cc_start: 0.8479 (tpt) cc_final: 0.8236 (tpp) REVERT: G 484 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8236 (p0) REVERT: H 68 MET cc_start: 0.7040 (tpt) cc_final: 0.5144 (ttp) REVERT: H 69 SER cc_start: 0.8672 (m) cc_final: 0.8276 (t) REVERT: H 143 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7499 (mt-10) REVERT: H 215 TYR cc_start: 0.8313 (m-80) cc_final: 0.7768 (m-80) REVERT: H 234 MET cc_start: 0.8977 (mmt) cc_final: 0.8525 (mmt) REVERT: H 261 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7907 (mpp) REVERT: I 40 ASN cc_start: 0.9131 (t0) cc_final: 0.8858 (t0) REVERT: I 98 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7631 (mtt-85) REVERT: P 134 TRP cc_start: 0.9030 (p90) cc_final: 0.8778 (p90) REVERT: P 205 ASP cc_start: 0.7325 (p0) cc_final: 0.6649 (m-30) REVERT: P 233 PHE cc_start: 0.8262 (m-80) cc_final: 0.7972 (m-80) REVERT: P 355 ARG cc_start: 0.7335 (ptp-170) cc_final: 0.6398 (mmt-90) REVERT: Q 94 THR cc_start: 0.8915 (m) cc_final: 0.8562 (p) REVERT: Q 146 ASP cc_start: 0.8433 (p0) cc_final: 0.8166 (p0) REVERT: R 45 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8417 (mtp180) REVERT: R 77 ILE cc_start: 0.8905 (tp) cc_final: 0.8612 (tt) REVERT: S 64 LYS cc_start: 0.8843 (mtpp) cc_final: 0.7826 (mtmt) REVERT: S 83 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8007 (p) REVERT: S 88 THR cc_start: 0.7981 (m) cc_final: 0.7708 (p) REVERT: S 92 GLN cc_start: 0.8743 (tp40) cc_final: 0.8401 (tp-100) REVERT: T 80 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8377 (ttpt) REVERT: T 104 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6974 (p90) REVERT: T 108 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6561 (tt) REVERT: T 123 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7922 (mt-10) REVERT: V 33 ASP cc_start: 0.8895 (t0) cc_final: 0.8590 (m-30) REVERT: W 58 THR cc_start: 0.8378 (m) cc_final: 0.8071 (p) REVERT: X 36 CYS cc_start: 0.8141 (m) cc_final: 0.7736 (m) REVERT: X 56 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7293 (m) REVERT: X 102 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6741 (tm-30) REVERT: X 104 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8256 (tm-30) REVERT: X 107 PHE cc_start: 0.8116 (t80) cc_final: 0.7653 (t80) REVERT: Z 35 MET cc_start: 0.8766 (ttm) cc_final: 0.8545 (mtp) REVERT: Z 76 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8539 (tp-100) REVERT: Z 79 LYS cc_start: 0.8982 (tttt) cc_final: 0.8605 (tttm) REVERT: Z 98 MET cc_start: 0.4867 (mmp) cc_final: 0.4618 (mtt) REVERT: Z 129 THR cc_start: 0.7965 (m) cc_final: 0.7741 (p) REVERT: a 47 LEU cc_start: 0.9210 (mp) cc_final: 0.8889 (mt) REVERT: a 51 ASP cc_start: 0.8039 (m-30) cc_final: 0.7717 (m-30) REVERT: q 42 ASP cc_start: 0.8113 (p0) cc_final: 0.7893 (p0) REVERT: q 47 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8534 (mtpp) REVERT: q 68 MET cc_start: 0.8885 (ttt) cc_final: 0.8589 (ttt) REVERT: q 122 GLU cc_start: 0.7942 (mp0) cc_final: 0.7692 (mp0) REVERT: q 136 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8614 (mp0) REVERT: r 30 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: r 60 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7110 (ttp-170) REVERT: r 105 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8380 (mm-30) outliers start: 133 outliers final: 103 residues processed: 819 average time/residue: 0.2191 time to fit residues: 290.1081 Evaluate side-chains 834 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 716 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 484 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain W residue 24 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 20 ASP Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 133 MET Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 76 ASP Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 60 ARG Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 370 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 310 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS E 152 GLN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 ASN G 202 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101715 restraints weight = 55267.046| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.84 r_work: 0.3146 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 35406 Z= 0.134 Angle : 0.812 67.473 48017 Z= 0.311 Chirality : 0.042 0.187 5232 Planarity : 0.005 0.067 6088 Dihedral : 8.847 175.545 5007 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.38 % Allowed : 19.97 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4209 helix: 1.15 (0.12), residues: 1891 sheet: -1.35 (0.25), residues: 394 loop : -0.65 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 37 TYR 0.023 0.001 TYR P 241 PHE 0.027 0.001 PHE E 242 TRP 0.012 0.001 TRP b 26 HIS 0.005 0.001 HIS F 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (35366) covalent geometry : angle 0.61338 / 0.31 (47927) SS BOND : bond 0.00469 / 0.23 ( 3) SS BOND : angle 0.98008 / 0.44 ( 6) hydrogen bonds : bond 0.03723 / 2.39 ( 1468) hydrogen bonds : angle 4.77790 / 3.34 ( 4209) metal coordination : bond 0.01687 / 1.21 ( 37) metal coordination : angle 12.73487 / 7.72 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 756 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8019 (tt) cc_final: 0.7770 (mp) REVERT: A 90 MET cc_start: 0.8297 (mmm) cc_final: 0.7849 (mmt) REVERT: C 74 GLN cc_start: 0.8763 (mt0) cc_final: 0.8134 (pt0) REVERT: D 84 PHE cc_start: 0.7651 (t80) cc_final: 0.7268 (t80) REVERT: D 105 MET cc_start: 0.5885 (ttm) cc_final: 0.5669 (tpp) REVERT: D 107 ARG cc_start: 0.8434 (mmt180) cc_final: 0.7920 (mmt-90) REVERT: D 212 GLU cc_start: 0.8275 (tt0) cc_final: 0.7960 (mt-10) REVERT: D 229 PRO cc_start: 0.8571 (Cg_endo) cc_final: 0.8361 (Cg_exo) REVERT: D 356 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8873 (pp) REVERT: D 360 ASP cc_start: 0.8362 (m-30) cc_final: 0.8098 (t0) REVERT: E 41 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6983 (mtm-85) REVERT: E 124 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7309 (mtpp) REVERT: E 143 ASP cc_start: 0.8642 (t0) cc_final: 0.7902 (t70) REVERT: E 146 SER cc_start: 0.8767 (t) cc_final: 0.8196 (m) REVERT: E 221 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7537 (ttp80) REVERT: F 147 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8509 (tpt170) REVERT: F 351 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9124 (t) REVERT: F 450 MET cc_start: 0.8630 (mmt) cc_final: 0.7735 (mmt) REVERT: G 145 MET cc_start: 0.9280 (mmt) cc_final: 0.8874 (mmt) REVERT: H 68 MET cc_start: 0.6996 (tpt) cc_final: 0.5151 (ttp) REVERT: H 69 SER cc_start: 0.8688 (m) cc_final: 0.8288 (t) REVERT: H 215 TYR cc_start: 0.8228 (m-80) cc_final: 0.7717 (m-80) REVERT: H 225 MET cc_start: 0.9110 (mtm) cc_final: 0.8910 (mtp) REVERT: H 234 MET cc_start: 0.8965 (mmt) cc_final: 0.8563 (mmt) REVERT: H 261 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7929 (mtp) REVERT: I 40 ASN cc_start: 0.9095 (t0) cc_final: 0.8829 (t0) REVERT: I 98 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7589 (mtt-85) REVERT: P 134 TRP cc_start: 0.9014 (p90) cc_final: 0.8768 (p90) REVERT: P 205 ASP cc_start: 0.7324 (p0) cc_final: 0.6664 (m-30) REVERT: P 233 PHE cc_start: 0.8271 (m-80) cc_final: 0.8006 (m-80) REVERT: P 355 ARG cc_start: 0.7313 (ptp-170) cc_final: 0.6362 (mmt-90) REVERT: Q 78 ARG cc_start: 0.8664 (ttp80) cc_final: 0.7775 (ttp80) REVERT: Q 94 THR cc_start: 0.8915 (m) cc_final: 0.8557 (p) REVERT: Q 146 ASP cc_start: 0.8393 (p0) cc_final: 0.8105 (p0) REVERT: R 45 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8383 (mtp180) REVERT: R 77 ILE cc_start: 0.8894 (tp) cc_final: 0.8588 (tt) REVERT: S 64 LYS cc_start: 0.8789 (mtpp) cc_final: 0.7871 (mtmt) REVERT: S 83 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7936 (p) REVERT: S 88 THR cc_start: 0.7994 (m) cc_final: 0.7747 (p) REVERT: T 80 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8213 (ttpt) REVERT: T 104 PHE cc_start: 0.7371 (OUTLIER) cc_final: 0.6812 (p90) REVERT: V 33 ASP cc_start: 0.8867 (t0) cc_final: 0.8509 (m-30) REVERT: W 58 THR cc_start: 0.8335 (m) cc_final: 0.8025 (p) REVERT: W 126 TYR cc_start: 0.9056 (m-80) cc_final: 0.8745 (m-10) REVERT: X 36 CYS cc_start: 0.8165 (m) cc_final: 0.7771 (m) REVERT: X 56 CYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7192 (m) REVERT: X 102 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6713 (tm-30) REVERT: X 104 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8255 (tm-30) REVERT: X 107 PHE cc_start: 0.8126 (t80) cc_final: 0.7888 (t80) REVERT: Z 35 MET cc_start: 0.8761 (ttm) cc_final: 0.8559 (mtp) REVERT: Z 76 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8459 (tp-100) REVERT: Z 79 LYS cc_start: 0.8941 (tttt) cc_final: 0.8585 (tttm) REVERT: Z 94 GLU cc_start: 0.8623 (tt0) cc_final: 0.7998 (tp30) REVERT: Z 98 MET cc_start: 0.4838 (mmp) cc_final: 0.4634 (mmp) REVERT: a 47 LEU cc_start: 0.9200 (mp) cc_final: 0.8866 (mt) REVERT: a 51 ASP cc_start: 0.8040 (m-30) cc_final: 0.7716 (m-30) REVERT: b 74 LEU cc_start: 0.8173 (mt) cc_final: 0.7937 (tp) REVERT: q 28 PHE cc_start: 0.8742 (m-80) cc_final: 0.8412 (m-10) REVERT: q 68 MET cc_start: 0.8852 (ttt) cc_final: 0.8455 (ttt) REVERT: q 78 ASP cc_start: 0.7863 (p0) cc_final: 0.7580 (p0) REVERT: q 122 GLU cc_start: 0.7808 (mp0) cc_final: 0.7353 (mp0) REVERT: r 30 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: r 105 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8372 (mm-30) outliers start: 125 outliers final: 96 residues processed: 832 average time/residue: 0.2213 time to fit residues: 298.5135 Evaluate side-chains 816 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 709 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 95 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain X residue 56 CYS Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 106 optimal weight: 0.9980 chunk 405 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 367 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 412 optimal weight: 9.9990 chunk 190 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN E 40 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101543 restraints weight = 55282.306| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.77 r_work: 0.3132 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35406 Z= 0.143 Angle : 0.824 67.761 48017 Z= 0.319 Chirality : 0.043 0.319 5232 Planarity : 0.005 0.095 6088 Dihedral : 8.805 174.292 5007 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.14 % Allowed : 20.29 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 4209 helix: 1.15 (0.12), residues: 1891 sheet: -1.27 (0.25), residues: 396 loop : -0.64 (0.14), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 135 TYR 0.032 0.001 TYR I 76 PHE 0.027 0.001 PHE E 242 TRP 0.020 0.001 TRP H 86 HIS 0.004 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (35366) covalent geometry : angle 0.62993 / 0.32 (47927) SS BOND : bond 0.00302 / 0.15 ( 3) SS BOND : angle 1.22141 / 0.52 ( 6) hydrogen bonds : bond 0.03787 / 2.43 ( 1468) hydrogen bonds : angle 4.79613 / 3.36 ( 4209) metal coordination : bond 0.01811 / 1.27 ( 37) metal coordination : angle 12.69785 / 7.68 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8418 Ramachandran restraints generated. 4209 Oldfield, 0 Emsley, 4209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 720 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8099 (tt) cc_final: 0.7888 (mp) REVERT: A 90 MET cc_start: 0.8083 (mmm) cc_final: 0.7629 (mmt) REVERT: C 74 GLN cc_start: 0.8656 (mt0) cc_final: 0.8087 (pt0) REVERT: D 84 PHE cc_start: 0.7617 (t80) cc_final: 0.7211 (t80) REVERT: D 107 ARG cc_start: 0.8436 (mmt180) cc_final: 0.7931 (mmt-90) REVERT: D 212 GLU cc_start: 0.8194 (tt0) cc_final: 0.7951 (mt-10) REVERT: D 229 PRO cc_start: 0.8475 (Cg_endo) cc_final: 0.8270 (Cg_exo) REVERT: D 261 MET cc_start: 0.8827 (tpp) cc_final: 0.8535 (tpp) REVERT: D 360 ASP cc_start: 0.8387 (m-30) cc_final: 0.8127 (t0) REVERT: E 41 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6995 (mtm-85) REVERT: E 124 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7383 (mtpp) REVERT: E 143 ASP cc_start: 0.8593 (t0) cc_final: 0.7855 (t70) REVERT: E 146 SER cc_start: 0.8774 (t) cc_final: 0.8210 (m) REVERT: E 218 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6526 (ttm110) REVERT: F 147 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8416 (tpt170) REVERT: F 450 MET cc_start: 0.8591 (mmt) cc_final: 0.7736 (mmt) REVERT: G 145 MET cc_start: 0.9256 (mmt) cc_final: 0.8883 (mmt) REVERT: G 215 MET cc_start: 0.7597 (ptm) cc_final: 0.7343 (ptm) REVERT: H 68 MET cc_start: 0.6937 (tpt) cc_final: 0.5162 (ttp) REVERT: H 69 SER cc_start: 0.8627 (m) cc_final: 0.8249 (t) REVERT: H 215 TYR cc_start: 0.8222 (m-80) cc_final: 0.7706 (m-80) REVERT: H 261 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: I 40 ASN cc_start: 0.9066 (t0) cc_final: 0.8850 (t0) REVERT: I 98 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: P 134 TRP cc_start: 0.9005 (p90) cc_final: 0.8762 (p90) REVERT: P 205 ASP cc_start: 0.7320 (p0) cc_final: 0.6718 (m-30) REVERT: P 233 PHE cc_start: 0.8272 (m-80) cc_final: 0.8031 (m-80) REVERT: P 355 ARG cc_start: 0.7289 (ptp-170) cc_final: 0.6417 (mmt-90) REVERT: Q 78 ARG cc_start: 0.8638 (ttp80) cc_final: 0.7825 (ttp80) REVERT: Q 94 THR cc_start: 0.8918 (m) cc_final: 0.8596 (p) REVERT: Q 146 ASP cc_start: 0.8295 (p0) cc_final: 0.8024 (p0) REVERT: R 45 ARG cc_start: 0.8987 (mtm110) cc_final: 0.8500 (mtp180) REVERT: R 77 ILE cc_start: 0.8928 (tp) cc_final: 0.8626 (tt) REVERT: S 64 LYS cc_start: 0.8832 (mtpp) cc_final: 0.7874 (mtmt) REVERT: S 88 THR cc_start: 0.8104 (m) cc_final: 0.7847 (p) REVERT: T 80 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8343 (ttpt) REVERT: T 104 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6469 (p90) REVERT: V 33 ASP cc_start: 0.8819 (t0) cc_final: 0.8500 (m-30) REVERT: W 58 THR cc_start: 0.8291 (m) cc_final: 0.8020 (p) REVERT: X 36 CYS cc_start: 0.8125 (m) cc_final: 0.7801 (m) REVERT: X 102 GLN cc_start: 0.7205 (tm-30) cc_final: 0.6720 (tm-30) REVERT: X 104 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8278 (tm-30) REVERT: X 107 PHE cc_start: 0.8147 (t80) cc_final: 0.7943 (t80) REVERT: Z 79 LYS cc_start: 0.8922 (tttt) cc_final: 0.8564 (tttm) REVERT: Z 94 GLU cc_start: 0.8494 (tt0) cc_final: 0.7959 (tp30) REVERT: Z 98 MET cc_start: 0.4839 (mmp) cc_final: 0.4638 (mmp) REVERT: a 47 LEU cc_start: 0.9206 (mp) cc_final: 0.8877 (mt) REVERT: a 51 ASP cc_start: 0.8007 (m-30) cc_final: 0.7687 (m-30) REVERT: b 74 LEU cc_start: 0.8164 (mt) cc_final: 0.7947 (tp) REVERT: q 28 PHE cc_start: 0.8727 (m-80) cc_final: 0.8420 (m-10) REVERT: q 78 ASP cc_start: 0.7866 (p0) cc_final: 0.7612 (p0) REVERT: q 122 GLU cc_start: 0.7704 (mp0) cc_final: 0.7298 (mp0) REVERT: r 30 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: r 60 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7020 (ttp-170) REVERT: r 105 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8475 (mm-30) outliers start: 116 outliers final: 94 residues processed: 792 average time/residue: 0.2284 time to fit residues: 292.9331 Evaluate side-chains 806 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 704 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 124 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 271 SER Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 264 SER Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 289 ILE Chi-restraints excluded: chain P residue 300 TRP Chi-restraints excluded: chain P residue 325 SER Chi-restraints excluded: chain P residue 340 VAL Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain T residue 91 ASP Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain W residue 122 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 GLU Chi-restraints excluded: chain X residue 111 VAL Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain b residue 36 SER Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 30 GLU Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 60 ARG Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 67 SER Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 239 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 362 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 411 optimal weight: 0.8980 chunk 366 optimal weight: 0.6980 chunk 325 optimal weight: 8.9990 chunk 377 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 GLN Z 76 GLN q 12 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102026 restraints weight = 54927.351| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.75 r_work: 0.3139 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 35406 Z= 0.135 Angle : 0.817 68.033 48017 Z= 0.315 Chirality : 0.044 0.362 5232 Planarity : 0.005 0.095 6088 Dihedral : 8.765 173.643 5007 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.98 % Allowed : 20.59 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.13), residues: 4209 helix: 1.19 (0.12), residues: 1893 sheet: -1.16 (0.26), residues: 382 loop : -0.63 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 79 TYR 0.025 0.001 TYR I 76 PHE 0.028 0.001 PHE E 242 TRP 0.016 0.001 TRP H 86 HIS 0.004 0.001 HIS F 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (35366) covalent geometry : angle 0.62216 / 0.31 (47927) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 1.14311 / 0.49 ( 6) hydrogen bonds : bond 0.03732 / 2.39 ( 1468) hydrogen bonds : angle 4.76687 / 3.34 ( 4209) metal coordination : bond 0.01690 / 1.18 ( 37) metal coordination : angle 12.66041 / 7.65 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11203.42 seconds wall clock time: 192 minutes 3.52 seconds (11523.52 seconds total)