Starting phenix.real_space_refine on Tue May 5 22:25:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic3_35353/05_2026/8ic3_35353_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic3_35353/05_2026/8ic3_35353.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/8ic3_35353/05_2026/8ic3_35353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic3_35353/05_2026/8ic3_35353.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic3_35353/05_2026/8ic3_35353_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic3_35353/05_2026/8ic3_35353_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= 0.005 sd= 0.077 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 11 5.49 5 S 245 5.16 5 C 21718 2.51 5 N 5768 2.21 5 O 6163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33934 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 737 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} 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: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3273 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 21, 'TRANS': 402} 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: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2531 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 22, 'TRANS': 294} Chain breaks: 1 Chain: "I" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1389 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 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: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1020 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 9, 'TRANS': 112} Chain breaks: 1 Chain: "r" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 3, 'TRANS': 25} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'3PE': 2, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 989 SG CYS B 99 79.478 61.343 106.554 1.00 29.52 S ATOM 1492 SG CYS B 164 77.279 56.542 111.106 1.00 28.96 S ATOM 1722 SG CYS B 194 82.437 56.512 110.374 1.00 29.28 S ATOM 995 SG CYS B 100 78.780 56.648 104.821 1.00 30.11 S ATOM 7502 SG CYS E 134 139.373 51.993 153.065 1.00 56.01 S ATOM 7536 SG CYS E 139 142.226 53.193 152.759 1.00 56.50 S ATOM 7843 SG CYS E 179 140.566 57.319 156.312 1.00 57.95 S ATOM 10997 SG CYS F 379 118.413 55.308 155.251 1.00 43.09 S ATOM 11016 SG CYS F 382 116.296 59.573 151.731 1.00 40.29 S ATOM 11036 SG CYS F 385 120.713 58.344 150.196 1.00 39.95 S ATOM 11358 SG CYS F 425 120.573 60.716 156.032 1.00 45.60 S ATOM 12406 SG CYS G 131 100.551 48.188 138.546 1.00 31.31 S ATOM 12385 SG CYS G 128 102.538 52.153 134.044 1.00 30.26 S ATOM 12446 SG CYS G 137 100.097 54.057 140.079 1.00 33.13 S ATOM 13131 SG CYS G 226 101.997 48.054 147.147 1.00 34.31 S ATOM 12802 SG CYS G 182 105.112 46.323 152.900 1.00 36.31 S ATOM 12778 SG CYS G 179 104.416 51.939 150.461 1.00 35.62 S ATOM 12755 SG CYS G 176 107.962 47.784 147.944 1.00 34.05 S ATOM 11892 SG CYS G 64 105.592 58.439 153.693 1.00 35.53 S ATOM 11978 SG CYS G 75 106.291 59.781 150.942 1.00 36.47 S ATOM 12003 SG CYS G 78 105.402 64.216 152.992 1.00 36.76 S ATOM 12104 SG CYS G 92 104.972 62.466 156.317 1.00 39.04 S ATOM 20116 SG CYS I 123 85.547 51.440 120.080 1.00 27.30 S ATOM 20342 SG CYS I 152 86.073 50.289 113.677 1.00 27.39 S ATOM 20389 SG CYS I 158 91.836 50.568 116.540 1.00 26.60 S ATOM 20368 SG CYS I 155 89.074 55.358 116.419 1.00 27.04 S ATOM 20065 SG CYS I 116 96.174 47.402 126.933 1.00 29.24 S ATOM 20088 SG CYS I 119 92.166 47.017 123.169 1.00 28.85 S ATOM 20046 SG CYS I 113 95.175 42.312 123.547 1.00 28.61 S ATOM 20418 SG CYS I 162 98.008 47.013 121.582 1.00 28.07 S ATOM 24917 SG CYS R 79 111.759 40.325 126.275 1.00 32.60 S ATOM 25093 SG CYS R 104 109.305 38.831 127.657 1.00 32.49 S ATOM 25115 SG CYS R 107 108.684 39.516 124.228 1.00 30.78 S Time building chain proxies: 6.85, per 1000 atoms: 0.20 Number of scatterers: 33934 At special positions: 0 Unit cell: (166, 128.65, 203.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 245 16.00 P 11 15.00 O 6163 8.00 N 5768 7.00 C 21718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.36 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 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: 3.37 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE3 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="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " 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=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7840 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 35 sheets defined 50.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.548A pdb=" N ALA B 128 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.591A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.602A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A 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 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.773A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.861A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.706A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 262 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.528A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.619A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.525A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 84 removed outlier: 3.602A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Proline residue: F 73 - end of helix Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.234A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.649A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.846A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.711A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 168 " --> pdb=" O ASN F 164 " (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: 3.832A 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 258 removed outlier: 3.601A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 265 removed outlier: 3.919A pdb=" N PHE F 262 " --> pdb=" O GLY F 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.061A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.660A 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: 4.349A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.713A 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 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.931A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 297 No H-bonds generated for 'chain 'G' and resid 295 through 297' Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 395 removed outlier: 4.190A pdb=" N GLU G 395 " --> pdb=" O ILE G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 458 removed outlier: 4.287A pdb=" N GLN G 453 " --> pdb=" O PRO G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 removed outlier: 4.114A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.522A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.573A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 86 Proline residue: H 75 - end of helix removed outlier: 3.625A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 4.465A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.553A 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: 3.736A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 removed outlier: 3.908A pdb=" N GLY H 203 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 removed outlier: 3.548A pdb=" N VAL H 213 " --> pdb=" O GLY H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.932A 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 63 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.620A pdb=" N GLY I 69 " --> pdb=" O GLU I 65 " (cutoff:3.500A) 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: 3.865A 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: 5.145A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.783A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.900A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 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: 3.624A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 219 removed outlier: 4.163A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA P 218 " --> pdb=" O LEU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 223 Processing helix chain 'P' and resid 229 through 233 Processing helix chain 'P' and resid 242 through 255 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.622A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 323 Processing helix chain 'P' and resid 335 through 339 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: 5.689A 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 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.550A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.446A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.810A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.585A 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: 3.929A 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: 3.528A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.623A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 53 through 55 No H-bonds generated for 'chain 'X' and resid 53 through 55' Processing helix chain 'X' and resid 56 through 77 removed outlier: 3.814A pdb=" N ALA X 67 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN X 69 " --> pdb=" O GLY X 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE X 70 " --> pdb=" O CYS X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.905A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.634A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.537A 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: 3.759A 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: 3.551A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.602A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.537A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.127A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 43 through 53 Processing helix chain 's' and resid 54 through 56 No H-bonds generated for 'chain 's' and resid 54 through 56' Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.066A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 74 removed outlier: 3.522A 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: 6.045A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.874A 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: 7.149A 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: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.616A pdb=" N MET D 80 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.309A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 397 through 401 Processing sheet with id=AB1, first strand: chain 'E' and resid 171 through 173 removed outlier: 3.701A pdb=" N CYS E 134 " --> pdb=" O MET E 184 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 199 removed outlier: 7.392A pdb=" N ARG F 152 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE F 196 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS F 111 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N TYR F 155 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 286 through 287 removed outlier: 6.347A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 294 through 295 removed outlier: 4.075A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.730A pdb=" N VAL G 34 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AB7, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'G' and resid 246 through 251 removed outlier: 8.152A pdb=" N ASN G 260 " --> pdb=" O PRO G 275 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL G 262 " --> pdb=" O ILE G 273 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE G 273 " --> pdb=" O VAL G 262 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N SER G 264 " --> pdb=" O MET G 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 299 through 301 removed outlier: 5.944A pdb=" N HIS q 135 " --> pdb=" O ARG G 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.093A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU G 548 " --> pdb=" O ALA G 339 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE G 341 " --> pdb=" O LEU G 548 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.204A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.516A 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=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.408A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.226A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL P 126 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL P 167 " --> pdb=" O VAL P 126 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN P 128 " --> pdb=" O VAL P 167 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.217A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 226 through 227 removed outlier: 5.711A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 76 through 79 removed outlier: 4.032A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD8, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.239A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1435 hydrogen bonds defined for protein. 4140 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: 6.38 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.35: 11003 1.35 - 1.58: 23253 1.58 - 1.80: 205 1.80 - 2.02: 205 2.02 - 2.24: 80 Bond restraints: 34746 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.646 0.732 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C ALA E 227 " pdb=" O ALA E 227 " ideal model delta sigma weight residual 1.236 1.420 -0.184 1.16e-02 7.43e+03 2.51e+02 bond pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 1.473 1.261 0.212 1.40e-02 5.10e+03 2.29e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.284 0.189 1.40e-02 5.10e+03 1.82e+02 bond pdb=" N PRO P 371 " pdb=" CD PRO P 371 " ideal model delta sigma weight residual 1.473 1.654 -0.181 1.40e-02 5.10e+03 1.67e+02 ... (remaining 34741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.68: 46390 6.68 - 13.36: 521 13.36 - 20.03: 170 20.03 - 26.71: 4 26.71 - 33.39: 2 Bond angle restraints: 47087 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.46 -21.81 1.13e+00 7.83e-01 3.73e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.53 17.89 9.40e-01 1.13e+00 3.62e+02 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 111.02 130.04 -19.02 1.22e+00 6.72e-01 2.43e+02 angle pdb=" N GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta sigma weight residual 110.50 135.18 -24.68 1.70e+00 3.46e-01 2.11e+02 ... (remaining 47082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.60: 20388 29.60 - 59.20: 525 59.20 - 88.80: 54 88.80 - 118.40: 6 118.40 - 148.00: 5 Dihedral angle restraints: 20978 sinusoidal: 8817 harmonic: 12161 Sorted by residual: dihedral pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual 122.80 167.13 -44.33 0 2.50e+00 1.60e-01 3.14e+02 dihedral pdb=" C GLU r 91 " pdb=" N GLU r 91 " pdb=" CA GLU r 91 " pdb=" CB GLU r 91 " ideal model delta harmonic sigma weight residual -122.60 -162.72 40.12 0 2.50e+00 1.60e-01 2.58e+02 dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.21 -21.39 0 2.50e+00 1.60e-01 7.32e+01 ... (remaining 20975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.348: 5069 0.348 - 0.696: 55 0.696 - 1.044: 24 1.044 - 1.392: 0 1.392 - 1.740: 1 Chirality restraints: 5149 Sorted by residual: chirality pdb=" CA GLU r 91 " pdb=" N GLU r 91 " pdb=" C GLU r 91 " pdb=" CB GLU r 91 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.57e+01 chirality pdb="FE4 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " 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="FE2 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5146 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " 0.054 2.00e-02 2.50e+03 2.68e-01 2.16e+03 pdb=" C1M UQ9 H 401 " 0.316 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.096 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " 0.076 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " -0.077 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " 0.103 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " -0.048 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " -0.328 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.378 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " 0.396 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " -0.407 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " 0.391 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 401 " 0.151 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C11 UQ9 H 401 " 0.122 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.342 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 401 " -0.511 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 401 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 H 401 " -0.233 2.00e-02 2.50e+03 1.97e-01 4.83e+02 pdb=" C13 UQ9 H 401 " 0.326 2.00e-02 2.50e+03 pdb=" C14 UQ9 H 401 " 0.071 2.00e-02 2.50e+03 pdb=" C15 UQ9 H 401 " 0.001 2.00e-02 2.50e+03 pdb=" C16 UQ9 H 401 " -0.165 2.00e-02 2.50e+03 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 46 2.34 - 2.98: 21125 2.98 - 3.62: 52811 3.62 - 4.26: 84767 4.26 - 4.90: 137606 Nonbonded interactions: 296355 Sorted by model distance: nonbonded pdb=" O ASN F 270 " pdb=" OD1 ASN F 270 " model vdw 1.702 3.040 nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.903 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.980 3.120 ... (remaining 296350 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: 11.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 36.830 Find NCS groups from input model: 0.160 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 1.141 34787 Z= 1.015 Angle : 2.171 41.471 47179 Z= 1.451 Chirality : 0.125 1.740 5149 Planarity : 0.009 0.292 5980 Dihedral : 13.172 148.000 13126 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 41.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 0.22 % Allowed : 7.02 % Favored : 92.76 % Cbeta Deviations : 1.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4138 helix: -0.67 (0.11), residues: 1795 sheet: -1.09 (0.30), residues: 313 loop : -2.11 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.047 0.002 TYR B 112 PHE 0.051 0.002 PHE a 3 TRP 0.036 0.002 TRP G 285 HIS 0.012 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01455 (34746) covalent geometry : angle 2.05538 (47087) SS BOND : bond 0.16653 ( 4) SS BOND : angle 4.96999 ( 8) hydrogen bonds : bond 0.23951 ( 1435) hydrogen bonds : angle 8.83546 ( 4140) metal coordination : bond 0.45800 ( 37) metal coordination : angle 16.65953 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1517 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 MET cc_start: 0.8416 (tpp) cc_final: 0.8128 (tpp) REVERT: E 152 GLN cc_start: 0.6852 (mt0) cc_final: 0.6467 (mt0) REVERT: F 390 ASP cc_start: 0.6571 (t0) cc_final: 0.6341 (t0) REVERT: G 192 VAL cc_start: 0.7938 (t) cc_final: 0.7713 (t) REVERT: G 318 SER cc_start: 0.8077 (t) cc_final: 0.7636 (p) REVERT: G 561 PRO cc_start: 0.5371 (Cg_exo) cc_final: 0.4765 (Cg_endo) REVERT: I 120 GLU cc_start: 0.7726 (tt0) cc_final: 0.7391 (tt0) REVERT: P 301 ILE cc_start: 0.8046 (mm) cc_final: 0.7770 (mm) REVERT: S 55 ILE cc_start: 0.8284 (mm) cc_final: 0.7929 (mm) REVERT: T 92 LYS cc_start: 0.7725 (tttm) cc_final: 0.6942 (tmtt) REVERT: W 27 ASP cc_start: 0.7199 (p0) cc_final: 0.6943 (p0) REVERT: W 69 MET cc_start: 0.7362 (mmt) cc_final: 0.7152 (mmt) REVERT: Z 91 LEU cc_start: 0.6657 (tm) cc_final: 0.6355 (tp) REVERT: a 3 PHE cc_start: 0.5870 (m-10) cc_final: 0.5433 (m-10) REVERT: r 25 GLN cc_start: 0.5141 (tp-100) cc_final: 0.4884 (pm20) outliers start: 8 outliers final: 1 residues processed: 1523 average time/residue: 0.2224 time to fit residues: 531.8722 Evaluate side-chains 853 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 852 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 103 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 179 ASN C 180 HIS D 79 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS D 131 GLN D 147 ASN D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS E 68 ASN E 245 GLN F 168 ASN ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 424 HIS G 444 HIS G 495 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN G 676 ASN H 47 GLN H 169 GLN H 292 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 GLN I 159 GLN P 71 ASN P 166 HIS P 323 HIS Q 51 GLN Q 167 ASN R 56 ASN S 39 GLN ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 HIS W 54 GLN X 104 GLN X 124 GLN X 140 ASN Z 55 GLN Z 103 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 HIS q 31 ASN q 54 GLN q 87 HIS q 91 HIS r 21 GLN r 25 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.128844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101791 restraints weight = 69861.313| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.41 r_work: 0.3414 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 34787 Z= 0.246 Angle : 0.984 50.231 47179 Z= 0.429 Chirality : 0.050 0.233 5149 Planarity : 0.006 0.088 5980 Dihedral : 10.343 168.041 4871 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.69 % Allowed : 16.32 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 4138 helix: 0.38 (0.12), residues: 1866 sheet: -1.26 (0.28), residues: 343 loop : -1.41 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 107 TYR 0.032 0.002 TYR a 60 PHE 0.031 0.003 PHE P 64 TRP 0.019 0.002 TRP V 114 HIS 0.009 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00571 (34746) covalent geometry : angle 0.81990 (47087) SS BOND : bond 0.01048 ( 4) SS BOND : angle 6.43405 ( 8) hydrogen bonds : bond 0.05994 ( 1435) hydrogen bonds : angle 5.73571 ( 4140) metal coordination : bond 0.03171 ( 37) metal coordination : angle 12.76663 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 885 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.8803 (mm) cc_final: 0.8586 (mm) REVERT: B 141 MET cc_start: 0.9014 (tpp) cc_final: 0.8740 (tpp) REVERT: C 148 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: D 79 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6946 (m-40) REVERT: D 144 MET cc_start: 0.7663 (mpp) cc_final: 0.6944 (mpp) REVERT: D 263 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8713 (m) REVERT: D 298 ILE cc_start: 0.8890 (mt) cc_final: 0.8686 (mm) REVERT: D 458 PHE cc_start: 0.8649 (m-80) cc_final: 0.8372 (m-80) REVERT: E 94 ILE cc_start: 0.9243 (tp) cc_final: 0.8922 (tp) REVERT: E 157 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6497 (tp) REVERT: E 171 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9021 (tp) REVERT: E 238 LYS cc_start: 0.5893 (mmtm) cc_final: 0.5045 (mmmt) REVERT: F 45 LEU cc_start: 0.7888 (mp) cc_final: 0.7685 (mt) REVERT: F 81 LYS cc_start: 0.7722 (mmtp) cc_final: 0.7214 (ttmt) REVERT: F 97 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8209 (tp) REVERT: F 119 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7105 (mt-10) REVERT: F 159 ARG cc_start: 0.7926 (ttp80) cc_final: 0.6909 (ttp80) REVERT: F 161 GLU cc_start: 0.7991 (mp0) cc_final: 0.7165 (mp0) REVERT: F 286 CYS cc_start: 0.7269 (p) cc_final: 0.7016 (t) REVERT: F 450 MET cc_start: 0.8470 (mmt) cc_final: 0.8066 (mmt) REVERT: F 451 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8049 (pp30) REVERT: F 452 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8278 (mpp80) REVERT: G 189 ILE cc_start: 0.9044 (mm) cc_final: 0.8835 (mt) REVERT: I 38 TYR cc_start: 0.8324 (m-80) cc_final: 0.8096 (m-80) REVERT: I 59 ARG cc_start: 0.7424 (ttp80) cc_final: 0.7090 (ttm170) REVERT: I 89 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7367 (mt-10) REVERT: I 111 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (pm20) REVERT: P 146 VAL cc_start: 0.7519 (OUTLIER) cc_final: 0.7257 (p) REVERT: P 317 ASP cc_start: 0.7702 (m-30) cc_final: 0.7267 (t70) REVERT: P 322 ILE cc_start: 0.8823 (mt) cc_final: 0.8566 (mm) REVERT: P 351 GLU cc_start: 0.8458 (pt0) cc_final: 0.8134 (pm20) REVERT: P 355 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7458 (ttm170) REVERT: P 361 TRP cc_start: 0.7456 (m100) cc_final: 0.6944 (m100) REVERT: S 46 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8802 (mtmm) REVERT: S 73 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7717 (mm-40) REVERT: T 92 LYS cc_start: 0.8718 (tttm) cc_final: 0.7928 (ttmt) REVERT: T 98 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7832 (mp) REVERT: T 120 MET cc_start: 0.8756 (mtm) cc_final: 0.8393 (mtp) REVERT: W 65 LYS cc_start: 0.8835 (tptt) cc_final: 0.8497 (tptt) REVERT: W 92 GLU cc_start: 0.9101 (tp30) cc_final: 0.8648 (tp30) REVERT: X 69 ASN cc_start: 0.7289 (p0) cc_final: 0.6797 (m-40) REVERT: X 91 TYR cc_start: 0.7633 (t80) cc_final: 0.7342 (t80) REVERT: X 109 GLN cc_start: 0.8382 (pt0) cc_final: 0.7938 (tp40) REVERT: X 140 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6092 (m110) REVERT: Z 76 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8019 (tm-30) REVERT: a 3 PHE cc_start: 0.6363 (m-10) cc_final: 0.6053 (m-10) outliers start: 134 outliers final: 70 residues processed: 957 average time/residue: 0.2049 time to fit residues: 317.3365 Evaluate side-chains 804 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 723 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 249 GLU Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 326 ASP Chi-restraints excluded: chain P residue 347 LEU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 73 ASN Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 50 GLU Chi-restraints excluded: chain X residue 104 GLN Chi-restraints excluded: chain X residue 140 ASN Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 148 optimal weight: 0.0980 chunk 198 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 88 HIS C 123 ASN D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN G 142 GLN G 260 ASN G 424 HIS G 514 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 604 GLN G 676 ASN H 157 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN R 56 ASN S 93 ASN ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN W 105 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 103 ASN a 58 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101282 restraints weight = 70016.567| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.41 r_work: 0.3406 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 34787 Z= 0.174 Angle : 0.866 63.851 47179 Z= 0.352 Chirality : 0.045 0.212 5149 Planarity : 0.005 0.063 5980 Dihedral : 9.981 149.984 4871 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.80 % Allowed : 17.75 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 4138 helix: 0.72 (0.12), residues: 1876 sheet: -1.00 (0.28), residues: 347 loop : -1.16 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 119 TYR 0.027 0.002 TYR W 43 PHE 0.027 0.002 PHE B 121 TRP 0.021 0.001 TRP E 91 HIS 0.005 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00403 (34746) covalent geometry : angle 0.67824 (47087) SS BOND : bond 0.01619 ( 4) SS BOND : angle 2.78528 ( 8) hydrogen bonds : bond 0.04984 ( 1435) hydrogen bonds : angle 5.23352 ( 4140) metal coordination : bond 0.02620 ( 37) metal coordination : angle 12.75439 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 803 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.9157 (p) cc_final: 0.8760 (t) REVERT: A 65 PHE cc_start: 0.8383 (m-80) cc_final: 0.8043 (m-80) REVERT: A 87 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4753 (mmt) REVERT: B 141 MET cc_start: 0.8931 (tpp) cc_final: 0.8708 (tpp) REVERT: D 263 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8783 (m) REVERT: E 46 ASN cc_start: 0.6661 (t0) cc_final: 0.6315 (t0) REVERT: E 94 ILE cc_start: 0.9181 (tp) cc_final: 0.8897 (tp) REVERT: E 153 ARG cc_start: 0.8800 (mmm160) cc_final: 0.8432 (ppt170) REVERT: E 168 PHE cc_start: 0.7597 (m-80) cc_final: 0.7262 (m-80) REVERT: E 207 LEU cc_start: 0.8223 (mt) cc_final: 0.7960 (mp) REVERT: E 238 LYS cc_start: 0.5398 (mmtm) cc_final: 0.4976 (mmmt) REVERT: F 81 LYS cc_start: 0.7716 (mmtp) cc_final: 0.7170 (ttmt) REVERT: F 97 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8242 (tp) REVERT: F 159 ARG cc_start: 0.8019 (ttp80) cc_final: 0.6950 (ttp80) REVERT: F 161 GLU cc_start: 0.8147 (mp0) cc_final: 0.7167 (mp0) REVERT: F 286 CYS cc_start: 0.7466 (p) cc_final: 0.7056 (t) REVERT: F 344 GLN cc_start: 0.8886 (tp40) cc_final: 0.8235 (mp10) REVERT: F 450 MET cc_start: 0.8532 (mmt) cc_final: 0.8234 (mmt) REVERT: G 513 MET cc_start: 0.9073 (tpp) cc_final: 0.8837 (tpp) REVERT: G 579 MET cc_start: 0.6646 (ptp) cc_final: 0.6372 (ptm) REVERT: H 39 ILE cc_start: 0.8576 (tt) cc_final: 0.8286 (tp) REVERT: H 47 GLN cc_start: 0.9001 (tp40) cc_final: 0.8794 (tp40) REVERT: I 38 TYR cc_start: 0.8368 (m-80) cc_final: 0.8159 (m-80) REVERT: I 59 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7032 (ttm170) REVERT: I 89 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7568 (mt-10) REVERT: I 110 GLU cc_start: 0.7635 (tp30) cc_final: 0.7296 (tp30) REVERT: P 72 HIS cc_start: 0.7604 (m90) cc_final: 0.7368 (m-70) REVERT: P 146 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7228 (p) REVERT: P 351 GLU cc_start: 0.8455 (pt0) cc_final: 0.8159 (pm20) REVERT: P 355 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7455 (ttm170) REVERT: P 361 TRP cc_start: 0.7415 (m100) cc_final: 0.6953 (m100) REVERT: Q 132 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: S 85 ASP cc_start: 0.8736 (m-30) cc_final: 0.8140 (p0) REVERT: T 92 LYS cc_start: 0.8724 (tttm) cc_final: 0.8232 (ttmt) REVERT: T 120 MET cc_start: 0.8833 (mtm) cc_final: 0.8500 (mtp) REVERT: X 17 GLU cc_start: 0.4625 (OUTLIER) cc_final: 0.3433 (mm-30) REVERT: X 69 ASN cc_start: 0.7097 (p0) cc_final: 0.6648 (m-40) REVERT: X 109 GLN cc_start: 0.8385 (pt0) cc_final: 0.7756 (tp40) REVERT: X 113 ASP cc_start: 0.8312 (m-30) cc_final: 0.8070 (m-30) REVERT: X 140 ASN cc_start: 0.6444 (p0) cc_final: 0.5968 (m110) REVERT: Z 76 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8022 (tm-30) REVERT: Z 130 LYS cc_start: 0.7444 (tttt) cc_final: 0.7042 (tttp) REVERT: a 31 ASN cc_start: 0.7921 (m110) cc_final: 0.7569 (m-40) REVERT: a 58 ASN cc_start: 0.6743 (OUTLIER) cc_final: 0.6406 (p0) REVERT: b 11 ASN cc_start: 0.7651 (p0) cc_final: 0.7202 (m-40) REVERT: b 32 MET cc_start: 0.8573 (mmm) cc_final: 0.8048 (tpt) REVERT: r 9 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8030 (mp10) outliers start: 138 outliers final: 79 residues processed: 877 average time/residue: 0.1980 time to fit residues: 283.3332 Evaluate side-chains 794 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 707 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 253 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 330 LEU Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 347 LEU Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 103 HIS Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 35 MET Chi-restraints excluded: chain Z residue 72 MET Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 114 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 244 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 322 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN F 220 GLN F 451 GLN F 455 GLN G 424 HIS G 514 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 676 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN Q 71 HIS Q 167 ASN R 56 ASN S 39 GLN T 142 GLN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 ASN Z 103 ASN a 58 ASN q 72 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.129382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102375 restraints weight = 69469.131| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.47 r_work: 0.3425 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34787 Z= 0.140 Angle : 0.829 68.651 47179 Z= 0.330 Chirality : 0.043 0.261 5149 Planarity : 0.005 0.066 5980 Dihedral : 9.604 154.345 4871 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.07 % Allowed : 19.04 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4138 helix: 0.87 (0.12), residues: 1878 sheet: -1.03 (0.27), residues: 354 loop : -0.98 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 55 TYR 0.028 0.002 TYR W 43 PHE 0.029 0.002 PHE B 121 TRP 0.020 0.001 TRP F 62 HIS 0.007 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00302 (34746) covalent geometry : angle 0.63624 (47087) SS BOND : bond 0.02071 ( 4) SS BOND : angle 3.18436 ( 8) hydrogen bonds : bond 0.04356 ( 1435) hydrogen bonds : angle 4.99202 ( 4140) metal coordination : bond 0.01804 ( 37) metal coordination : angle 12.56049 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 791 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.9147 (t) cc_final: 0.8860 (t) REVERT: A 61 THR cc_start: 0.9110 (p) cc_final: 0.8791 (t) REVERT: A 65 PHE cc_start: 0.8387 (m-80) cc_final: 0.8085 (m-80) REVERT: A 87 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4990 (mmt) REVERT: A 88 MET cc_start: 0.7873 (tmm) cc_final: 0.7665 (tmm) REVERT: A 89 ILE cc_start: 0.8900 (mm) cc_final: 0.8683 (mm) REVERT: B 120 VAL cc_start: 0.8952 (m) cc_final: 0.8739 (p) REVERT: B 122 ARG cc_start: 0.7107 (tpt90) cc_final: 0.6618 (tpp-160) REVERT: C 214 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: D 263 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8793 (m) REVERT: D 461 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8563 (mp) REVERT: E 46 ASN cc_start: 0.6607 (t0) cc_final: 0.6239 (t0) REVERT: E 49 ASP cc_start: 0.7234 (t0) cc_final: 0.7014 (m-30) REVERT: E 94 ILE cc_start: 0.9149 (tp) cc_final: 0.8820 (tp) REVERT: E 153 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8474 (ptt90) REVERT: E 194 ASP cc_start: 0.7442 (t0) cc_final: 0.6903 (m-30) REVERT: F 45 LEU cc_start: 0.7104 (mt) cc_final: 0.6769 (mp) REVERT: F 81 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7167 (tttt) REVERT: F 97 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8191 (tp) REVERT: F 159 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7613 (ttp80) REVERT: F 162 PHE cc_start: 0.7543 (m-80) cc_final: 0.6991 (m-10) REVERT: F 344 GLN cc_start: 0.8872 (tp40) cc_final: 0.8265 (mp10) REVERT: F 450 MET cc_start: 0.8481 (mmt) cc_final: 0.8199 (mmt) REVERT: G 454 ASP cc_start: 0.8385 (m-30) cc_final: 0.7538 (t0) REVERT: G 471 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: G 513 MET cc_start: 0.9074 (tpp) cc_final: 0.8422 (tpp) REVERT: H 39 ILE cc_start: 0.8592 (tt) cc_final: 0.8272 (tp) REVERT: H 47 GLN cc_start: 0.8946 (tp40) cc_final: 0.8742 (tp40) REVERT: I 59 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7018 (ttm170) REVERT: I 110 GLU cc_start: 0.7625 (tp30) cc_final: 0.7413 (tp30) REVERT: I 111 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8623 (pm20) REVERT: P 233 PHE cc_start: 0.7994 (m-80) cc_final: 0.7676 (m-80) REVERT: P 317 ASP cc_start: 0.7745 (m-30) cc_final: 0.7324 (t70) REVERT: P 327 VAL cc_start: 0.8288 (t) cc_final: 0.8075 (m) REVERT: P 351 GLU cc_start: 0.8368 (pt0) cc_final: 0.8111 (pm20) REVERT: P 355 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7319 (ttm170) REVERT: P 361 TRP cc_start: 0.7495 (m100) cc_final: 0.7148 (m100) REVERT: Q 132 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: Q 164 PHE cc_start: 0.8342 (m-10) cc_final: 0.7925 (m-10) REVERT: R 43 TYR cc_start: 0.5612 (p90) cc_final: 0.5343 (p90) REVERT: R 51 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7925 (mtm110) REVERT: S 53 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7886 (mt) REVERT: S 85 ASP cc_start: 0.8598 (m-30) cc_final: 0.8189 (p0) REVERT: T 97 LYS cc_start: 0.7323 (tptp) cc_final: 0.6924 (mmtp) REVERT: T 120 MET cc_start: 0.8798 (mtm) cc_final: 0.8485 (mtp) REVERT: T 138 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6811 (pp) REVERT: W 45 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8111 (tp30) REVERT: X 17 GLU cc_start: 0.4576 (OUTLIER) cc_final: 0.3476 (mm-30) REVERT: X 50 GLU cc_start: 0.7607 (tt0) cc_final: 0.7314 (pp20) REVERT: X 69 ASN cc_start: 0.7106 (p0) cc_final: 0.6509 (m-40) REVERT: X 103 GLN cc_start: 0.8083 (mp10) cc_final: 0.7842 (mt0) REVERT: X 109 GLN cc_start: 0.8446 (pt0) cc_final: 0.7780 (tp40) REVERT: X 113 ASP cc_start: 0.8359 (m-30) cc_final: 0.8086 (m-30) REVERT: X 125 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8111 (tt) REVERT: X 140 ASN cc_start: 0.6789 (p0) cc_final: 0.5882 (m110) REVERT: Z 21 TYR cc_start: 0.8142 (p90) cc_final: 0.7873 (p90) REVERT: Z 76 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8034 (tm-30) REVERT: Z 91 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7290 (tp) REVERT: Z 130 LYS cc_start: 0.7409 (tttt) cc_final: 0.7063 (tttp) REVERT: Z 138 PHE cc_start: 0.8128 (m-80) cc_final: 0.7896 (m-80) REVERT: a 59 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7514 (ptt-90) REVERT: b 11 ASN cc_start: 0.7581 (p0) cc_final: 0.7135 (m-40) REVERT: b 32 MET cc_start: 0.8535 (mmm) cc_final: 0.8034 (tpt) REVERT: q 124 TYR cc_start: 0.8747 (t80) cc_final: 0.8496 (t80) REVERT: r 9 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: s 52 LEU cc_start: 0.7534 (mm) cc_final: 0.7272 (mp) outliers start: 148 outliers final: 80 residues processed: 876 average time/residue: 0.2011 time to fit residues: 288.4671 Evaluate side-chains 801 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 706 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 471 LYS Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 265 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 59 ARG Chi-restraints excluded: chain a residue 62 VAL Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 151 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 301 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 315 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN F 220 GLN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 ASN R 56 ASN W 105 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099660 restraints weight = 70071.574| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.47 r_work: 0.3370 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 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 : 0.004 0.090 34787 Z= 0.166 Angle : 0.837 72.375 47179 Z= 0.328 Chirality : 0.044 0.210 5149 Planarity : 0.005 0.077 5980 Dihedral : 9.315 157.461 4869 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.10 % Allowed : 19.54 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4138 helix: 0.91 (0.12), residues: 1898 sheet: -1.00 (0.27), residues: 361 loop : -0.96 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG s 64 TYR 0.027 0.002 TYR W 43 PHE 0.030 0.002 PHE B 121 TRP 0.014 0.001 TRP X 86 HIS 0.007 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00388 (34746) covalent geometry : angle 0.63258 (47087) SS BOND : bond 0.00732 ( 4) SS BOND : angle 3.26347 ( 8) hydrogen bonds : bond 0.04329 ( 1435) hydrogen bonds : angle 4.92121 ( 4140) metal coordination : bond 0.02301 ( 37) metal coordination : angle 12.94937 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 739 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.8448 (m-80) cc_final: 0.8239 (m-80) REVERT: B 103 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 122 ARG cc_start: 0.7140 (tpt90) cc_final: 0.6607 (tpp-160) REVERT: C 214 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: D 139 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 263 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8793 (m) REVERT: D 461 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8603 (mp) REVERT: E 94 ILE cc_start: 0.9129 (tp) cc_final: 0.8839 (tp) REVERT: E 153 ARG cc_start: 0.8836 (mmm160) cc_final: 0.8517 (ptt90) REVERT: E 187 ILE cc_start: 0.7831 (mm) cc_final: 0.7486 (mm) REVERT: E 194 ASP cc_start: 0.7358 (t0) cc_final: 0.6951 (m-30) REVERT: F 81 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7102 (ttmt) REVERT: F 97 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8314 (tp) REVERT: F 159 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7555 (ttp80) REVERT: F 162 PHE cc_start: 0.7606 (m-80) cc_final: 0.7074 (m-10) REVERT: F 292 MET cc_start: 0.6583 (ttp) cc_final: 0.6263 (ptm) REVERT: F 344 GLN cc_start: 0.8872 (tp40) cc_final: 0.8326 (mt0) REVERT: F 450 MET cc_start: 0.8567 (mmt) cc_final: 0.8328 (mmt) REVERT: G 145 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7840 (mtt) REVERT: G 454 ASP cc_start: 0.8382 (m-30) cc_final: 0.7588 (t0) REVERT: G 471 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8373 (mtpp) REVERT: G 513 MET cc_start: 0.9014 (tpp) cc_final: 0.8345 (tpp) REVERT: G 555 ILE cc_start: 0.8781 (mm) cc_final: 0.8485 (mt) REVERT: H 199 ASP cc_start: 0.7580 (t0) cc_final: 0.7312 (t0) REVERT: I 59 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7076 (ttm170) REVERT: I 111 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: P 233 PHE cc_start: 0.8037 (m-80) cc_final: 0.7692 (m-80) REVERT: P 351 GLU cc_start: 0.8423 (pt0) cc_final: 0.8115 (pm20) REVERT: P 355 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7392 (ttm170) REVERT: P 361 TRP cc_start: 0.7487 (m100) cc_final: 0.7140 (m100) REVERT: Q 132 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: Q 164 PHE cc_start: 0.8396 (m-10) cc_final: 0.8020 (m-10) REVERT: R 43 TYR cc_start: 0.5856 (p90) cc_final: 0.5583 (p90) REVERT: S 85 ASP cc_start: 0.8720 (m-30) cc_final: 0.8312 (p0) REVERT: T 97 LYS cc_start: 0.7476 (tptp) cc_final: 0.7058 (mmmt) REVERT: T 120 MET cc_start: 0.8834 (mtm) cc_final: 0.8494 (mtp) REVERT: T 138 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6939 (pp) REVERT: W 45 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8159 (tp30) REVERT: X 46 CYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6440 (t) REVERT: X 64 ASN cc_start: 0.8079 (t0) cc_final: 0.7850 (t0) REVERT: X 68 LEU cc_start: 0.8010 (mt) cc_final: 0.7611 (mt) REVERT: X 69 ASN cc_start: 0.7147 (p0) cc_final: 0.6635 (m-40) REVERT: X 109 GLN cc_start: 0.8434 (pt0) cc_final: 0.7829 (tp40) REVERT: X 140 ASN cc_start: 0.6726 (p0) cc_final: 0.6071 (m110) REVERT: X 142 TYR cc_start: 0.6456 (p90) cc_final: 0.6174 (p90) REVERT: Z 21 TYR cc_start: 0.8242 (p90) cc_final: 0.7980 (p90) REVERT: Z 76 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8189 (tm-30) REVERT: Z 91 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7355 (tp) REVERT: Z 111 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.4591 (t80) REVERT: Z 130 LYS cc_start: 0.7516 (tttt) cc_final: 0.7186 (tttp) REVERT: b 11 ASN cc_start: 0.7655 (p0) cc_final: 0.7249 (m-40) REVERT: b 32 MET cc_start: 0.8607 (mmm) cc_final: 0.8371 (tpp) REVERT: q 124 TYR cc_start: 0.8751 (t80) cc_final: 0.8499 (t80) REVERT: r 9 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: s 41 ASN cc_start: 0.7307 (t0) cc_final: 0.6768 (t0) outliers start: 149 outliers final: 78 residues processed: 830 average time/residue: 0.2010 time to fit residues: 271.4259 Evaluate side-chains 762 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 671 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 91 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 111 PHE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 295 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 183 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 368 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 303 HIS F 451 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN P 72 HIS P 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.128350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101495 restraints weight = 69159.156| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.46 r_work: 0.3410 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 34787 Z= 0.129 Angle : 0.807 63.814 47179 Z= 0.317 Chirality : 0.043 0.301 5149 Planarity : 0.005 0.053 5980 Dihedral : 8.939 161.229 4869 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.44 % Allowed : 20.47 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.13), residues: 4138 helix: 0.98 (0.12), residues: 1907 sheet: -1.06 (0.27), residues: 368 loop : -0.89 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 89 TYR 0.030 0.001 TYR W 43 PHE 0.036 0.001 PHE B 121 TRP 0.019 0.001 TRP A 106 HIS 0.007 0.001 HIS P 216 Details of bonding type rmsd covalent geometry : bond 0.00293 (34746) covalent geometry : angle 0.61631 (47087) SS BOND : bond 0.00454 ( 4) SS BOND : angle 2.56448 ( 8) hydrogen bonds : bond 0.03992 ( 1435) hydrogen bonds : angle 4.81359 ( 4140) metal coordination : bond 0.01752 ( 37) metal coordination : angle 12.32830 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 754 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4838 (mmp) REVERT: B 122 ARG cc_start: 0.7132 (tpt90) cc_final: 0.6525 (tpp-160) REVERT: D 83 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7971 (p0) REVERT: D 263 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8801 (m) REVERT: D 443 MET cc_start: 0.7683 (mtt) cc_final: 0.7481 (mtm) REVERT: E 94 ILE cc_start: 0.9120 (tp) cc_final: 0.8774 (tp) REVERT: E 105 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7822 (mt0) REVERT: E 153 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8504 (ptt90) REVERT: E 186 GLN cc_start: 0.7935 (tt0) cc_final: 0.7715 (tt0) REVERT: F 81 LYS cc_start: 0.7631 (mmtp) cc_final: 0.7073 (ttmt) REVERT: F 97 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8187 (tp) REVERT: F 101 PHE cc_start: 0.8060 (m-80) cc_final: 0.7434 (m-80) REVERT: F 162 PHE cc_start: 0.7373 (m-80) cc_final: 0.7101 (m-80) REVERT: F 208 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7825 (tm-30) REVERT: F 344 GLN cc_start: 0.8865 (tp40) cc_final: 0.8260 (mt0) REVERT: F 450 MET cc_start: 0.8528 (mmt) cc_final: 0.8272 (mmt) REVERT: G 77 MET cc_start: 0.9081 (tpt) cc_final: 0.8776 (tpt) REVERT: G 145 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: G 231 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8727 (pp) REVERT: G 441 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7555 (ttp-110) REVERT: G 454 ASP cc_start: 0.8344 (m-30) cc_final: 0.7636 (t0) REVERT: G 513 MET cc_start: 0.9017 (tpp) cc_final: 0.8486 (tpt) REVERT: G 539 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: G 555 ILE cc_start: 0.8776 (mm) cc_final: 0.8463 (mt) REVERT: H 17 MET cc_start: 0.8634 (tmm) cc_final: 0.8300 (tmm) REVERT: H 199 ASP cc_start: 0.7564 (t0) cc_final: 0.7362 (t0) REVERT: H 202 GLU cc_start: 0.7617 (mt-10) cc_final: 0.6971 (mt-10) REVERT: H 283 ASP cc_start: 0.8236 (t0) cc_final: 0.7528 (t0) REVERT: H 287 HIS cc_start: 0.7924 (t-90) cc_final: 0.7692 (m-70) REVERT: I 40 ASN cc_start: 0.8871 (t0) cc_final: 0.8219 (t0) REVERT: I 59 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7093 (ttm170) REVERT: I 94 SER cc_start: 0.9029 (p) cc_final: 0.8741 (p) REVERT: I 111 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: I 209 TYR cc_start: 0.9245 (p90) cc_final: 0.9004 (p90) REVERT: P 233 PHE cc_start: 0.8013 (m-80) cc_final: 0.7707 (m-80) REVERT: P 317 ASP cc_start: 0.7668 (m-30) cc_final: 0.7074 (t0) REVERT: P 351 GLU cc_start: 0.8342 (pt0) cc_final: 0.8084 (pm20) REVERT: P 355 ARG cc_start: 0.8197 (ttp-170) cc_final: 0.7391 (ttm170) REVERT: P 361 TRP cc_start: 0.7508 (m100) cc_final: 0.7148 (m100) REVERT: Q 132 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: Q 164 PHE cc_start: 0.8368 (m-10) cc_final: 0.8098 (m-10) REVERT: R 43 TYR cc_start: 0.5847 (p90) cc_final: 0.5558 (p90) REVERT: R 51 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7742 (mtm110) REVERT: S 91 MET cc_start: 0.8730 (tpt) cc_final: 0.8445 (tpt) REVERT: T 97 LYS cc_start: 0.7475 (tptp) cc_final: 0.7114 (mmmt) REVERT: T 120 MET cc_start: 0.8807 (mtm) cc_final: 0.8454 (mtp) REVERT: W 45 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7438 (tp30) REVERT: W 92 GLU cc_start: 0.9033 (tp30) cc_final: 0.8618 (tp30) REVERT: X 17 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.3702 (mm-30) REVERT: X 46 CYS cc_start: 0.6658 (OUTLIER) cc_final: 0.6343 (t) REVERT: X 64 ASN cc_start: 0.8065 (t0) cc_final: 0.7748 (t0) REVERT: X 68 LEU cc_start: 0.8043 (mt) cc_final: 0.7584 (mt) REVERT: X 69 ASN cc_start: 0.7229 (p0) cc_final: 0.6748 (m-40) REVERT: X 109 GLN cc_start: 0.8412 (pt0) cc_final: 0.7920 (tp40) REVERT: X 140 ASN cc_start: 0.6924 (p0) cc_final: 0.6011 (m110) REVERT: X 142 TYR cc_start: 0.6435 (p90) cc_final: 0.6096 (p90) REVERT: Z 21 TYR cc_start: 0.8239 (p90) cc_final: 0.7996 (p90) REVERT: Z 76 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8100 (tm-30) REVERT: Z 111 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.4724 (t80) REVERT: Z 124 MET cc_start: 0.8171 (mtp) cc_final: 0.7935 (ttt) REVERT: Z 130 LYS cc_start: 0.7586 (tttt) cc_final: 0.7255 (tttp) REVERT: a 18 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8190 (mm) REVERT: b 11 ASN cc_start: 0.7642 (p0) cc_final: 0.7249 (m-40) REVERT: b 32 MET cc_start: 0.8623 (mmm) cc_final: 0.8419 (tpp) REVERT: q 124 TYR cc_start: 0.8712 (t80) cc_final: 0.8464 (t80) REVERT: r 9 GLN cc_start: 0.8091 (mp10) cc_final: 0.7724 (mp10) outliers start: 125 outliers final: 78 residues processed: 824 average time/residue: 0.1953 time to fit residues: 262.2002 Evaluate side-chains 771 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 680 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 623 ILE Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 71 PHE Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 111 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 291 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 285 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 372 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 334 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 376 HIS F 451 GLN H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** 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 = 0.3916 r_free = 0.3916 target = 0.127177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100022 restraints weight = 69857.465| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.41 r_work: 0.3386 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34787 Z= 0.154 Angle : 0.823 66.874 47179 Z= 0.322 Chirality : 0.044 0.312 5149 Planarity : 0.005 0.076 5980 Dihedral : 8.785 163.875 4869 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.66 % Allowed : 20.97 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4138 helix: 0.99 (0.12), residues: 1890 sheet: -1.01 (0.27), residues: 388 loop : -0.86 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 89 TYR 0.037 0.002 TYR H 142 PHE 0.041 0.002 PHE B 121 TRP 0.016 0.001 TRP Z 48 HIS 0.006 0.001 HIS W 105 Details of bonding type rmsd covalent geometry : bond 0.00364 (34746) covalent geometry : angle 0.62410 (47087) SS BOND : bond 0.00384 ( 4) SS BOND : angle 2.72636 ( 8) hydrogen bonds : bond 0.04052 ( 1435) hydrogen bonds : angle 4.80951 ( 4140) metal coordination : bond 0.02108 ( 37) metal coordination : angle 12.68725 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 705 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8834 (mm) cc_final: 0.8630 (mt) REVERT: A 87 MET cc_start: 0.5157 (OUTLIER) cc_final: 0.4931 (mmp) REVERT: B 122 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6645 (tpp-160) REVERT: D 83 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7896 (p0) REVERT: D 263 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8808 (m) REVERT: E 47 ASN cc_start: 0.6582 (p0) cc_final: 0.5882 (p0) REVERT: E 61 ARG cc_start: 0.7753 (mmt90) cc_final: 0.7202 (mtm180) REVERT: E 105 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7860 (mt0) REVERT: E 153 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8518 (ptt90) REVERT: E 186 GLN cc_start: 0.7915 (tt0) cc_final: 0.7607 (tt0) REVERT: E 194 ASP cc_start: 0.7523 (t0) cc_final: 0.7200 (m-30) REVERT: E 202 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8361 (pp20) REVERT: F 97 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8326 (tp) REVERT: F 101 PHE cc_start: 0.8084 (m-80) cc_final: 0.7412 (m-80) REVERT: F 159 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7957 (ttp80) REVERT: F 162 PHE cc_start: 0.7360 (m-80) cc_final: 0.6709 (m-10) REVERT: F 208 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7922 (tm-30) REVERT: F 344 GLN cc_start: 0.8837 (tp40) cc_final: 0.8301 (mt0) REVERT: G 145 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: G 231 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8861 (pp) REVERT: G 441 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7592 (ttp-110) REVERT: G 454 ASP cc_start: 0.8305 (m-30) cc_final: 0.7623 (t0) REVERT: G 539 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7795 (ptpp) REVERT: G 555 ILE cc_start: 0.8772 (mm) cc_final: 0.8429 (mt) REVERT: H 17 MET cc_start: 0.8754 (tmm) cc_final: 0.8379 (tmm) REVERT: H 202 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7097 (mt-10) REVERT: H 239 THR cc_start: 0.8674 (m) cc_final: 0.8431 (m) REVERT: H 283 ASP cc_start: 0.8254 (t0) cc_final: 0.7805 (t0) REVERT: H 287 HIS cc_start: 0.7984 (t-90) cc_final: 0.7782 (m-70) REVERT: I 40 ASN cc_start: 0.8908 (t0) cc_final: 0.8254 (t0) REVERT: I 59 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7117 (ttm170) REVERT: I 94 SER cc_start: 0.9010 (p) cc_final: 0.8722 (p) REVERT: I 111 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: P 146 VAL cc_start: 0.7512 (p) cc_final: 0.7188 (p) REVERT: P 233 PHE cc_start: 0.8037 (m-80) cc_final: 0.7756 (m-80) REVERT: P 317 ASP cc_start: 0.7668 (m-30) cc_final: 0.7108 (t0) REVERT: P 351 GLU cc_start: 0.8342 (pt0) cc_final: 0.8096 (pm20) REVERT: P 355 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7384 (ttm170) REVERT: P 361 TRP cc_start: 0.7549 (m100) cc_final: 0.7182 (m100) REVERT: Q 132 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: Q 164 PHE cc_start: 0.8322 (m-10) cc_final: 0.8064 (m-10) REVERT: R 43 TYR cc_start: 0.5839 (p90) cc_final: 0.5548 (p90) REVERT: R 51 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7640 (mtm110) REVERT: T 97 LYS cc_start: 0.7626 (tptp) cc_final: 0.7277 (mmtm) REVERT: T 120 MET cc_start: 0.8853 (mtm) cc_final: 0.8453 (mtp) REVERT: W 45 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8118 (tp30) REVERT: W 92 GLU cc_start: 0.8997 (tp30) cc_final: 0.8667 (tp30) REVERT: X 46 CYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6194 (t) REVERT: X 68 LEU cc_start: 0.8071 (mt) cc_final: 0.7647 (mt) REVERT: X 69 ASN cc_start: 0.7236 (p0) cc_final: 0.6745 (m-40) REVERT: X 109 GLN cc_start: 0.8343 (pt0) cc_final: 0.7983 (tp40) REVERT: X 142 TYR cc_start: 0.6507 (p90) cc_final: 0.6228 (p90) REVERT: Z 21 TYR cc_start: 0.8279 (p90) cc_final: 0.8059 (p90) REVERT: Z 76 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8218 (tm-30) REVERT: Z 111 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.4729 (t80) REVERT: Z 124 MET cc_start: 0.8167 (mtp) cc_final: 0.7947 (ttt) REVERT: Z 130 LYS cc_start: 0.7631 (tttt) cc_final: 0.7331 (tttp) REVERT: a 18 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8229 (mm) REVERT: b 11 ASN cc_start: 0.7690 (p0) cc_final: 0.7298 (m-40) REVERT: b 32 MET cc_start: 0.8630 (mmm) cc_final: 0.8308 (tpt) REVERT: r 5 THR cc_start: 0.5550 (OUTLIER) cc_final: 0.5279 (t) REVERT: r 9 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7736 (mp10) outliers start: 133 outliers final: 88 residues processed: 787 average time/residue: 0.2031 time to fit residues: 259.1083 Evaluate side-chains 771 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 668 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 71 PHE Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 6 VAL Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain Z residue 111 PHE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 367 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 316 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 chunk 329 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 80 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 346 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 451 GLN H 235 ASN I 159 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.128083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101227 restraints weight = 69324.165| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.41 r_work: 0.3410 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34787 Z= 0.132 Angle : 0.820 67.362 47179 Z= 0.322 Chirality : 0.043 0.288 5149 Planarity : 0.005 0.058 5980 Dihedral : 8.605 166.325 4869 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.44 % Allowed : 21.22 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4138 helix: 1.01 (0.12), residues: 1894 sheet: -0.96 (0.27), residues: 383 loop : -0.81 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 89 TYR 0.036 0.001 TYR H 142 PHE 0.034 0.001 PHE B 121 TRP 0.018 0.001 TRP Z 48 HIS 0.006 0.001 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00306 (34746) covalent geometry : angle 0.62275 (47087) SS BOND : bond 0.00855 ( 4) SS BOND : angle 4.21048 ( 8) hydrogen bonds : bond 0.03936 ( 1435) hydrogen bonds : angle 4.80653 ( 4140) metal coordination : bond 0.01708 ( 37) metal coordination : angle 12.58588 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 710 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.5131 (OUTLIER) cc_final: 0.4922 (mmt) REVERT: B 122 ARG cc_start: 0.7216 (tpt90) cc_final: 0.6599 (tpp-160) REVERT: D 263 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8821 (m) REVERT: E 61 ARG cc_start: 0.7837 (mmt90) cc_final: 0.7315 (mtm180) REVERT: E 105 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7850 (mt0) REVERT: E 153 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8537 (ptt90) REVERT: F 97 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8294 (tp) REVERT: F 101 PHE cc_start: 0.8064 (m-80) cc_final: 0.7285 (m-80) REVERT: F 159 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7901 (ttp80) REVERT: F 162 PHE cc_start: 0.7449 (m-80) cc_final: 0.6722 (m-10) REVERT: F 208 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7942 (tm-30) REVERT: F 344 GLN cc_start: 0.8847 (tp40) cc_final: 0.8299 (mt0) REVERT: F 357 MET cc_start: 0.8246 (mtp) cc_final: 0.7907 (mmm) REVERT: G 308 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7721 (tpp-160) REVERT: G 441 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7601 (ttp-110) REVERT: G 454 ASP cc_start: 0.8305 (m-30) cc_final: 0.7675 (t0) REVERT: G 471 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8320 (mtpp) REVERT: G 539 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7790 (ptpp) REVERT: G 555 ILE cc_start: 0.8774 (mm) cc_final: 0.8452 (mt) REVERT: H 17 MET cc_start: 0.8869 (tmm) cc_final: 0.8471 (tmm) REVERT: H 202 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7168 (mt-10) REVERT: H 283 ASP cc_start: 0.8114 (t0) cc_final: 0.7375 (t0) REVERT: H 287 HIS cc_start: 0.7977 (t-90) cc_final: 0.7750 (m-70) REVERT: I 59 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7104 (ttm170) REVERT: I 94 SER cc_start: 0.8962 (p) cc_final: 0.8737 (p) REVERT: I 111 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: I 209 TYR cc_start: 0.9230 (p90) cc_final: 0.9003 (p90) REVERT: P 146 VAL cc_start: 0.7526 (p) cc_final: 0.7208 (p) REVERT: P 233 PHE cc_start: 0.8075 (m-80) cc_final: 0.7759 (m-80) REVERT: P 317 ASP cc_start: 0.7608 (m-30) cc_final: 0.7055 (t0) REVERT: P 351 GLU cc_start: 0.8307 (pt0) cc_final: 0.8010 (pm20) REVERT: P 355 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7383 (ttm170) REVERT: P 361 TRP cc_start: 0.7537 (m100) cc_final: 0.7178 (m100) REVERT: Q 132 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: Q 164 PHE cc_start: 0.8326 (m-10) cc_final: 0.8121 (m-10) REVERT: R 43 TYR cc_start: 0.5840 (p90) cc_final: 0.5513 (p90) REVERT: R 51 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7628 (mtm110) REVERT: S 91 MET cc_start: 0.8716 (tpt) cc_final: 0.8394 (tpt) REVERT: T 97 LYS cc_start: 0.7623 (tptp) cc_final: 0.7336 (mmtp) REVERT: T 120 MET cc_start: 0.8810 (mtm) cc_final: 0.8381 (mtp) REVERT: W 45 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7437 (tp30) REVERT: X 17 GLU cc_start: 0.4837 (OUTLIER) cc_final: 0.3760 (mm-30) REVERT: X 46 CYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6148 (t) REVERT: X 68 LEU cc_start: 0.8091 (mt) cc_final: 0.7778 (mt) REVERT: X 69 ASN cc_start: 0.7196 (p0) cc_final: 0.6603 (m-40) REVERT: X 109 GLN cc_start: 0.8314 (pt0) cc_final: 0.7919 (tp40) REVERT: X 140 ASN cc_start: 0.7611 (p0) cc_final: 0.6383 (m110) REVERT: X 142 TYR cc_start: 0.6439 (p90) cc_final: 0.6204 (p90) REVERT: Z 76 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8244 (tm-30) REVERT: Z 130 LYS cc_start: 0.7613 (tttt) cc_final: 0.7332 (tttp) REVERT: a 12 MET cc_start: 0.8299 (ttm) cc_final: 0.7940 (ttm) REVERT: a 18 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8241 (mm) REVERT: b 11 ASN cc_start: 0.7617 (p0) cc_final: 0.7243 (m-40) REVERT: r 5 THR cc_start: 0.5462 (OUTLIER) cc_final: 0.5209 (t) REVERT: r 9 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7835 (mp10) outliers start: 125 outliers final: 85 residues processed: 788 average time/residue: 0.2002 time to fit residues: 257.1054 Evaluate side-chains 764 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 668 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 87 MET Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 695 TYR Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 360 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 314 optimal weight: 0.6980 chunk 287 optimal weight: 20.0000 chunk 195 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 451 GLN ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN I 159 GLN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.127292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100289 restraints weight = 69219.917| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.40 r_work: 0.3391 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34787 Z= 0.146 Angle : 0.835 68.248 47179 Z= 0.327 Chirality : 0.044 0.284 5149 Planarity : 0.005 0.077 5980 Dihedral : 8.572 168.925 4869 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.08 % Allowed : 21.66 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.13), residues: 4138 helix: 1.02 (0.12), residues: 1883 sheet: -0.94 (0.27), residues: 387 loop : -0.82 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 68 TYR 0.038 0.002 TYR H 142 PHE 0.036 0.001 PHE B 121 TRP 0.019 0.001 TRP Z 48 HIS 0.008 0.001 HIS H 287 Details of bonding type rmsd covalent geometry : bond 0.00345 (34746) covalent geometry : angle 0.63888 (47087) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.76919 ( 8) hydrogen bonds : bond 0.03964 ( 1435) hydrogen bonds : angle 4.80687 ( 4140) metal coordination : bond 0.01955 ( 37) metal coordination : angle 12.71465 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 692 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4886 (mmt) REVERT: B 122 ARG cc_start: 0.7234 (tpt90) cc_final: 0.6639 (tpp-160) REVERT: D 84 PHE cc_start: 0.7585 (t80) cc_final: 0.6814 (t80) REVERT: D 263 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (m) REVERT: E 61 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7416 (mtt-85) REVERT: E 105 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7846 (mt0) REVERT: E 153 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8580 (ptt90) REVERT: F 97 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8291 (tp) REVERT: F 101 PHE cc_start: 0.8124 (m-80) cc_final: 0.7302 (m-80) REVERT: F 159 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7930 (ttp80) REVERT: F 162 PHE cc_start: 0.7447 (m-80) cc_final: 0.6756 (m-10) REVERT: F 344 GLN cc_start: 0.8850 (tp40) cc_final: 0.8349 (mt0) REVERT: F 357 MET cc_start: 0.8248 (mtp) cc_final: 0.7913 (mmm) REVERT: G 441 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7605 (ttp-110) REVERT: G 454 ASP cc_start: 0.8346 (m-30) cc_final: 0.7734 (t0) REVERT: G 539 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7815 (ptpp) REVERT: G 555 ILE cc_start: 0.8763 (mm) cc_final: 0.8444 (mt) REVERT: H 17 MET cc_start: 0.8886 (tmm) cc_final: 0.8518 (tmm) REVERT: H 202 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7030 (mt-10) REVERT: H 239 THR cc_start: 0.8569 (m) cc_final: 0.8237 (m) REVERT: H 283 ASP cc_start: 0.8166 (t0) cc_final: 0.7530 (t0) REVERT: I 59 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7223 (ttm170) REVERT: I 94 SER cc_start: 0.8980 (p) cc_final: 0.8723 (p) REVERT: I 111 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: P 146 VAL cc_start: 0.7589 (p) cc_final: 0.7257 (p) REVERT: P 233 PHE cc_start: 0.8106 (m-80) cc_final: 0.7768 (m-80) REVERT: P 317 ASP cc_start: 0.7604 (m-30) cc_final: 0.7060 (t0) REVERT: P 351 GLU cc_start: 0.8314 (pt0) cc_final: 0.8036 (pm20) REVERT: P 355 ARG cc_start: 0.8173 (ttp-170) cc_final: 0.7406 (ttm170) REVERT: P 361 TRP cc_start: 0.7565 (m100) cc_final: 0.7180 (m100) REVERT: Q 132 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: Q 164 PHE cc_start: 0.8329 (m-10) cc_final: 0.8118 (m-10) REVERT: R 43 TYR cc_start: 0.5953 (p90) cc_final: 0.5630 (p90) REVERT: R 51 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7622 (mtm110) REVERT: S 53 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8024 (mt) REVERT: S 91 MET cc_start: 0.8704 (tpt) cc_final: 0.8385 (tpt) REVERT: T 97 LYS cc_start: 0.7636 (tptp) cc_final: 0.7328 (mmtp) REVERT: T 120 MET cc_start: 0.8839 (mtm) cc_final: 0.8382 (mtp) REVERT: W 45 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7510 (tp30) REVERT: X 46 CYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6160 (t) REVERT: X 68 LEU cc_start: 0.8078 (mt) cc_final: 0.7665 (mt) REVERT: X 69 ASN cc_start: 0.7287 (p0) cc_final: 0.6831 (m-40) REVERT: X 109 GLN cc_start: 0.8303 (pt0) cc_final: 0.7947 (tp40) REVERT: X 140 ASN cc_start: 0.7590 (p0) cc_final: 0.6271 (m110) REVERT: X 142 TYR cc_start: 0.6436 (p90) cc_final: 0.6222 (p90) REVERT: Z 76 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8254 (tm-30) REVERT: a 12 MET cc_start: 0.8366 (ttm) cc_final: 0.8052 (ttm) REVERT: a 18 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8239 (mm) REVERT: b 11 ASN cc_start: 0.7637 (p0) cc_final: 0.7279 (m110) REVERT: b 32 MET cc_start: 0.8795 (tpp) cc_final: 0.8546 (mmm) REVERT: q 136 GLU cc_start: 0.8267 (pm20) cc_final: 0.7927 (pm20) REVERT: r 5 THR cc_start: 0.5389 (OUTLIER) cc_final: 0.5163 (t) REVERT: r 9 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7789 (mp10) outliers start: 112 outliers final: 86 residues processed: 764 average time/residue: 0.2024 time to fit residues: 251.1250 Evaluate side-chains 766 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 669 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 62 ARG Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 113 LYS Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 302 optimal weight: 0.0040 chunk 145 optimal weight: 7.9990 chunk 306 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 149 optimal weight: 0.0030 chunk 242 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 393 optimal weight: 20.0000 chunk 386 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 305 optimal weight: 10.0000 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 451 GLN G 453 GLN ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 235 ASN I 159 GLN b 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.128276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101499 restraints weight = 69952.929| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.43 r_work: 0.3412 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34787 Z= 0.129 Angle : 0.829 69.122 47179 Z= 0.325 Chirality : 0.043 0.282 5149 Planarity : 0.005 0.109 5980 Dihedral : 8.433 171.621 4869 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.67 % Allowed : 22.18 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 4138 helix: 1.06 (0.12), residues: 1885 sheet: -0.98 (0.27), residues: 391 loop : -0.79 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG s 64 TYR 0.036 0.002 TYR H 142 PHE 0.037 0.001 PHE B 121 TRP 0.021 0.001 TRP Z 48 HIS 0.007 0.001 HIS H 287 Details of bonding type rmsd covalent geometry : bond 0.00296 (34746) covalent geometry : angle 0.63466 (47087) SS BOND : bond 0.00266 ( 4) SS BOND : angle 2.44209 ( 8) hydrogen bonds : bond 0.03837 ( 1435) hydrogen bonds : angle 4.78288 ( 4140) metal coordination : bond 0.01578 ( 37) metal coordination : angle 12.63338 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 717 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4815 (mmp) REVERT: B 122 ARG cc_start: 0.7279 (tpt90) cc_final: 0.6739 (tpp-160) REVERT: D 263 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8814 (m) REVERT: E 61 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7426 (mtt-85) REVERT: E 105 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7844 (mt0) REVERT: E 153 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8606 (ptt90) REVERT: F 97 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8299 (tp) REVERT: F 101 PHE cc_start: 0.8108 (m-80) cc_final: 0.7331 (m-80) REVERT: F 159 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7920 (ttp80) REVERT: F 162 PHE cc_start: 0.7438 (m-80) cc_final: 0.6761 (m-10) REVERT: F 344 GLN cc_start: 0.8840 (tp40) cc_final: 0.8328 (mt0) REVERT: F 357 MET cc_start: 0.8168 (mtp) cc_final: 0.7831 (mmm) REVERT: G 441 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7654 (ttp-110) REVERT: G 454 ASP cc_start: 0.8348 (m-30) cc_final: 0.7784 (t0) REVERT: G 539 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7826 (ptpp) REVERT: G 555 ILE cc_start: 0.8752 (mm) cc_final: 0.8450 (mt) REVERT: H 17 MET cc_start: 0.8879 (tmm) cc_final: 0.8522 (tmm) REVERT: H 239 THR cc_start: 0.8495 (m) cc_final: 0.8185 (m) REVERT: H 283 ASP cc_start: 0.8309 (t0) cc_final: 0.7860 (t0) REVERT: H 287 HIS cc_start: 0.7961 (m-70) cc_final: 0.7729 (m-70) REVERT: I 59 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7140 (ttm170) REVERT: I 111 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: P 72 HIS cc_start: 0.7637 (m90) cc_final: 0.7399 (m170) REVERT: P 146 VAL cc_start: 0.7573 (p) cc_final: 0.7229 (p) REVERT: P 213 PHE cc_start: 0.8957 (t80) cc_final: 0.8642 (t80) REVERT: P 233 PHE cc_start: 0.8089 (m-80) cc_final: 0.7755 (m-80) REVERT: P 317 ASP cc_start: 0.7523 (m-30) cc_final: 0.7012 (t0) REVERT: P 351 GLU cc_start: 0.8332 (pt0) cc_final: 0.8095 (pm20) REVERT: P 355 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7375 (ttm170) REVERT: P 361 TRP cc_start: 0.7585 (m100) cc_final: 0.7192 (m100) REVERT: Q 132 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: Q 165 SER cc_start: 0.8468 (t) cc_final: 0.7755 (p) REVERT: R 43 TYR cc_start: 0.5898 (p90) cc_final: 0.5552 (p90) REVERT: R 51 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7627 (mtm110) REVERT: S 18 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7319 (pt0) REVERT: S 53 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8046 (mt) REVERT: S 91 MET cc_start: 0.8669 (tpt) cc_final: 0.8329 (tpt) REVERT: T 97 LYS cc_start: 0.7609 (tptp) cc_final: 0.7294 (mmmt) REVERT: T 120 MET cc_start: 0.8808 (mtm) cc_final: 0.8335 (mtp) REVERT: W 45 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7458 (tp30) REVERT: X 46 CYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6099 (t) REVERT: X 69 ASN cc_start: 0.7245 (p0) cc_final: 0.6742 (m-40) REVERT: X 109 GLN cc_start: 0.8283 (pt0) cc_final: 0.7970 (tp40) REVERT: X 140 ASN cc_start: 0.7544 (p0) cc_final: 0.6227 (m110) REVERT: a 18 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8257 (mm) REVERT: b 11 ASN cc_start: 0.7582 (p0) cc_final: 0.7228 (m110) REVERT: b 32 MET cc_start: 0.8798 (tpp) cc_final: 0.8545 (mmm) REVERT: q 136 GLU cc_start: 0.8273 (pm20) cc_final: 0.7900 (pm20) REVERT: r 5 THR cc_start: 0.5347 (OUTLIER) cc_final: 0.5140 (t) REVERT: r 9 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7740 (mp10) outliers start: 97 outliers final: 74 residues processed: 778 average time/residue: 0.1972 time to fit residues: 249.7468 Evaluate side-chains 755 residues out of total 3634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 670 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 TYR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 451 GLN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 539 LYS Chi-restraints excluded: chain G residue 597 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 706 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 111 GLU Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 214 LEU Chi-restraints excluded: chain P residue 296 PHE Chi-restraints excluded: chain P residue 374 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 132 GLU Chi-restraints excluded: chain Q residue 147 VAL Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 122 MET Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 72 LYS Chi-restraints excluded: chain W residue 86 VAL Chi-restraints excluded: chain X residue 21 SER Chi-restraints excluded: chain X residue 45 LEU Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 115 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 8 PHE Chi-restraints excluded: chain b residue 44 MET Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 5 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 9 GLN Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 39 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 265 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 342 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 394 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 451 GLN ** G 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 HIS b 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.128167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101340 restraints weight = 69214.917| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.41 r_work: 0.3410 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34787 Z= 0.135 Angle : 0.838 70.282 47179 Z= 0.331 Chirality : 0.043 0.281 5149 Planarity : 0.005 0.071 5980 Dihedral : 8.341 174.052 4869 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.42 % Allowed : 22.70 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4138 helix: 1.07 (0.12), residues: 1880 sheet: -0.94 (0.27), residues: 386 loop : -0.80 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 68 TYR 0.026 0.002 TYR H 142 PHE 0.042 0.001 PHE B 121 TRP 0.021 0.001 TRP Z 48 HIS 0.007 0.001 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00315 (34746) covalent geometry : angle 0.64057 (47087) SS BOND : bond 0.00368 ( 4) SS BOND : angle 3.72002 ( 8) hydrogen bonds : bond 0.03915 ( 1435) hydrogen bonds : angle 4.78769 ( 4140) metal coordination : bond 0.01670 ( 37) metal coordination : angle 12.77343 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9524.92 seconds wall clock time: 163 minutes 42.50 seconds (9822.50 seconds total)