Starting phenix.real_space_refine on Tue May 5 20:52:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519.map" model { file = "/net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xny_38519/05_2026/8xny_38519_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 9 5.49 5 S 244 5.16 5 C 21236 2.51 5 N 5649 2.21 5 O 6009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 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: 33176 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 735 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1643 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3074 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 1 Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2502 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 22, 'TRANS': 290} Chain breaks: 1 Chain: "I" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1380 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 1 Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "R" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 336 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1145 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 833 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain breaks: 2 Chain: "r" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 389 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain breaks: 2 Chain: "s" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 193 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 2, 'TRANS': 20} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'PC1': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 981 SG CYS B 99 84.108 63.733 104.874 1.00 29.52 S ATOM 987 SG CYS B 100 83.141 59.668 103.425 1.00 30.11 S ATOM 1484 SG CYS B 164 80.562 59.304 107.288 1.00 28.96 S ATOM 1714 SG CYS B 194 86.888 59.968 107.764 1.00 29.28 S ATOM 7482 SG CYS E 134 146.453 56.593 147.561 1.00 56.01 S ATOM 7516 SG CYS E 139 149.117 58.537 146.558 1.00 56.50 S ATOM 7800 SG CYS E 175 144.147 60.002 150.324 1.00 54.42 S ATOM 7823 SG CYS E 179 147.260 62.068 149.964 1.00 57.95 S ATOM 11353 SG CYS F 425 127.600 64.832 151.513 1.00 45.60 S ATOM 11031 SG CYS F 385 127.467 62.575 145.632 1.00 39.95 S ATOM 11011 SG CYS F 382 123.267 63.429 148.148 1.00 40.29 S ATOM 10992 SG CYS F 379 125.573 59.369 150.752 1.00 43.09 S ATOM 12401 SG CYS G 131 107.087 51.905 134.931 1.00 31.31 S ATOM 12380 SG CYS G 128 108.675 56.006 130.394 1.00 30.26 S ATOM 12441 SG CYS G 137 106.525 57.730 136.592 1.00 33.13 S ATOM 13126 SG CYS G 226 109.034 51.690 143.434 1.00 34.31 S ATOM 12797 SG CYS G 182 112.415 50.272 148.456 1.00 36.31 S ATOM 12773 SG CYS G 179 111.512 55.604 146.669 1.00 35.62 S ATOM 12750 SG CYS G 176 115.040 51.614 143.882 1.00 34.05 S ATOM 11887 SG CYS G 64 112.707 61.635 148.842 1.00 35.53 S ATOM 11973 SG CYS G 75 113.249 63.770 147.224 1.00 36.47 S ATOM 11998 SG CYS G 78 111.998 68.190 149.587 1.00 36.76 S ATOM 12099 SG CYS G 92 109.744 65.927 151.562 1.00 39.04 S ATOM 20299 SG CYS I 152 91.421 53.902 111.720 1.00 27.39 S ATOM 20073 SG CYS I 123 91.273 54.848 117.125 1.00 27.30 S ATOM 20325 SG CYS I 155 93.711 58.785 113.354 1.00 27.04 S ATOM 20346 SG CYS I 158 97.090 53.689 113.920 1.00 26.60 S ATOM 20045 SG CYS I 119 96.910 49.831 120.490 1.00 28.85 S ATOM 20375 SG CYS I 162 103.933 50.927 117.847 1.00 28.07 S ATOM 20003 SG CYS I 113 100.835 45.827 120.198 1.00 28.61 S ATOM 20022 SG CYS I 116 101.461 51.242 123.449 1.00 29.24 S ATOM 24533 SG CYS R 79 117.567 44.671 121.918 1.00 32.60 S ATOM 24709 SG CYS R 104 115.262 43.145 123.438 1.00 32.49 S ATOM 24731 SG CYS R 107 114.399 43.884 120.075 1.00 30.78 S Time building chain proxies: 6.94, per 1000 atoms: 0.21 Number of scatterers: 33176 At special positions: 0 Unit cell: (173.8, 132, 199.1, 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 244 16.00 P 9 15.00 O 6009 8.00 N 5649 7.00 C 21236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.04 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 164 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 152 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 123 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 155 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 158 " pdb="FE1 SF4 I 301 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 302 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 119 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7694 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 33 sheets defined 49.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 removed outlier: 3.508A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 removed outlier: 4.082A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 83 through 109 removed outlier: 3.922A pdb=" N MET A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.694A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.911A pdb=" N ASP B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.631A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.227A pdb=" N ILE B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.960A 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 155 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.035A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.924A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.736A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 138' Processing helix chain 'D' and resid 143 through 159 removed outlier: 4.131A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 216 removed outlier: 3.829A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.087A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.750A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.524A pdb=" N LYS D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.677A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.834A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.609A pdb=" N ASN E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.613A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 209 Processing helix chain 'F' and resid 36 through 40 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.557A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.296A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 133 removed outlier: 4.185A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET F 131 " --> pdb=" O ASP F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 4.032A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.635A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 4.260A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 257 removed outlier: 3.587A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix Processing helix chain 'F' and resid 258 through 266 removed outlier: 4.016A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 303 removed outlier: 3.861A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.732A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.547A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.724A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.520A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.775A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.713A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.821A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 361 Processing helix chain 'G' and resid 377 through 386 removed outlier: 4.304A pdb=" N LEU G 381 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG G 382 " --> pdb=" O THR G 379 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER G 383 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.589A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.027A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.009A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.677A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 529 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 556 through 560 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 665 through 675 Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 2 through 32 removed outlier: 3.605A pdb=" N VAL H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Proline residue: H 12 - end of helix removed outlier: 4.399A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 58 Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 73 through 87 removed outlier: 3.703A pdb=" N LEU H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 124 removed outlier: 3.672A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 158 removed outlier: 3.517A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 169 removed outlier: 3.674A pdb=" N LEU H 165 " --> pdb=" O SER H 161 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 191 Processing helix chain 'H' and resid 216 through 237 removed outlier: 3.586A pdb=" N PHE H 220 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU H 233 " --> pdb=" O THR H 229 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 252 through 275 removed outlier: 4.396A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU H 265 " --> pdb=" O MET H 261 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE H 273 " --> pdb=" O THR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.608A pdb=" N MET H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 312 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 59 Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.770A pdb=" N MET I 72 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR I 76 " --> pdb=" O MET I 72 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 122 removed outlier: 3.749A pdb=" N ILE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 187 through 195 removed outlier: 3.584A pdb=" N ASN I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN I 193 " --> pdb=" O LYS I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 209 removed outlier: 4.284A pdb=" N ALA I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN I 204 " --> pdb=" O GLU I 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 76 Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.589A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 114 through 122 removed outlier: 4.503A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 Processing helix chain 'P' and resid 178 through 195 Processing helix chain 'P' and resid 213 through 220 Processing helix chain 'P' and resid 228 through 233 removed outlier: 3.773A pdb=" N LEU P 231 " --> pdb=" O LEU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 273 through 284 removed outlier: 4.118A pdb=" N GLY P 282 " --> pdb=" O LYS P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.937A pdb=" N LEU P 304 " --> pdb=" O TRP P 300 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE P 305 " --> pdb=" O ILE P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 334 through 339 Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.446A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 72 Processing helix chain 'Q' and resid 130 through 142 removed outlier: 3.520A pdb=" N PHE Q 137 " --> pdb=" O ASP Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'S' and resid 32 through 48 removed outlier: 6.311A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS S 46 " --> pdb=" O VAL S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 127 removed outlier: 3.591A pdb=" N VAL T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU T 117 " --> pdb=" O LEU T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 35 Processing helix chain 'V' and resid 36 through 38 No H-bonds generated for 'chain 'V' and resid 36 through 38' Processing helix chain 'V' and resid 42 through 60 removed outlier: 3.708A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU V 54 " --> pdb=" O GLN V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 73 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.681A pdb=" N LYS V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.991A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 Processing helix chain 'W' and resid 78 through 98 removed outlier: 3.948A pdb=" N ILE W 87 " --> pdb=" O ASP W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 126 Processing helix chain 'X' and resid 9 through 14 Processing helix chain 'X' and resid 21 through 28 removed outlier: 3.545A pdb=" N LEU X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 35 Processing helix chain 'X' and resid 37 through 50 removed outlier: 3.680A pdb=" N GLU X 42 " --> pdb=" O LYS X 38 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE X 43 " --> pdb=" O THR X 39 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU X 49 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 77 removed outlier: 4.057A pdb=" N LEU X 68 " --> pdb=" O ASN X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 90 removed outlier: 3.893A pdb=" N CYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 removed outlier: 3.899A pdb=" N ALA X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS X 110 " --> pdb=" O LYS X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 144 Processing helix chain 'Z' and resid 31 through 87 removed outlier: 3.543A pdb=" N GLY Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR Z 47 " --> pdb=" O LEU Z 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG Z 68 " --> pdb=" O ASP Z 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) Proline residue: Z 73 - end of helix removed outlier: 3.659A pdb=" N LEU Z 87 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 96 removed outlier: 3.717A pdb=" N GLU Z 93 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 138 Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 16 through 27 removed outlier: 4.466A pdb=" N GLY a 20 " --> pdb=" O LEU a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 removed outlier: 3.740A pdb=" N TRP a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 4.032A pdb=" N ASN b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 24 through 35 removed outlier: 3.581A pdb=" N ALA b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) Proline residue: b 33 - end of helix Processing helix chain 'b' and resid 38 through 40 No H-bonds generated for 'chain 'b' and resid 38 through 40' Processing helix chain 'b' and resid 41 through 49 removed outlier: 3.533A pdb=" N ASN b 46 " --> pdb=" O ALA b 42 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS b 47 " --> pdb=" O SER b 43 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 16 removed outlier: 3.739A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS q 8 " --> pdb=" O VAL q 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 27 Processing helix chain 'q' and resid 78 through 82 removed outlier: 4.200A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 3.984A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 16 Processing helix chain 's' and resid 78 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.137A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 189 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.859A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 83 " --> pdb=" O ARG C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.398A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.766A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 105 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA7, first strand: chain 'E' and resid 168 through 171 removed outlier: 6.566A pdb=" N TYR E 129 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE E 171 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 131 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.598A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'G' and resid 35 through 36 removed outlier: 6.775A pdb=" N PHE G 35 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.350A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 306 through 309 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.096A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N CYS G 367 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA G 340 " --> pdb=" O CYS G 367 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.323A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASN G 514 " --> pdb=" O PRO G 472 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL G 474 " --> pdb=" O ASN G 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 132 through 134 removed outlier: 3.574A pdb=" N ARG I 141 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 146 through 148 Processing sheet with id=AC5, first strand: chain 'P' and resid 56 through 58 removed outlier: 5.864A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE P 201 " --> pdb=" O PHE P 164 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N HIS P 166 " --> pdb=" O ILE P 201 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE P 200 " --> pdb=" O PHE P 263 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE P 265 " --> pdb=" O ILE P 200 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ARG P 202 " --> pdb=" O PHE P 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 80 through 84 removed outlier: 3.849A pdb=" N LEU P 106 " --> pdb=" O ILE P 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 205 through 207 removed outlier: 6.369A pdb=" N ASP P 205 " --> pdb=" O VAL P 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'P' and resid 236 through 237 Processing sheet with id=AC9, first strand: chain 'Q' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'Q' and resid 78 through 80 removed outlier: 4.055A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU Q 126 " --> pdb=" O MET Q 99 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD3, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD4, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.508A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 55 through 57 Processing sheet with id=AD6, first strand: chain 'X' and resid 130 through 131 1320 hydrogen bonds defined for protein. 3759 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: 5.37 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 13204 1.38 - 1.60: 20319 1.60 - 1.81: 318 1.81 - 2.02: 57 2.02 - 2.23: 80 Bond restraints: 33978 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C ARG Q 106 " pdb=" O ARG Q 106 " ideal model delta sigma weight residual 1.236 1.339 -0.103 1.14e-02 7.69e+03 8.14e+01 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.182 0.174 2.00e-02 2.50e+03 7.61e+01 bond pdb=" O7 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 1.486 1.646 -0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 33973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 45363 6.45 - 12.90: 536 12.90 - 19.34: 161 19.34 - 25.79: 2 25.79 - 32.24: 2 Bond angle restraints: 46064 Sorted by residual: angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.06 25.58 1.52e+00 4.33e-01 2.83e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.47 19.70 1.26e+00 6.30e-01 2.44e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.81 16.52 1.14e+00 7.69e-01 2.10e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.56 16.77 1.20e+00 6.94e-01 1.95e+02 angle pdb=" N PRO H 197 " pdb=" CA PRO H 197 " pdb=" C PRO H 197 " ideal model delta sigma weight residual 113.86 96.73 17.13 1.25e+00 6.40e-01 1.88e+02 ... (remaining 46059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 19746 25.42 - 50.85: 671 50.85 - 76.27: 53 76.27 - 101.69: 24 101.69 - 127.11: 3 Dihedral angle restraints: 20497 sinusoidal: 8569 harmonic: 11928 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS X 78 " pdb=" SG CYS X 78 " pdb=" SG CYS X 110 " pdb=" CB CYS X 110 " ideal model delta sinusoidal sigma weight residual 93.00 154.28 -61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" C ARG D 329 " pdb=" N ARG D 329 " pdb=" CA ARG D 329 " pdb=" CB ARG D 329 " ideal model delta harmonic sigma weight residual -122.60 -138.79 16.19 0 2.50e+00 1.60e-01 4.20e+01 ... (remaining 20494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 4621 0.189 - 0.379: 387 0.379 - 0.568: 26 0.568 - 0.758: 1 0.758 - 0.947: 24 Chirality restraints: 5059 Sorted by residual: chirality pdb="FE3 SF4 I 301 " pdb=" S1 SF4 I 301 " pdb=" S2 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.61 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb="FE1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.63 -0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb="FE2 SF4 I 301 " pdb=" S1 SF4 I 301 " pdb=" S3 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False 10.55 9.64 0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 5056 not shown) Planarity restraints: 5846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 135 " 0.067 2.00e-02 2.50e+03 3.53e-02 2.49e+01 pdb=" CG TYR D 135 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 135 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 135 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR D 135 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 135 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 135 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 135 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 183 " -0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C LEU I 183 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU I 183 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU I 184 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 245 " 0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C PRO H 245 " -0.077 2.00e-02 2.50e+03 pdb=" O PRO H 245 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU H 246 " 0.026 2.00e-02 2.50e+03 ... (remaining 5843 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 390 2.53 - 3.13: 30337 3.13 - 3.72: 52872 3.72 - 4.31: 79720 4.31 - 4.90: 125601 Nonbonded interactions: 288920 Sorted by model distance: nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.942 3.040 nonbonded pdb=" OD1 ASP C 147 " pdb=" OE1 GLU C 148 " model vdw 1.999 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.006 3.400 nonbonded pdb=" O ASN Z 24 " pdb=" OD1 ASN Z 24 " model vdw 2.045 3.040 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.079 2.560 ... (remaining 288915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 37.190 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 1.241 34019 Z= 1.009 Angle : 2.179 56.970 46156 Z= 1.422 Chirality : 0.122 0.947 5059 Planarity : 0.007 0.108 5846 Dihedral : 12.592 127.114 12791 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 45.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.23 % Cbeta Deviations : 0.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.12), residues: 4054 helix: -1.84 (0.11), residues: 1754 sheet: -2.16 (0.27), residues: 310 loop : -2.46 (0.12), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 68 TYR 0.067 0.003 TYR D 135 PHE 0.037 0.003 PHE H 224 TRP 0.033 0.002 TRP G 285 HIS 0.011 0.002 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01454 (33978) covalent geometry : angle 2.04328 (46064) SS BOND : bond 0.00888 ( 4) SS BOND : angle 1.32213 ( 8) hydrogen bonds : bond 0.25160 ( 1320) hydrogen bonds : angle 9.71889 ( 3759) metal coordination : bond 0.48559 ( 37) metal coordination : angle 17.88117 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1533 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 1516 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 83 ASN cc_start: 0.6731 (m-40) cc_final: 0.5810 (m110) REVERT: B 187 VAL cc_start: 0.8099 (t) cc_final: 0.7748 (t) REVERT: D 202 TRP cc_start: 0.7464 (m-10) cc_final: 0.6942 (m-10) REVERT: E 46 ASN cc_start: 0.6274 (t0) cc_final: 0.6035 (t0) REVERT: G 153 PHE cc_start: 0.6982 (t80) cc_final: 0.6669 (t80) REVERT: G 693 ASP cc_start: 0.6274 (m-30) cc_final: 0.5597 (m-30) REVERT: H 57 MET cc_start: 0.7379 (mtt) cc_final: 0.7087 (mtt) REVERT: H 262 GLU cc_start: 0.6169 (mt-10) cc_final: 0.5178 (mt-10) REVERT: H 298 LEU cc_start: 0.8485 (mt) cc_final: 0.8281 (mt) REVERT: P 91 ILE cc_start: 0.7782 (pt) cc_final: 0.7148 (pt) REVERT: P 121 GLN cc_start: 0.6646 (tt0) cc_final: 0.6412 (tt0) REVERT: P 165 ILE cc_start: 0.7537 (mp) cc_final: 0.6961 (mp) REVERT: P 277 VAL cc_start: 0.7708 (t) cc_final: 0.7494 (p) REVERT: Q 67 VAL cc_start: 0.8834 (t) cc_final: 0.8581 (m) REVERT: Q 117 THR cc_start: 0.6832 (t) cc_final: 0.6453 (t) REVERT: Q 123 ASN cc_start: 0.7462 (m-40) cc_final: 0.7261 (m-40) REVERT: Q 147 VAL cc_start: 0.7505 (t) cc_final: 0.7024 (p) REVERT: R 92 TYR cc_start: 0.6122 (m-80) cc_final: 0.5812 (m-10) REVERT: T 130 ILE cc_start: 0.8281 (mm) cc_final: 0.7721 (mm) REVERT: V 88 LEU cc_start: 0.7947 (tp) cc_final: 0.7679 (tp) REVERT: V 90 LEU cc_start: 0.8007 (tp) cc_final: 0.6824 (tp) REVERT: W 55 LEU cc_start: 0.6953 (mt) cc_final: 0.6750 (mt) REVERT: X 94 MET cc_start: 0.7147 (mtp) cc_final: 0.6070 (mtp) REVERT: r 68 ILE cc_start: 0.5163 (pt) cc_final: 0.4895 (tt) outliers start: 17 outliers final: 3 residues processed: 1524 average time/residue: 0.2208 time to fit residues: 528.8526 Evaluate side-chains 834 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 831 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN C 102 HIS C 104 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS D 79 ASN D 88 HIS D 117 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN D 442 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN E 190 ASN E 245 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS F 455 GLN G 59 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 388 ASN G 444 HIS G 495 ASN G 571 HIS G 572 HIS G 604 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS H 235 ASN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN T 142 GLN V 37 HIS V 50 GLN W 54 GLN W 61 GLN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 ASN X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 54 ASN Z 90 ASN ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.078021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061712 restraints weight = 172672.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.063723 restraints weight = 104268.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.064960 restraints weight = 71907.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.066011 restraints weight = 55415.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.066633 restraints weight = 45635.621| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 34019 Z= 0.260 Angle : 1.153 63.176 46156 Z= 0.466 Chirality : 0.050 0.286 5059 Planarity : 0.007 0.127 5846 Dihedral : 8.533 133.738 4702 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.53 % Allowed : 4.82 % Favored : 94.64 % 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: -2.09 (0.12), residues: 4054 helix: -0.90 (0.11), residues: 1830 sheet: -2.11 (0.26), residues: 346 loop : -1.65 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 146 TYR 0.036 0.003 TYR E 112 PHE 0.035 0.003 PHE X 71 TRP 0.031 0.002 TRP V 97 HIS 0.020 0.002 HIS P 169 Details of bonding type rmsd covalent geometry : bond 0.00568 (33978) covalent geometry : angle 0.89059 (46064) SS BOND : bond 0.00348 ( 4) SS BOND : angle 1.48202 ( 8) hydrogen bonds : bond 0.06277 ( 1320) hydrogen bonds : angle 6.09759 ( 3759) metal coordination : bond 0.02941 ( 37) metal coordination : angle 17.17339 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1022 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7934 (t-100) cc_final: 0.7642 (t-100) REVERT: A 26 GLN cc_start: 0.8639 (pp30) cc_final: 0.8289 (tt0) REVERT: A 61 THR cc_start: 0.9574 (m) cc_final: 0.9330 (m) REVERT: A 63 LEU cc_start: 0.9356 (tp) cc_final: 0.9105 (tp) REVERT: A 89 ILE cc_start: 0.9629 (mt) cc_final: 0.9408 (mt) REVERT: A 94 LEU cc_start: 0.8729 (tp) cc_final: 0.8323 (tp) REVERT: B 76 THR cc_start: 0.9436 (p) cc_final: 0.9018 (p) REVERT: B 80 ASP cc_start: 0.8960 (m-30) cc_final: 0.8735 (m-30) REVERT: B 91 TRP cc_start: 0.9071 (m-10) cc_final: 0.8472 (m-10) REVERT: B 105 MET cc_start: 0.9228 (mmp) cc_final: 0.8649 (mmm) REVERT: B 115 ASP cc_start: 0.8182 (m-30) cc_final: 0.7970 (m-30) REVERT: B 117 PHE cc_start: 0.8721 (m-80) cc_final: 0.8173 (m-80) REVERT: B 152 MET cc_start: 0.8072 (mtp) cc_final: 0.7384 (mtp) REVERT: B 187 VAL cc_start: 0.8693 (t) cc_final: 0.8436 (t) REVERT: C 154 SER cc_start: 0.7824 (p) cc_final: 0.7582 (m) REVERT: C 176 PHE cc_start: 0.8143 (t80) cc_final: 0.7774 (t80) REVERT: C 182 ASP cc_start: 0.7658 (t0) cc_final: 0.6285 (t0) REVERT: C 187 LEU cc_start: 0.8688 (pp) cc_final: 0.8377 (pp) REVERT: C 190 TYR cc_start: 0.8723 (m-80) cc_final: 0.8395 (m-80) REVERT: C 225 LEU cc_start: 0.9511 (mp) cc_final: 0.8571 (mp) REVERT: D 124 ILE cc_start: 0.9610 (OUTLIER) cc_final: 0.9375 (mp) REVERT: D 138 ARG cc_start: 0.9024 (mtt90) cc_final: 0.7540 (mtt90) REVERT: D 172 VAL cc_start: 0.9664 (t) cc_final: 0.9203 (t) REVERT: D 176 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8390 (mm-30) REVERT: D 180 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9472 (mp) REVERT: D 185 MET cc_start: 0.9157 (tpt) cc_final: 0.8681 (tpt) REVERT: D 202 TRP cc_start: 0.8718 (m-10) cc_final: 0.8148 (m-10) REVERT: D 288 PHE cc_start: 0.8681 (m-10) cc_final: 0.8296 (m-10) REVERT: D 302 LEU cc_start: 0.9204 (mp) cc_final: 0.8989 (mp) REVERT: D 363 VAL cc_start: 0.9615 (t) cc_final: 0.9289 (p) REVERT: D 371 MET cc_start: 0.8976 (ppp) cc_final: 0.7923 (ppp) REVERT: D 431 HIS cc_start: 0.8141 (m170) cc_final: 0.7717 (m170) REVERT: D 436 ASP cc_start: 0.8733 (t0) cc_final: 0.8507 (p0) REVERT: E 46 ASN cc_start: 0.6701 (t0) cc_final: 0.5293 (t0) REVERT: E 65 ILE cc_start: 0.9046 (mm) cc_final: 0.8818 (mm) REVERT: E 129 TYR cc_start: 0.9375 (m-80) cc_final: 0.8873 (m-80) REVERT: F 42 PHE cc_start: 0.7491 (m-80) cc_final: 0.7106 (m-80) REVERT: F 155 TYR cc_start: 0.8279 (m-80) cc_final: 0.7477 (m-80) REVERT: F 157 TYR cc_start: 0.8845 (t80) cc_final: 0.8550 (t80) REVERT: F 204 TYR cc_start: 0.7061 (t80) cc_final: 0.6766 (t80) REVERT: F 261 TRP cc_start: 0.6313 (t60) cc_final: 0.6086 (t60) REVERT: F 422 HIS cc_start: 0.6895 (m90) cc_final: 0.6391 (m-70) REVERT: F 424 ILE cc_start: 0.8090 (mm) cc_final: 0.7622 (mm) REVERT: G 97 MET cc_start: 0.6978 (mmp) cc_final: 0.6643 (mmt) REVERT: G 117 MET cc_start: 0.9294 (mmt) cc_final: 0.9089 (mmp) REVERT: G 118 GLU cc_start: 0.8899 (tt0) cc_final: 0.8695 (tt0) REVERT: G 121 LEU cc_start: 0.9750 (mt) cc_final: 0.9467 (mt) REVERT: G 144 MET cc_start: 0.8846 (tpt) cc_final: 0.8507 (tpt) REVERT: G 306 MET cc_start: 0.8393 (mtm) cc_final: 0.7652 (mpp) REVERT: G 405 THR cc_start: 0.8927 (t) cc_final: 0.8667 (t) REVERT: G 425 ASN cc_start: 0.8142 (t0) cc_final: 0.7905 (t0) REVERT: G 473 MET cc_start: 0.8245 (ttp) cc_final: 0.7803 (tpp) REVERT: G 546 PHE cc_start: 0.8488 (m-80) cc_final: 0.8092 (m-80) REVERT: G 598 ASN cc_start: 0.8837 (p0) cc_final: 0.8112 (p0) REVERT: G 615 LEU cc_start: 0.9336 (mt) cc_final: 0.9012 (mp) REVERT: G 659 ILE cc_start: 0.8574 (pt) cc_final: 0.8348 (mm) REVERT: G 693 ASP cc_start: 0.8094 (m-30) cc_final: 0.7598 (t0) REVERT: G 694 PHE cc_start: 0.8566 (t80) cc_final: 0.8298 (t80) REVERT: H 15 ILE cc_start: 0.9288 (mm) cc_final: 0.9003 (mm) REVERT: H 17 MET cc_start: 0.8582 (tmm) cc_final: 0.8287 (tmm) REVERT: H 31 MET cc_start: 0.9118 (mmm) cc_final: 0.8817 (mmt) REVERT: H 35 LYS cc_start: 0.8343 (mtmt) cc_final: 0.7996 (mmtm) REVERT: H 53 MET cc_start: 0.9360 (tpt) cc_final: 0.9125 (tpp) REVERT: H 86 TRP cc_start: 0.8714 (m100) cc_final: 0.8500 (m100) REVERT: H 89 LEU cc_start: 0.8815 (tp) cc_final: 0.8235 (tp) REVERT: H 138 GLN cc_start: 0.9272 (pt0) cc_final: 0.9020 (pt0) REVERT: H 195 ARG cc_start: 0.7959 (tpt90) cc_final: 0.7491 (tpt90) REVERT: H 255 TYR cc_start: 0.8760 (t80) cc_final: 0.8385 (t80) REVERT: H 272 TRP cc_start: 0.9142 (m-10) cc_final: 0.8822 (m-10) REVERT: H 282 TYR cc_start: 0.8909 (t80) cc_final: 0.8348 (t80) REVERT: H 296 LEU cc_start: 0.9738 (tp) cc_final: 0.9507 (tp) REVERT: H 302 MET cc_start: 0.9409 (ttm) cc_final: 0.8675 (ttp) REVERT: I 38 TYR cc_start: 0.8109 (m-80) cc_final: 0.7876 (m-10) REVERT: I 40 ASN cc_start: 0.8151 (t0) cc_final: 0.7948 (t0) REVERT: I 56 ASN cc_start: 0.8441 (t0) cc_final: 0.7849 (t0) REVERT: I 62 MET cc_start: 0.8992 (ptt) cc_final: 0.8711 (tmm) REVERT: I 74 LEU cc_start: 0.9533 (tp) cc_final: 0.9314 (mm) REVERT: I 117 LYS cc_start: 0.9212 (mttp) cc_final: 0.8446 (mtmt) REVERT: P 65 LEU cc_start: 0.8535 (mt) cc_final: 0.8310 (mt) REVERT: P 92 MET cc_start: 0.8754 (mmp) cc_final: 0.8127 (mmm) REVERT: P 97 MET cc_start: 0.7818 (mmm) cc_final: 0.7047 (mmp) REVERT: P 114 ASP cc_start: 0.8101 (t0) cc_final: 0.7467 (t0) REVERT: P 134 TRP cc_start: 0.8183 (p90) cc_final: 0.7615 (t60) REVERT: P 148 ILE cc_start: 0.9145 (mm) cc_final: 0.8878 (mt) REVERT: P 220 TYR cc_start: 0.8976 (m-10) cc_final: 0.8720 (m-80) REVERT: P 265 PHE cc_start: 0.7656 (m-10) cc_final: 0.7011 (m-10) REVERT: P 300 TRP cc_start: 0.7429 (m100) cc_final: 0.6919 (m-10) REVERT: P 318 LYS cc_start: 0.8325 (tmtt) cc_final: 0.8091 (tptt) REVERT: Q 64 LEU cc_start: 0.8935 (mp) cc_final: 0.8713 (mp) REVERT: Q 87 MET cc_start: 0.8004 (mmp) cc_final: 0.7574 (mmt) REVERT: Q 88 GLN cc_start: 0.8286 (mt0) cc_final: 0.7163 (mm-40) REVERT: Q 105 GLU cc_start: 0.7252 (tt0) cc_final: 0.6634 (tt0) REVERT: Q 117 THR cc_start: 0.7649 (t) cc_final: 0.7124 (t) REVERT: Q 121 LEU cc_start: 0.9247 (mt) cc_final: 0.9032 (mt) REVERT: Q 160 TYR cc_start: 0.8271 (t80) cc_final: 0.7848 (t80) REVERT: R 95 LEU cc_start: 0.8186 (mp) cc_final: 0.7977 (mt) REVERT: S 62 GLN cc_start: 0.9420 (pm20) cc_final: 0.9202 (pm20) REVERT: T 83 VAL cc_start: 0.8930 (t) cc_final: 0.8531 (t) REVERT: T 97 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7941 (tmtt) REVERT: T 113 LEU cc_start: 0.9124 (tp) cc_final: 0.8826 (tp) REVERT: T 119 ILE cc_start: 0.9697 (mm) cc_final: 0.9487 (mm) REVERT: T 130 ILE cc_start: 0.9284 (mm) cc_final: 0.8723 (mm) REVERT: T 136 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8516 (pp20) REVERT: T 138 LEU cc_start: 0.9220 (pt) cc_final: 0.8848 (pt) REVERT: T 139 MET cc_start: 0.8432 (ptm) cc_final: 0.8207 (ttm) REVERT: T 142 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8838 (pp30) REVERT: V 24 LEU cc_start: 0.9678 (mt) cc_final: 0.9398 (mt) REVERT: V 28 TYR cc_start: 0.8803 (m-80) cc_final: 0.8399 (m-80) REVERT: V 58 MET cc_start: 0.9333 (mtp) cc_final: 0.8835 (mtp) REVERT: V 90 LEU cc_start: 0.9538 (tp) cc_final: 0.9131 (tp) REVERT: V 94 MET cc_start: 0.8499 (mmt) cc_final: 0.8195 (mmp) REVERT: W 32 LYS cc_start: 0.9431 (ptpt) cc_final: 0.9029 (ptpp) REVERT: W 55 LEU cc_start: 0.9372 (mt) cc_final: 0.8692 (mt) REVERT: W 69 MET cc_start: 0.9451 (mmp) cc_final: 0.9148 (mmp) REVERT: W 90 LYS cc_start: 0.9345 (tptp) cc_final: 0.9042 (tptp) REVERT: W 94 GLN cc_start: 0.9017 (tp-100) cc_final: 0.7980 (tp-100) REVERT: W 98 LYS cc_start: 0.9720 (mmpt) cc_final: 0.9077 (mmtm) REVERT: W 106 VAL cc_start: 0.9688 (m) cc_final: 0.9383 (m) REVERT: X 26 LYS cc_start: 0.9624 (tttp) cc_final: 0.9378 (ttpt) REVERT: X 32 TYR cc_start: 0.9128 (t80) cc_final: 0.8920 (t80) REVERT: X 43 PHE cc_start: 0.8487 (t80) cc_final: 0.8120 (t80) REVERT: Z 10 MET cc_start: 0.9023 (mtp) cc_final: 0.8653 (tpp) REVERT: Z 43 LEU cc_start: 0.9463 (tp) cc_final: 0.9161 (tp) REVERT: Z 47 TYR cc_start: 0.8769 (m-10) cc_final: 0.8331 (m-80) REVERT: Z 84 LEU cc_start: 0.9257 (mm) cc_final: 0.8959 (mt) REVERT: Z 137 ASN cc_start: 0.8842 (t0) cc_final: 0.8423 (t0) REVERT: a 15 CYS cc_start: 0.9379 (m) cc_final: 0.9156 (m) REVERT: b 32 MET cc_start: 0.9112 (tpt) cc_final: 0.8868 (tpp) REVERT: b 44 MET cc_start: 0.8929 (mtp) cc_final: 0.8072 (mtt) REVERT: b 63 MET cc_start: 0.9021 (mmm) cc_final: 0.8724 (pmm) REVERT: q 93 MET cc_start: 0.6282 (mtt) cc_final: 0.4885 (ttm) REVERT: r 68 ILE cc_start: 0.7080 (pt) cc_final: 0.6709 (tt) outliers start: 19 outliers final: 3 residues processed: 1033 average time/residue: 0.2128 time to fit residues: 354.6105 Evaluate side-chains 778 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 771 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 175 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 390 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 313 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 375 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 442 HIS ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS G 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN P 219 ASN P 323 HIS ** S 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN V 41 HIS ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN ** W 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.072782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.057233 restraints weight = 175999.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059068 restraints weight = 106448.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060338 restraints weight = 74187.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061201 restraints weight = 57238.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061824 restraints weight = 47748.475| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 34019 Z= 0.296 Angle : 1.174 72.224 46156 Z= 0.443 Chirality : 0.049 0.291 5059 Planarity : 0.007 0.061 5846 Dihedral : 8.262 136.939 4702 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4054 helix: -0.52 (0.11), residues: 1854 sheet: -1.77 (0.26), residues: 369 loop : -1.41 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 184 TYR 0.032 0.003 TYR D 135 PHE 0.032 0.003 PHE X 71 TRP 0.037 0.003 TRP V 114 HIS 0.012 0.002 HIS R 88 Details of bonding type rmsd covalent geometry : bond 0.00631 (33978) covalent geometry : angle 0.84806 (46064) SS BOND : bond 0.00429 ( 4) SS BOND : angle 1.47770 ( 8) hydrogen bonds : bond 0.05245 ( 1320) hydrogen bonds : angle 5.81864 ( 3759) metal coordination : bond 0.03779 ( 37) metal coordination : angle 19.04925 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 933 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7909 (t-100) cc_final: 0.7705 (t-100) REVERT: A 63 LEU cc_start: 0.9450 (tp) cc_final: 0.9247 (tp) REVERT: A 89 ILE cc_start: 0.9626 (mt) cc_final: 0.9405 (mt) REVERT: A 94 LEU cc_start: 0.8917 (tp) cc_final: 0.8646 (tp) REVERT: B 76 THR cc_start: 0.9438 (p) cc_final: 0.8979 (p) REVERT: B 115 ASP cc_start: 0.7983 (m-30) cc_final: 0.7723 (m-30) REVERT: B 117 PHE cc_start: 0.8749 (m-80) cc_final: 0.8282 (m-80) REVERT: B 141 MET cc_start: 0.9049 (mmt) cc_final: 0.8848 (mmt) REVERT: B 154 GLU cc_start: 0.7928 (pp20) cc_final: 0.7447 (pt0) REVERT: B 190 TYR cc_start: 0.9007 (m-80) cc_final: 0.8345 (m-80) REVERT: B 205 ILE cc_start: 0.9736 (mm) cc_final: 0.9503 (mm) REVERT: B 209 GLN cc_start: 0.9412 (mm110) cc_final: 0.9082 (mm110) REVERT: B 212 ILE cc_start: 0.9385 (tp) cc_final: 0.9123 (tp) REVERT: B 218 LEU cc_start: 0.9311 (mm) cc_final: 0.8779 (mm) REVERT: C 154 SER cc_start: 0.8467 (p) cc_final: 0.8117 (m) REVERT: C 176 PHE cc_start: 0.8444 (t80) cc_final: 0.7911 (t80) REVERT: C 190 TYR cc_start: 0.8925 (m-80) cc_final: 0.8444 (m-80) REVERT: C 214 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8887 (mm-30) REVERT: D 124 ILE cc_start: 0.9738 (OUTLIER) cc_final: 0.9395 (mm) REVERT: D 185 MET cc_start: 0.9030 (tpt) cc_final: 0.8653 (tpt) REVERT: D 202 TRP cc_start: 0.8911 (m-10) cc_final: 0.7830 (m-90) REVERT: D 261 MET cc_start: 0.8692 (mmt) cc_final: 0.8280 (mtt) REVERT: D 285 ASN cc_start: 0.9324 (t0) cc_final: 0.8958 (t0) REVERT: D 371 MET cc_start: 0.9045 (ppp) cc_final: 0.8030 (ppp) REVERT: D 425 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8381 (tptt) REVERT: D 443 MET cc_start: 0.8807 (tmm) cc_final: 0.8495 (tmm) REVERT: E 46 ASN cc_start: 0.6201 (t0) cc_final: 0.5697 (t0) REVERT: E 47 ASN cc_start: 0.7333 (p0) cc_final: 0.6998 (p0) REVERT: E 54 PHE cc_start: 0.8521 (m-80) cc_final: 0.7926 (m-80) REVERT: E 65 ILE cc_start: 0.9128 (mm) cc_final: 0.8862 (mm) REVERT: E 89 ASN cc_start: 0.8926 (t0) cc_final: 0.8567 (t0) REVERT: E 121 TYR cc_start: 0.7835 (m-80) cc_final: 0.7360 (m-80) REVERT: E 129 TYR cc_start: 0.9431 (m-80) cc_final: 0.9212 (m-80) REVERT: F 99 TRP cc_start: 0.9132 (m100) cc_final: 0.8770 (m100) REVERT: F 204 TYR cc_start: 0.6969 (t80) cc_final: 0.6696 (t80) REVERT: F 337 MET cc_start: 0.8940 (mtm) cc_final: 0.8330 (ptm) REVERT: F 442 PHE cc_start: 0.8709 (m-80) cc_final: 0.8449 (m-80) REVERT: G 49 VAL cc_start: 0.9377 (t) cc_final: 0.9143 (t) REVERT: G 67 GLU cc_start: 0.9242 (pt0) cc_final: 0.8679 (pt0) REVERT: G 97 MET cc_start: 0.7695 (mmp) cc_final: 0.6898 (mmm) REVERT: G 120 LEU cc_start: 0.9674 (mt) cc_final: 0.9449 (mt) REVERT: G 145 MET cc_start: 0.8582 (ttp) cc_final: 0.8121 (ttm) REVERT: G 294 TYR cc_start: 0.8716 (p90) cc_final: 0.8468 (p90) REVERT: G 297 LEU cc_start: 0.9675 (mt) cc_final: 0.9411 (mp) REVERT: G 425 ASN cc_start: 0.8453 (t0) cc_final: 0.8217 (t0) REVERT: G 544 MET cc_start: 0.6842 (ptm) cc_final: 0.6631 (ptm) REVERT: G 546 PHE cc_start: 0.8394 (m-80) cc_final: 0.8037 (m-80) REVERT: G 548 LEU cc_start: 0.8795 (tp) cc_final: 0.8491 (tp) REVERT: G 598 ASN cc_start: 0.8689 (p0) cc_final: 0.8220 (p0) REVERT: G 615 LEU cc_start: 0.9378 (mt) cc_final: 0.9012 (mp) REVERT: G 694 PHE cc_start: 0.8621 (t80) cc_final: 0.8010 (t80) REVERT: H 15 ILE cc_start: 0.9433 (mm) cc_final: 0.9231 (mm) REVERT: H 17 MET cc_start: 0.8777 (tmm) cc_final: 0.8343 (tmm) REVERT: H 31 MET cc_start: 0.9291 (mmt) cc_final: 0.8507 (mmp) REVERT: H 35 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8179 (mmtm) REVERT: H 53 MET cc_start: 0.9421 (tpt) cc_final: 0.8831 (tpp) REVERT: H 57 MET cc_start: 0.9235 (mmp) cc_final: 0.8625 (mmm) REVERT: H 85 LEU cc_start: 0.9489 (mt) cc_final: 0.9255 (mt) REVERT: H 91 MET cc_start: 0.9111 (mmm) cc_final: 0.8883 (mmm) REVERT: H 150 LEU cc_start: 0.9505 (tp) cc_final: 0.9302 (tp) REVERT: H 174 LEU cc_start: 0.9502 (mt) cc_final: 0.9286 (mt) REVERT: H 184 MET cc_start: 0.9171 (mtt) cc_final: 0.8865 (mtt) REVERT: H 272 TRP cc_start: 0.9118 (m-10) cc_final: 0.8802 (m100) REVERT: H 282 TYR cc_start: 0.8994 (t80) cc_final: 0.8079 (t80) REVERT: H 288 LEU cc_start: 0.9382 (tp) cc_final: 0.9146 (tp) REVERT: H 302 MET cc_start: 0.9487 (ttm) cc_final: 0.8665 (ttp) REVERT: I 38 TYR cc_start: 0.8149 (m-80) cc_final: 0.7844 (m-10) REVERT: I 40 ASN cc_start: 0.8196 (t0) cc_final: 0.7842 (t0) REVERT: I 56 ASN cc_start: 0.8536 (t0) cc_final: 0.8219 (t0) REVERT: I 62 MET cc_start: 0.9141 (ptt) cc_final: 0.8858 (tmm) REVERT: I 72 MET cc_start: 0.7882 (mmp) cc_final: 0.7288 (mmp) REVERT: I 146 ASP cc_start: 0.8061 (t0) cc_final: 0.7420 (m-30) REVERT: I 147 ILE cc_start: 0.9505 (mp) cc_final: 0.9062 (pt) REVERT: I 149 MET cc_start: 0.9038 (mmp) cc_final: 0.8824 (mmp) REVERT: I 153 ILE cc_start: 0.9609 (pt) cc_final: 0.9390 (mm) REVERT: P 65 LEU cc_start: 0.8663 (mt) cc_final: 0.8460 (mt) REVERT: P 92 MET cc_start: 0.8878 (mmp) cc_final: 0.8197 (mmm) REVERT: P 114 ASP cc_start: 0.8095 (t0) cc_final: 0.7761 (t0) REVERT: P 217 PHE cc_start: 0.9254 (m-10) cc_final: 0.9010 (m-80) REVERT: P 220 TYR cc_start: 0.8961 (m-10) cc_final: 0.8372 (m-10) REVERT: P 265 PHE cc_start: 0.7600 (m-10) cc_final: 0.7047 (m-10) REVERT: P 298 TYR cc_start: 0.8528 (m-80) cc_final: 0.7995 (m-80) REVERT: P 300 TRP cc_start: 0.7557 (m100) cc_final: 0.7165 (m-10) REVERT: Q 63 THR cc_start: 0.8458 (p) cc_final: 0.8055 (p) REVERT: Q 85 ASN cc_start: 0.8896 (t0) cc_final: 0.8623 (t0) REVERT: Q 87 MET cc_start: 0.7488 (mmp) cc_final: 0.7276 (mmt) REVERT: Q 88 GLN cc_start: 0.8145 (mt0) cc_final: 0.6805 (mm-40) REVERT: Q 99 MET cc_start: 0.7785 (tmm) cc_final: 0.7535 (tmm) REVERT: Q 105 GLU cc_start: 0.7336 (tt0) cc_final: 0.6906 (tt0) REVERT: Q 117 THR cc_start: 0.7391 (t) cc_final: 0.7083 (m) REVERT: Q 141 ASN cc_start: 0.9256 (m110) cc_final: 0.7779 (m110) REVERT: Q 160 TYR cc_start: 0.8207 (t80) cc_final: 0.7862 (t80) REVERT: R 95 LEU cc_start: 0.8540 (mp) cc_final: 0.8291 (mt) REVERT: S 62 GLN cc_start: 0.9447 (pm20) cc_final: 0.9197 (pm20) REVERT: T 97 LYS cc_start: 0.8610 (tmmt) cc_final: 0.8375 (tmtt) REVERT: T 105 MET cc_start: 0.8328 (mpp) cc_final: 0.8003 (mpp) REVERT: T 110 LEU cc_start: 0.6976 (mp) cc_final: 0.6656 (tt) REVERT: T 130 ILE cc_start: 0.9344 (mm) cc_final: 0.8911 (mm) REVERT: T 138 LEU cc_start: 0.9166 (pt) cc_final: 0.8886 (pt) REVERT: V 24 LEU cc_start: 0.9688 (mt) cc_final: 0.9358 (mt) REVERT: V 28 TYR cc_start: 0.8798 (m-80) cc_final: 0.8436 (m-80) REVERT: V 90 LEU cc_start: 0.9530 (tp) cc_final: 0.9321 (tp) REVERT: V 94 MET cc_start: 0.8655 (mmt) cc_final: 0.8419 (mmp) REVERT: W 73 ASN cc_start: 0.9586 (m110) cc_final: 0.9334 (m-40) REVERT: W 90 LYS cc_start: 0.9513 (tptp) cc_final: 0.9274 (tptp) REVERT: W 94 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8132 (tp-100) REVERT: W 98 LYS cc_start: 0.9720 (mmpt) cc_final: 0.9311 (mmtm) REVERT: W 111 HIS cc_start: 0.7182 (p90) cc_final: 0.6860 (m90) REVERT: W 129 HIS cc_start: 0.6672 (m-70) cc_final: 0.6357 (m-70) REVERT: X 26 LYS cc_start: 0.9494 (tttp) cc_final: 0.9288 (ttpt) REVERT: X 94 MET cc_start: 0.8798 (mtp) cc_final: 0.8525 (mtt) REVERT: Z 43 LEU cc_start: 0.9424 (tp) cc_final: 0.8790 (tp) REVERT: Z 44 ILE cc_start: 0.9462 (tp) cc_final: 0.9252 (mm) REVERT: Z 47 TYR cc_start: 0.9153 (m-10) cc_final: 0.8648 (m-80) REVERT: Z 137 ASN cc_start: 0.8951 (t0) cc_final: 0.8421 (t0) REVERT: a 15 CYS cc_start: 0.9347 (m) cc_final: 0.9110 (m) REVERT: b 19 LEU cc_start: 0.9340 (mt) cc_final: 0.9056 (mt) REVERT: b 44 MET cc_start: 0.8900 (mtp) cc_final: 0.7918 (mtt) REVERT: q 93 MET cc_start: 0.6843 (mtt) cc_final: 0.5655 (ttm) REVERT: r 68 ILE cc_start: 0.6989 (pt) cc_final: 0.6441 (tt) outliers start: 4 outliers final: 0 residues processed: 936 average time/residue: 0.2084 time to fit residues: 315.3276 Evaluate side-chains 708 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 707 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 338 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 317 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN C 130 ASN C 195 HIS C 227 GLN D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 152 GLN E 190 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN G 142 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 285 HIS S 22 HIS S 48 HIS V 50 GLN X 35 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 GLN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.075138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.059394 restraints weight = 170674.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061298 restraints weight = 105855.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062639 restraints weight = 74198.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063485 restraints weight = 57212.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064202 restraints weight = 47837.671| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34019 Z= 0.159 Angle : 1.046 74.333 46156 Z= 0.381 Chirality : 0.046 0.254 5059 Planarity : 0.005 0.064 5846 Dihedral : 8.254 141.682 4702 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4054 helix: -0.11 (0.12), residues: 1859 sheet: -1.72 (0.26), residues: 384 loop : -1.24 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 218 TYR 0.050 0.002 TYR D 135 PHE 0.041 0.002 PHE B 95 TRP 0.049 0.002 TRP V 97 HIS 0.011 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00362 (33978) covalent geometry : angle 0.74520 (46064) SS BOND : bond 0.00752 ( 4) SS BOND : angle 2.27586 ( 8) hydrogen bonds : bond 0.04562 ( 1320) hydrogen bonds : angle 5.43276 ( 3759) metal coordination : bond 0.01870 ( 37) metal coordination : angle 17.19648 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 937 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8014 (t-100) cc_final: 0.7713 (t-100) REVERT: A 61 THR cc_start: 0.9609 (m) cc_final: 0.9218 (p) REVERT: A 94 LEU cc_start: 0.8950 (tp) cc_final: 0.8725 (tp) REVERT: A 109 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8919 (tmtt) REVERT: B 76 THR cc_start: 0.9323 (p) cc_final: 0.8938 (p) REVERT: B 80 ASP cc_start: 0.9132 (m-30) cc_final: 0.8896 (m-30) REVERT: B 115 ASP cc_start: 0.7875 (m-30) cc_final: 0.7662 (m-30) REVERT: B 117 PHE cc_start: 0.8652 (m-80) cc_final: 0.8171 (m-80) REVERT: B 126 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7854 (mmm-85) REVERT: B 190 TYR cc_start: 0.9048 (m-80) cc_final: 0.8361 (m-80) REVERT: B 205 ILE cc_start: 0.9720 (mm) cc_final: 0.9422 (mm) REVERT: B 207 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9207 (tt0) REVERT: B 209 GLN cc_start: 0.9376 (mm110) cc_final: 0.9033 (mm-40) REVERT: C 113 LEU cc_start: 0.9138 (tt) cc_final: 0.8775 (tt) REVERT: C 154 SER cc_start: 0.8309 (p) cc_final: 0.8023 (m) REVERT: C 176 PHE cc_start: 0.8199 (t80) cc_final: 0.7624 (t80) REVERT: C 230 ARG cc_start: 0.8631 (ptp90) cc_final: 0.8173 (ptt-90) REVERT: D 124 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9412 (mm) REVERT: D 176 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8299 (mm-30) REVERT: D 185 MET cc_start: 0.8862 (tpt) cc_final: 0.8530 (tpt) REVERT: D 202 TRP cc_start: 0.8631 (m-10) cc_final: 0.8018 (m-90) REVERT: D 285 ASN cc_start: 0.9317 (t0) cc_final: 0.8946 (t0) REVERT: D 422 CYS cc_start: 0.8146 (t) cc_final: 0.7871 (t) REVERT: D 425 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8154 (tptt) REVERT: D 458 PHE cc_start: 0.8618 (m-80) cc_final: 0.8313 (m-10) REVERT: E 46 ASN cc_start: 0.6197 (t0) cc_final: 0.5469 (t0) REVERT: E 65 ILE cc_start: 0.9166 (mm) cc_final: 0.8841 (mm) REVERT: F 99 TRP cc_start: 0.9066 (m100) cc_final: 0.8843 (m100) REVERT: F 102 MET cc_start: 0.7856 (tpp) cc_final: 0.6657 (tpp) REVERT: F 149 MET cc_start: 0.3987 (mmt) cc_final: 0.3457 (mmt) REVERT: F 191 TYR cc_start: 0.7238 (t80) cc_final: 0.7012 (t80) REVERT: F 204 TYR cc_start: 0.6827 (t80) cc_final: 0.6578 (t80) REVERT: F 275 LEU cc_start: 0.8940 (mm) cc_final: 0.8134 (tp) REVERT: F 337 MET cc_start: 0.8912 (mtm) cc_final: 0.8609 (mtm) REVERT: F 357 MET cc_start: 0.9204 (ttt) cc_final: 0.8918 (ttt) REVERT: F 442 PHE cc_start: 0.8907 (m-80) cc_final: 0.8597 (m-80) REVERT: G 47 THR cc_start: 0.8522 (p) cc_final: 0.8150 (p) REVERT: G 49 VAL cc_start: 0.9454 (t) cc_final: 0.9230 (t) REVERT: G 306 MET cc_start: 0.8289 (mtm) cc_final: 0.7580 (mpp) REVERT: G 425 ASN cc_start: 0.8377 (t0) cc_final: 0.8127 (t0) REVERT: G 546 PHE cc_start: 0.8488 (m-80) cc_final: 0.7768 (m-80) REVERT: G 548 LEU cc_start: 0.8828 (tp) cc_final: 0.8576 (tp) REVERT: G 598 ASN cc_start: 0.8795 (p0) cc_final: 0.8214 (p0) REVERT: G 615 LEU cc_start: 0.9484 (mt) cc_final: 0.9144 (mp) REVERT: G 694 PHE cc_start: 0.8565 (t80) cc_final: 0.7873 (t80) REVERT: H 17 MET cc_start: 0.8741 (tmm) cc_final: 0.8231 (tmm) REVERT: H 31 MET cc_start: 0.9288 (mmt) cc_final: 0.8686 (mmp) REVERT: H 33 LEU cc_start: 0.8694 (mp) cc_final: 0.8476 (mp) REVERT: H 35 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8079 (mmtm) REVERT: H 53 MET cc_start: 0.9412 (tpt) cc_final: 0.8676 (tpp) REVERT: H 57 MET cc_start: 0.9227 (mmp) cc_final: 0.8405 (mmp) REVERT: H 89 LEU cc_start: 0.8806 (tp) cc_final: 0.8570 (tp) REVERT: H 146 MET cc_start: 0.9063 (tpp) cc_final: 0.7970 (tpp) REVERT: H 150 LEU cc_start: 0.9483 (tp) cc_final: 0.9232 (tp) REVERT: H 185 TRP cc_start: 0.9470 (t-100) cc_final: 0.8979 (t-100) REVERT: H 195 ARG cc_start: 0.8426 (tpt90) cc_final: 0.8209 (tpt90) REVERT: H 228 TYR cc_start: 0.9351 (m-10) cc_final: 0.8961 (m-10) REVERT: H 273 ILE cc_start: 0.9519 (tt) cc_final: 0.9117 (tt) REVERT: H 277 TYR cc_start: 0.7654 (m-80) cc_final: 0.6959 (m-80) REVERT: H 282 TYR cc_start: 0.8844 (t80) cc_final: 0.8443 (t80) REVERT: H 302 MET cc_start: 0.9333 (ttm) cc_final: 0.8453 (ttp) REVERT: I 40 ASN cc_start: 0.8045 (t0) cc_final: 0.7819 (t0) REVERT: I 70 LEU cc_start: 0.9085 (mt) cc_final: 0.8624 (mt) REVERT: I 72 MET cc_start: 0.7904 (mmp) cc_final: 0.7570 (mmt) REVERT: I 114 ILE cc_start: 0.9525 (pt) cc_final: 0.9201 (mp) REVERT: I 117 LYS cc_start: 0.9204 (mttt) cc_final: 0.8511 (mtmt) REVERT: I 146 ASP cc_start: 0.8262 (t0) cc_final: 0.7579 (m-30) REVERT: I 147 ILE cc_start: 0.9515 (mp) cc_final: 0.9113 (mp) REVERT: I 153 ILE cc_start: 0.9599 (pt) cc_final: 0.9264 (mm) REVERT: P 65 LEU cc_start: 0.8540 (mt) cc_final: 0.8339 (mt) REVERT: P 67 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7714 (ptp-110) REVERT: P 92 MET cc_start: 0.8836 (mmp) cc_final: 0.8299 (mmm) REVERT: P 96 LEU cc_start: 0.8984 (pt) cc_final: 0.8701 (pt) REVERT: P 97 MET cc_start: 0.8053 (mmm) cc_final: 0.7141 (mmp) REVERT: P 102 GLN cc_start: 0.8308 (mp10) cc_final: 0.7933 (mp10) REVERT: P 114 ASP cc_start: 0.8127 (t0) cc_final: 0.7789 (t0) REVERT: P 220 TYR cc_start: 0.9029 (m-10) cc_final: 0.8389 (m-10) REVERT: P 300 TRP cc_start: 0.7587 (m100) cc_final: 0.7129 (m-10) REVERT: Q 63 THR cc_start: 0.8486 (p) cc_final: 0.8190 (p) REVERT: Q 84 ARG cc_start: 0.8585 (tmm160) cc_final: 0.8360 (tmm-80) REVERT: Q 88 GLN cc_start: 0.7671 (mt0) cc_final: 0.6495 (mm-40) REVERT: Q 99 MET cc_start: 0.8064 (tmm) cc_final: 0.7701 (tmm) REVERT: Q 117 THR cc_start: 0.7373 (t) cc_final: 0.6540 (t) REVERT: Q 121 LEU cc_start: 0.9270 (mt) cc_final: 0.8973 (mt) REVERT: Q 160 TYR cc_start: 0.8108 (t80) cc_final: 0.7845 (t80) REVERT: R 76 ILE cc_start: 0.8560 (mt) cc_final: 0.8359 (mp) REVERT: R 95 LEU cc_start: 0.8188 (mp) cc_final: 0.7974 (mt) REVERT: S 44 LEU cc_start: 0.8891 (tp) cc_final: 0.8577 (pp) REVERT: S 62 GLN cc_start: 0.9408 (pm20) cc_final: 0.9198 (pm20) REVERT: T 93 ILE cc_start: 0.8602 (mp) cc_final: 0.8336 (mp) REVERT: T 96 GLU cc_start: 0.7636 (mp0) cc_final: 0.7298 (mp0) REVERT: T 113 LEU cc_start: 0.9242 (tp) cc_final: 0.9030 (tp) REVERT: T 130 ILE cc_start: 0.9415 (mm) cc_final: 0.8876 (mm) REVERT: T 138 LEU cc_start: 0.9165 (pt) cc_final: 0.8879 (pt) REVERT: V 24 LEU cc_start: 0.9643 (mt) cc_final: 0.9232 (mt) REVERT: V 28 TYR cc_start: 0.8716 (m-80) cc_final: 0.8436 (m-80) REVERT: V 81 ILE cc_start: 0.9422 (mt) cc_final: 0.9218 (mt) REVERT: V 93 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9278 (ptpt) REVERT: W 32 LYS cc_start: 0.9335 (ptpt) cc_final: 0.9050 (pttp) REVERT: W 38 LEU cc_start: 0.9318 (tp) cc_final: 0.8913 (tt) REVERT: W 45 GLU cc_start: 0.8502 (tp30) cc_final: 0.7788 (tp30) REVERT: W 64 ASP cc_start: 0.9239 (m-30) cc_final: 0.9013 (m-30) REVERT: W 66 VAL cc_start: 0.9461 (t) cc_final: 0.9141 (t) REVERT: W 73 ASN cc_start: 0.9569 (m110) cc_final: 0.9113 (m-40) REVERT: W 85 LEU cc_start: 0.9714 (mt) cc_final: 0.9458 (mt) REVERT: W 90 LYS cc_start: 0.9499 (tptp) cc_final: 0.9147 (tptp) REVERT: W 94 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8410 (tp-100) REVERT: W 98 LYS cc_start: 0.9614 (mmpt) cc_final: 0.9255 (mmmt) REVERT: W 129 HIS cc_start: 0.6282 (m-70) cc_final: 0.5995 (m-70) REVERT: X 94 MET cc_start: 0.8759 (mtp) cc_final: 0.8478 (mtt) REVERT: Z 24 ASN cc_start: 0.7848 (m-40) cc_final: 0.7495 (m-40) REVERT: Z 43 LEU cc_start: 0.9422 (tp) cc_final: 0.8644 (tp) REVERT: Z 47 TYR cc_start: 0.9085 (m-10) cc_final: 0.8590 (m-80) REVERT: Z 84 LEU cc_start: 0.9362 (mt) cc_final: 0.9140 (mt) REVERT: Z 137 ASN cc_start: 0.8948 (t0) cc_final: 0.8307 (t0) REVERT: a 15 CYS cc_start: 0.9270 (m) cc_final: 0.8997 (m) REVERT: b 19 LEU cc_start: 0.9391 (mt) cc_final: 0.9062 (mt) REVERT: q 87 HIS cc_start: 0.2370 (t70) cc_final: 0.1852 (t-170) outliers start: 4 outliers final: 0 residues processed: 939 average time/residue: 0.1989 time to fit residues: 304.2612 Evaluate side-chains 707 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 706 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 56 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 285 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 329 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 390 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN B 139 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN G 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN P 171 ASN W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.073568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058011 restraints weight = 173546.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.059892 restraints weight = 105127.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061202 restraints weight = 73400.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062104 restraints weight = 56598.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062682 restraints weight = 46889.753| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34019 Z= 0.181 Angle : 1.053 75.949 46156 Z= 0.376 Chirality : 0.046 0.247 5059 Planarity : 0.005 0.065 5846 Dihedral : 8.185 146.053 4702 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4054 helix: -0.01 (0.12), residues: 1863 sheet: -1.69 (0.26), residues: 385 loop : -1.13 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 153 TYR 0.046 0.002 TYR D 135 PHE 0.021 0.002 PHE X 71 TRP 0.044 0.002 TRP V 97 HIS 0.012 0.002 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00407 (33978) covalent geometry : angle 0.72824 (46064) SS BOND : bond 0.00955 ( 4) SS BOND : angle 2.16530 ( 8) hydrogen bonds : bond 0.04355 ( 1320) hydrogen bonds : angle 5.42285 ( 3759) metal coordination : bond 0.02185 ( 37) metal coordination : angle 17.82243 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 899 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9426 (mm) cc_final: 0.9089 (tp) REVERT: A 61 THR cc_start: 0.9625 (m) cc_final: 0.9381 (m) REVERT: B 76 THR cc_start: 0.9346 (p) cc_final: 0.8940 (p) REVERT: B 80 ASP cc_start: 0.9158 (m-30) cc_final: 0.8946 (m-30) REVERT: B 105 MET cc_start: 0.8891 (mmt) cc_final: 0.8394 (mmm) REVERT: B 115 ASP cc_start: 0.7874 (m-30) cc_final: 0.7600 (m-30) REVERT: B 117 PHE cc_start: 0.8734 (m-80) cc_final: 0.8432 (m-80) REVERT: B 126 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: B 152 MET cc_start: 0.8890 (ttm) cc_final: 0.8625 (ttm) REVERT: B 161 MET cc_start: 0.8670 (ttp) cc_final: 0.8395 (tmm) REVERT: B 190 TYR cc_start: 0.9042 (m-80) cc_final: 0.8391 (m-80) REVERT: B 205 ILE cc_start: 0.9733 (mm) cc_final: 0.9492 (mm) REVERT: B 218 LEU cc_start: 0.9074 (mm) cc_final: 0.8700 (mm) REVERT: C 93 ILE cc_start: 0.9558 (pt) cc_final: 0.8994 (mm) REVERT: C 165 TYR cc_start: 0.9227 (m-80) cc_final: 0.8819 (m-80) REVERT: C 176 PHE cc_start: 0.8058 (t80) cc_final: 0.7500 (t80) REVERT: C 189 ASP cc_start: 0.8814 (m-30) cc_final: 0.8255 (m-30) REVERT: C 230 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8195 (ptt-90) REVERT: D 124 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9479 (mm) REVERT: D 185 MET cc_start: 0.8878 (tpt) cc_final: 0.8512 (tpt) REVERT: D 192 LEU cc_start: 0.9596 (tp) cc_final: 0.9220 (mm) REVERT: D 197 MET cc_start: 0.8112 (mtp) cc_final: 0.7839 (mtm) REVERT: D 202 TRP cc_start: 0.8527 (m-10) cc_final: 0.7600 (m-90) REVERT: D 261 MET cc_start: 0.8636 (mmt) cc_final: 0.7862 (mtt) REVERT: D 422 CYS cc_start: 0.8133 (t) cc_final: 0.7861 (t) REVERT: D 425 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8158 (tptt) REVERT: E 46 ASN cc_start: 0.6285 (t0) cc_final: 0.5971 (t0) REVERT: E 65 ILE cc_start: 0.9204 (mm) cc_final: 0.8887 (mm) REVERT: F 99 TRP cc_start: 0.9042 (m100) cc_final: 0.8841 (m100) REVERT: F 102 MET cc_start: 0.7949 (tpp) cc_final: 0.6547 (tpp) REVERT: F 149 MET cc_start: 0.4161 (mmt) cc_final: 0.3583 (mmt) REVERT: F 191 TYR cc_start: 0.7385 (t80) cc_final: 0.7137 (t80) REVERT: F 204 TYR cc_start: 0.6951 (t80) cc_final: 0.6667 (t80) REVERT: F 292 MET cc_start: 0.7953 (ppp) cc_final: 0.7549 (ppp) REVERT: F 337 MET cc_start: 0.8914 (mtm) cc_final: 0.8590 (mtm) REVERT: F 357 MET cc_start: 0.9240 (ttt) cc_final: 0.8912 (ttt) REVERT: F 442 PHE cc_start: 0.8799 (m-80) cc_final: 0.8479 (m-80) REVERT: G 47 THR cc_start: 0.8516 (p) cc_final: 0.8163 (t) REVERT: G 49 VAL cc_start: 0.9469 (t) cc_final: 0.9250 (t) REVERT: G 77 MET cc_start: 0.9268 (tpt) cc_final: 0.8857 (tpp) REVERT: G 118 GLU cc_start: 0.9197 (tt0) cc_final: 0.8791 (tt0) REVERT: G 306 MET cc_start: 0.8395 (mtm) cc_final: 0.7747 (mpp) REVERT: G 425 ASN cc_start: 0.8465 (t0) cc_final: 0.8202 (t0) REVERT: G 473 MET cc_start: 0.8375 (ttt) cc_final: 0.7934 (tpp) REVERT: G 546 PHE cc_start: 0.8458 (m-80) cc_final: 0.7941 (m-80) REVERT: G 548 LEU cc_start: 0.8660 (tp) cc_final: 0.8347 (tp) REVERT: G 598 ASN cc_start: 0.8848 (p0) cc_final: 0.8299 (p0) REVERT: G 693 ASP cc_start: 0.8378 (m-30) cc_final: 0.7835 (t0) REVERT: G 694 PHE cc_start: 0.8510 (t80) cc_final: 0.7705 (t80) REVERT: H 4 ILE cc_start: 0.8993 (mt) cc_final: 0.8733 (mp) REVERT: H 6 ILE cc_start: 0.9542 (mm) cc_final: 0.9336 (mm) REVERT: H 7 LEU cc_start: 0.9557 (mm) cc_final: 0.9038 (pp) REVERT: H 15 ILE cc_start: 0.9246 (mp) cc_final: 0.8973 (mp) REVERT: H 17 MET cc_start: 0.8881 (tmm) cc_final: 0.8358 (tmm) REVERT: H 19 PHE cc_start: 0.9300 (m-80) cc_final: 0.9034 (m-80) REVERT: H 31 MET cc_start: 0.9289 (mmt) cc_final: 0.8722 (mmp) REVERT: H 35 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8123 (mmtm) REVERT: H 53 MET cc_start: 0.9415 (tpt) cc_final: 0.8663 (tpp) REVERT: H 57 MET cc_start: 0.9235 (mmp) cc_final: 0.8408 (mmp) REVERT: H 91 MET cc_start: 0.8962 (mpp) cc_final: 0.8587 (mmm) REVERT: H 172 MET cc_start: 0.8232 (tpt) cc_final: 0.7972 (tpt) REVERT: H 185 TRP cc_start: 0.9551 (t-100) cc_final: 0.8717 (t-100) REVERT: H 272 TRP cc_start: 0.9121 (m-10) cc_final: 0.8643 (m100) REVERT: H 273 ILE cc_start: 0.9512 (tt) cc_final: 0.9130 (tt) REVERT: H 282 TYR cc_start: 0.8842 (t80) cc_final: 0.8456 (t80) REVERT: H 302 MET cc_start: 0.9439 (ttm) cc_final: 0.8714 (ttp) REVERT: I 40 ASN cc_start: 0.8087 (t0) cc_final: 0.7815 (t0) REVERT: I 56 ASN cc_start: 0.8608 (t0) cc_final: 0.8094 (t0) REVERT: I 114 ILE cc_start: 0.9586 (pt) cc_final: 0.9305 (mp) REVERT: I 146 ASP cc_start: 0.8200 (t0) cc_final: 0.7931 (m-30) REVERT: I 147 ILE cc_start: 0.9515 (mp) cc_final: 0.9110 (mp) REVERT: I 153 ILE cc_start: 0.9634 (pt) cc_final: 0.9334 (mm) REVERT: P 67 ARG cc_start: 0.8122 (ptm160) cc_final: 0.7802 (ptp-110) REVERT: P 92 MET cc_start: 0.8815 (mmp) cc_final: 0.8221 (mmm) REVERT: P 96 LEU cc_start: 0.9000 (pt) cc_final: 0.8692 (pt) REVERT: P 97 MET cc_start: 0.8128 (mmm) cc_final: 0.7217 (mmp) REVERT: P 220 TYR cc_start: 0.9099 (m-10) cc_final: 0.8795 (m-10) REVERT: P 300 TRP cc_start: 0.7499 (m100) cc_final: 0.7126 (m-10) REVERT: Q 84 ARG cc_start: 0.8420 (tmm160) cc_final: 0.8199 (tmm-80) REVERT: Q 88 GLN cc_start: 0.7621 (mt0) cc_final: 0.6749 (mm-40) REVERT: Q 96 LYS cc_start: 0.9358 (mptt) cc_final: 0.8838 (mtmt) REVERT: Q 117 THR cc_start: 0.7493 (t) cc_final: 0.6234 (t) REVERT: Q 160 TYR cc_start: 0.8155 (t80) cc_final: 0.7903 (t80) REVERT: S 44 LEU cc_start: 0.8948 (tp) cc_final: 0.8619 (pp) REVERT: S 62 GLN cc_start: 0.9417 (pm20) cc_final: 0.9216 (pm20) REVERT: T 96 GLU cc_start: 0.7541 (mp0) cc_final: 0.7260 (mp0) REVERT: T 113 LEU cc_start: 0.9338 (tp) cc_final: 0.9099 (tp) REVERT: T 130 ILE cc_start: 0.9461 (mm) cc_final: 0.8176 (mm) REVERT: T 136 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8233 (pp20) REVERT: T 138 LEU cc_start: 0.9229 (pt) cc_final: 0.8905 (pt) REVERT: T 147 TYR cc_start: 0.7702 (t80) cc_final: 0.7216 (t80) REVERT: V 24 LEU cc_start: 0.9624 (mt) cc_final: 0.8847 (mt) REVERT: V 28 TYR cc_start: 0.8728 (m-80) cc_final: 0.8276 (m-80) REVERT: V 58 MET cc_start: 0.9218 (mtm) cc_final: 0.8939 (mtp) REVERT: V 90 LEU cc_start: 0.9542 (tp) cc_final: 0.9190 (tt) REVERT: V 94 MET cc_start: 0.8343 (mmp) cc_final: 0.8051 (mmp) REVERT: W 32 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9034 (pttp) REVERT: W 38 LEU cc_start: 0.9424 (tp) cc_final: 0.9110 (tt) REVERT: W 66 VAL cc_start: 0.9451 (t) cc_final: 0.9166 (t) REVERT: W 73 ASN cc_start: 0.9607 (m110) cc_final: 0.9192 (m110) REVERT: W 85 LEU cc_start: 0.9717 (mt) cc_final: 0.9485 (mt) REVERT: W 90 LYS cc_start: 0.9564 (tptp) cc_final: 0.9212 (tptp) REVERT: W 94 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8458 (tp-100) REVERT: W 98 LYS cc_start: 0.9565 (mmpt) cc_final: 0.9224 (mmmt) REVERT: Z 43 LEU cc_start: 0.9384 (tp) cc_final: 0.8613 (tp) REVERT: Z 47 TYR cc_start: 0.9157 (m-10) cc_final: 0.8661 (m-80) REVERT: Z 84 LEU cc_start: 0.9394 (mt) cc_final: 0.9104 (mt) REVERT: Z 98 MET cc_start: 0.1498 (tpt) cc_final: 0.1210 (tpt) REVERT: Z 137 ASN cc_start: 0.8956 (t0) cc_final: 0.8276 (t0) REVERT: a 15 CYS cc_start: 0.9253 (m) cc_final: 0.8985 (m) REVERT: b 19 LEU cc_start: 0.9485 (mt) cc_final: 0.9190 (mt) REVERT: b 23 PHE cc_start: 0.8516 (m-80) cc_final: 0.8261 (m-80) REVERT: b 62 ASN cc_start: 0.8186 (p0) cc_final: 0.7894 (p0) REVERT: q 87 HIS cc_start: 0.2334 (t70) cc_final: 0.1685 (t-170) REVERT: q 93 MET cc_start: 0.6570 (mtt) cc_final: 0.6019 (ttm) REVERT: r 112 TYR cc_start: 0.8618 (m-80) cc_final: 0.8323 (m-10) outliers start: 4 outliers final: 1 residues processed: 902 average time/residue: 0.2016 time to fit residues: 296.4222 Evaluate side-chains 695 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 692 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 30.0000 chunk 212 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN B 127 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN F 133 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 HIS ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.074171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.058444 restraints weight = 175810.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.060379 restraints weight = 103552.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061660 restraints weight = 71133.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.062553 restraints weight = 54279.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063129 restraints weight = 44723.690| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34019 Z= 0.170 Angle : 1.032 75.989 46156 Z= 0.371 Chirality : 0.046 0.263 5059 Planarity : 0.005 0.064 5846 Dihedral : 8.138 149.779 4702 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 4054 helix: 0.03 (0.12), residues: 1860 sheet: -1.68 (0.26), residues: 383 loop : -1.11 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 106 TYR 0.023 0.002 TYR D 135 PHE 0.034 0.002 PHE I 175 TRP 0.033 0.002 TRP C 170 HIS 0.008 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00389 (33978) covalent geometry : angle 0.72237 (46064) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.75093 ( 8) hydrogen bonds : bond 0.04204 ( 1320) hydrogen bonds : angle 5.39397 ( 3759) metal coordination : bond 0.01911 ( 37) metal coordination : angle 17.29698 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 889 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.9602 (m) cc_final: 0.9250 (m) REVERT: B 76 THR cc_start: 0.9358 (p) cc_final: 0.8956 (p) REVERT: B 104 MET cc_start: 0.8691 (ppp) cc_final: 0.8230 (ppp) REVERT: B 105 MET cc_start: 0.8771 (mmt) cc_final: 0.8512 (mmm) REVERT: B 117 PHE cc_start: 0.8782 (m-80) cc_final: 0.8453 (m-80) REVERT: B 126 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7784 (mmm-85) REVERT: B 152 MET cc_start: 0.8783 (ttm) cc_final: 0.8504 (ttm) REVERT: B 190 TYR cc_start: 0.8991 (m-80) cc_final: 0.8343 (m-80) REVERT: B 203 TYR cc_start: 0.8306 (t80) cc_final: 0.8051 (t80) REVERT: B 205 ILE cc_start: 0.9753 (mm) cc_final: 0.9551 (mm) REVERT: B 207 GLN cc_start: 0.9410 (tp40) cc_final: 0.9155 (tp40) REVERT: B 218 LEU cc_start: 0.9053 (mm) cc_final: 0.8682 (mm) REVERT: C 93 ILE cc_start: 0.9536 (pt) cc_final: 0.9025 (mm) REVERT: C 165 TYR cc_start: 0.9232 (m-80) cc_final: 0.8764 (m-80) REVERT: C 176 PHE cc_start: 0.8202 (t80) cc_final: 0.7386 (t80) REVERT: C 187 LEU cc_start: 0.8658 (pp) cc_final: 0.8404 (pp) REVERT: C 214 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8206 (mm-30) REVERT: C 230 ARG cc_start: 0.8335 (ptp90) cc_final: 0.8111 (ptt-90) REVERT: D 124 ILE cc_start: 0.9718 (OUTLIER) cc_final: 0.9445 (mm) REVERT: D 185 MET cc_start: 0.8848 (tpt) cc_final: 0.8480 (tpt) REVERT: D 202 TRP cc_start: 0.8494 (m-10) cc_final: 0.7465 (m-90) REVERT: D 261 MET cc_start: 0.8833 (mmt) cc_final: 0.8452 (mtt) REVERT: E 46 ASN cc_start: 0.6255 (t0) cc_final: 0.5958 (t0) REVERT: E 65 ILE cc_start: 0.9203 (mm) cc_final: 0.8935 (mm) REVERT: E 165 ASP cc_start: 0.8747 (t70) cc_final: 0.8511 (p0) REVERT: F 99 TRP cc_start: 0.9155 (m100) cc_final: 0.8943 (m100) REVERT: F 102 MET cc_start: 0.7835 (tpp) cc_final: 0.7544 (tpp) REVERT: F 191 TYR cc_start: 0.7507 (t80) cc_final: 0.7211 (t80) REVERT: F 275 LEU cc_start: 0.8996 (mm) cc_final: 0.8198 (tp) REVERT: F 292 MET cc_start: 0.7767 (ppp) cc_final: 0.7339 (ppp) REVERT: F 337 MET cc_start: 0.8932 (mtm) cc_final: 0.8553 (mtm) REVERT: F 357 MET cc_start: 0.9295 (ttt) cc_final: 0.8961 (ttt) REVERT: F 442 PHE cc_start: 0.8717 (m-80) cc_final: 0.8418 (m-80) REVERT: G 49 VAL cc_start: 0.9457 (t) cc_final: 0.9218 (t) REVERT: G 77 MET cc_start: 0.9155 (tpt) cc_final: 0.8880 (tpp) REVERT: G 118 GLU cc_start: 0.9154 (tt0) cc_final: 0.8674 (tm-30) REVERT: G 173 MET cc_start: 0.8232 (tpt) cc_final: 0.7419 (tpt) REVERT: G 306 MET cc_start: 0.8332 (mtm) cc_final: 0.7684 (mpp) REVERT: G 425 ASN cc_start: 0.8521 (t0) cc_final: 0.8260 (t0) REVERT: G 544 MET cc_start: 0.6962 (ptt) cc_final: 0.6542 (ptt) REVERT: G 546 PHE cc_start: 0.8680 (m-80) cc_final: 0.8043 (m-80) REVERT: G 548 LEU cc_start: 0.8763 (tp) cc_final: 0.8505 (tp) REVERT: G 598 ASN cc_start: 0.8908 (p0) cc_final: 0.8409 (p0) REVERT: G 693 ASP cc_start: 0.8411 (m-30) cc_final: 0.7818 (t0) REVERT: G 694 PHE cc_start: 0.8522 (t80) cc_final: 0.7754 (t80) REVERT: H 4 ILE cc_start: 0.9000 (mt) cc_final: 0.8568 (mp) REVERT: H 6 ILE cc_start: 0.9556 (mm) cc_final: 0.9351 (mm) REVERT: H 7 LEU cc_start: 0.9563 (mm) cc_final: 0.9018 (pp) REVERT: H 15 ILE cc_start: 0.9272 (mp) cc_final: 0.9019 (mp) REVERT: H 17 MET cc_start: 0.8891 (tmm) cc_final: 0.8279 (tmm) REVERT: H 19 PHE cc_start: 0.9308 (m-80) cc_final: 0.9069 (m-10) REVERT: H 24 GLU cc_start: 0.9324 (tt0) cc_final: 0.8740 (tp30) REVERT: H 31 MET cc_start: 0.9186 (mmt) cc_final: 0.8702 (mmp) REVERT: H 35 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8101 (mmtm) REVERT: H 53 MET cc_start: 0.9407 (tpt) cc_final: 0.8634 (tpp) REVERT: H 57 MET cc_start: 0.9229 (mmp) cc_final: 0.8384 (mmp) REVERT: H 81 LEU cc_start: 0.9525 (mm) cc_final: 0.9259 (mm) REVERT: H 89 LEU cc_start: 0.8986 (tp) cc_final: 0.8776 (tp) REVERT: H 195 ARG cc_start: 0.8610 (tpt90) cc_final: 0.7608 (tpt90) REVERT: H 273 ILE cc_start: 0.9517 (tt) cc_final: 0.9109 (tt) REVERT: H 277 TYR cc_start: 0.8212 (m-80) cc_final: 0.7114 (m-80) REVERT: H 282 TYR cc_start: 0.8712 (t80) cc_final: 0.8425 (t80) REVERT: H 302 MET cc_start: 0.9469 (ttm) cc_final: 0.8793 (ttp) REVERT: I 38 TYR cc_start: 0.8137 (m-80) cc_final: 0.7763 (m-10) REVERT: I 40 ASN cc_start: 0.8078 (t0) cc_final: 0.7774 (t0) REVERT: I 56 ASN cc_start: 0.8589 (t0) cc_final: 0.8111 (t0) REVERT: I 70 LEU cc_start: 0.9221 (tt) cc_final: 0.9010 (mt) REVERT: I 114 ILE cc_start: 0.9552 (pt) cc_final: 0.9241 (mp) REVERT: I 146 ASP cc_start: 0.7863 (t0) cc_final: 0.7188 (t0) REVERT: I 153 ILE cc_start: 0.9640 (pt) cc_final: 0.9307 (mm) REVERT: P 92 MET cc_start: 0.8748 (mmp) cc_final: 0.8150 (mmm) REVERT: P 96 LEU cc_start: 0.8988 (pt) cc_final: 0.8655 (pt) REVERT: P 97 MET cc_start: 0.8154 (mmm) cc_final: 0.7121 (mmp) REVERT: P 102 GLN cc_start: 0.8303 (mp10) cc_final: 0.7944 (mp10) REVERT: P 300 TRP cc_start: 0.7655 (m100) cc_final: 0.7254 (m-10) REVERT: Q 84 ARG cc_start: 0.8304 (tmm160) cc_final: 0.8087 (tmm-80) REVERT: Q 88 GLN cc_start: 0.7897 (mt0) cc_final: 0.6641 (mm-40) REVERT: Q 96 LYS cc_start: 0.9362 (mptt) cc_final: 0.8918 (mtmt) REVERT: Q 121 LEU cc_start: 0.9263 (mt) cc_final: 0.9040 (mt) REVERT: Q 160 TYR cc_start: 0.8171 (t80) cc_final: 0.7940 (t80) REVERT: S 44 LEU cc_start: 0.8979 (tp) cc_final: 0.8624 (pp) REVERT: S 62 GLN cc_start: 0.9399 (pm20) cc_final: 0.9198 (pm20) REVERT: T 113 LEU cc_start: 0.9286 (tp) cc_final: 0.9044 (tp) REVERT: T 130 ILE cc_start: 0.9312 (mm) cc_final: 0.7855 (mm) REVERT: T 138 LEU cc_start: 0.9231 (pt) cc_final: 0.8977 (pt) REVERT: T 147 TYR cc_start: 0.7895 (t80) cc_final: 0.7315 (t80) REVERT: V 24 LEU cc_start: 0.9646 (mt) cc_final: 0.8817 (mt) REVERT: V 28 TYR cc_start: 0.8766 (m-80) cc_final: 0.8275 (m-80) REVERT: V 58 MET cc_start: 0.9171 (mtm) cc_final: 0.8826 (mtp) REVERT: V 90 LEU cc_start: 0.9608 (tp) cc_final: 0.9314 (tt) REVERT: V 94 MET cc_start: 0.8480 (mmp) cc_final: 0.8178 (mmp) REVERT: W 32 LYS cc_start: 0.9363 (ptpt) cc_final: 0.9034 (pttp) REVERT: W 45 GLU cc_start: 0.8617 (tp30) cc_final: 0.7774 (tp30) REVERT: W 66 VAL cc_start: 0.9438 (t) cc_final: 0.9226 (t) REVERT: W 73 ASN cc_start: 0.9576 (m110) cc_final: 0.9122 (m110) REVERT: W 85 LEU cc_start: 0.9721 (mt) cc_final: 0.9504 (mt) REVERT: W 90 LYS cc_start: 0.9564 (tptp) cc_final: 0.9248 (tptp) REVERT: W 94 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8580 (tp-100) REVERT: W 98 LYS cc_start: 0.9517 (mmpt) cc_final: 0.9253 (mmmt) REVERT: Z 24 ASN cc_start: 0.8347 (m-40) cc_final: 0.8047 (m-40) REVERT: Z 43 LEU cc_start: 0.9427 (tp) cc_final: 0.8674 (tp) REVERT: Z 47 TYR cc_start: 0.9158 (m-10) cc_final: 0.8687 (m-80) REVERT: Z 84 LEU cc_start: 0.9446 (mt) cc_final: 0.9183 (mt) REVERT: Z 137 ASN cc_start: 0.8950 (t0) cc_final: 0.8213 (t0) REVERT: a 11 ILE cc_start: 0.9464 (tt) cc_final: 0.9212 (tt) REVERT: a 15 CYS cc_start: 0.9268 (m) cc_final: 0.8986 (m) REVERT: a 48 MET cc_start: 0.8934 (ttm) cc_final: 0.8721 (mmm) REVERT: b 19 LEU cc_start: 0.9501 (mt) cc_final: 0.9221 (mt) REVERT: b 23 PHE cc_start: 0.8520 (m-80) cc_final: 0.8175 (m-80) REVERT: b 62 ASN cc_start: 0.8254 (p0) cc_final: 0.7587 (p0) REVERT: q 66 THR cc_start: 0.4015 (m) cc_final: 0.3583 (m) REVERT: q 87 HIS cc_start: 0.2242 (t70) cc_final: 0.1587 (t-170) REVERT: q 93 MET cc_start: 0.6370 (mtt) cc_final: 0.5809 (ttm) REVERT: r 112 TYR cc_start: 0.8557 (m-80) cc_final: 0.8290 (m-10) outliers start: 2 outliers final: 1 residues processed: 890 average time/residue: 0.2030 time to fit residues: 295.9142 Evaluate side-chains 692 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 690 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 360 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 333 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 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 = 0.3689 r_free = 0.3689 target = 0.073805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.058267 restraints weight = 174049.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.060155 restraints weight = 104363.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061471 restraints weight = 72594.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062326 restraints weight = 55549.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062984 restraints weight = 46189.293| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 34019 Z= 0.150 Angle : 1.006 74.283 46156 Z= 0.370 Chirality : 0.046 0.268 5059 Planarity : 0.005 0.064 5846 Dihedral : 8.057 152.312 4702 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.13), residues: 4054 helix: 0.14 (0.12), residues: 1857 sheet: -1.67 (0.26), residues: 377 loop : -1.07 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 254 TYR 0.036 0.002 TYR D 135 PHE 0.033 0.002 PHE B 95 TRP 0.039 0.002 TRP C 170 HIS 0.008 0.001 HIS D 223 Details of bonding type rmsd covalent geometry : bond 0.00344 (33978) covalent geometry : angle 0.72535 (46064) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.57855 ( 8) hydrogen bonds : bond 0.04062 ( 1320) hydrogen bonds : angle 5.36429 ( 3759) metal coordination : bond 0.01648 ( 37) metal coordination : angle 16.35713 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 880 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 THR cc_start: 0.9581 (m) cc_final: 0.9229 (m) REVERT: B 76 THR cc_start: 0.9378 (p) cc_final: 0.9004 (p) REVERT: B 117 PHE cc_start: 0.8781 (m-80) cc_final: 0.8458 (m-80) REVERT: B 126 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8053 (mmm-85) REVERT: B 152 MET cc_start: 0.8828 (ttm) cc_final: 0.8501 (ttm) REVERT: B 190 TYR cc_start: 0.9008 (m-80) cc_final: 0.8350 (m-80) REVERT: B 205 ILE cc_start: 0.9742 (mm) cc_final: 0.9528 (mm) REVERT: B 218 LEU cc_start: 0.9107 (mm) cc_final: 0.8728 (mp) REVERT: C 93 ILE cc_start: 0.9507 (pt) cc_final: 0.8988 (mm) REVERT: C 165 TYR cc_start: 0.9321 (m-80) cc_final: 0.8944 (m-80) REVERT: C 176 PHE cc_start: 0.8111 (t80) cc_final: 0.7155 (t80) REVERT: C 187 LEU cc_start: 0.8647 (pp) cc_final: 0.8303 (pp) REVERT: C 192 PHE cc_start: 0.9120 (t80) cc_final: 0.8838 (t80) REVERT: C 230 ARG cc_start: 0.8449 (ptp90) cc_final: 0.8084 (ptt-90) REVERT: D 185 MET cc_start: 0.8819 (tpt) cc_final: 0.8509 (tpt) REVERT: D 202 TRP cc_start: 0.8581 (m-10) cc_final: 0.7925 (m-90) REVERT: E 46 ASN cc_start: 0.6279 (t0) cc_final: 0.5996 (t0) REVERT: E 65 ILE cc_start: 0.9170 (mm) cc_final: 0.8844 (mm) REVERT: E 83 ASP cc_start: 0.9111 (m-30) cc_final: 0.8766 (m-30) REVERT: E 165 ASP cc_start: 0.8742 (t70) cc_final: 0.8532 (p0) REVERT: F 99 TRP cc_start: 0.9137 (m100) cc_final: 0.8806 (m100) REVERT: F 149 MET cc_start: 0.4234 (mmt) cc_final: 0.3886 (mmt) REVERT: F 191 TYR cc_start: 0.7453 (t80) cc_final: 0.7100 (t80) REVERT: F 204 TYR cc_start: 0.6765 (t80) cc_final: 0.6556 (t80) REVERT: F 275 LEU cc_start: 0.8983 (mm) cc_final: 0.8116 (tp) REVERT: F 292 MET cc_start: 0.7889 (ppp) cc_final: 0.7397 (ppp) REVERT: F 314 LEU cc_start: 0.9513 (mm) cc_final: 0.9248 (mt) REVERT: F 337 MET cc_start: 0.8842 (mtm) cc_final: 0.8430 (mtm) REVERT: F 357 MET cc_start: 0.9241 (ttt) cc_final: 0.8821 (ttt) REVERT: F 392 MET cc_start: 0.9301 (mmm) cc_final: 0.8949 (mmm) REVERT: F 442 PHE cc_start: 0.8707 (m-80) cc_final: 0.8427 (m-80) REVERT: G 77 MET cc_start: 0.9113 (tpt) cc_final: 0.8880 (tpp) REVERT: G 118 GLU cc_start: 0.9298 (tt0) cc_final: 0.8972 (tm-30) REVERT: G 144 MET cc_start: 0.9052 (tpp) cc_final: 0.8828 (tpt) REVERT: G 173 MET cc_start: 0.8201 (tpt) cc_final: 0.7414 (tpt) REVERT: G 306 MET cc_start: 0.8310 (mtm) cc_final: 0.7636 (mpp) REVERT: G 425 ASN cc_start: 0.8606 (t0) cc_final: 0.8278 (t0) REVERT: G 544 MET cc_start: 0.7080 (ptt) cc_final: 0.6622 (ptt) REVERT: G 546 PHE cc_start: 0.8421 (m-80) cc_final: 0.7753 (m-10) REVERT: G 548 LEU cc_start: 0.8811 (tp) cc_final: 0.8584 (tp) REVERT: G 598 ASN cc_start: 0.8925 (p0) cc_final: 0.8401 (p0) REVERT: G 607 LYS cc_start: 0.9296 (mppt) cc_final: 0.8917 (mmtm) REVERT: G 693 ASP cc_start: 0.8403 (m-30) cc_final: 0.7851 (t0) REVERT: G 694 PHE cc_start: 0.8555 (t80) cc_final: 0.7760 (t80) REVERT: H 7 LEU cc_start: 0.9552 (mm) cc_final: 0.9031 (pp) REVERT: H 15 ILE cc_start: 0.9255 (mp) cc_final: 0.9002 (mp) REVERT: H 17 MET cc_start: 0.8894 (tmm) cc_final: 0.8221 (tmm) REVERT: H 31 MET cc_start: 0.9114 (mmt) cc_final: 0.8446 (mmp) REVERT: H 35 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8141 (mtpp) REVERT: H 53 MET cc_start: 0.9453 (tpt) cc_final: 0.8789 (tpp) REVERT: H 57 MET cc_start: 0.9241 (mmp) cc_final: 0.8563 (mmp) REVERT: H 89 LEU cc_start: 0.8988 (tp) cc_final: 0.8773 (tp) REVERT: H 172 MET cc_start: 0.8168 (tpt) cc_final: 0.7852 (tpt) REVERT: H 174 LEU cc_start: 0.9528 (mt) cc_final: 0.9300 (mt) REVERT: H 195 ARG cc_start: 0.8500 (tpt90) cc_final: 0.8284 (tpt90) REVERT: H 227 GLU cc_start: 0.9072 (pp20) cc_final: 0.8641 (pp20) REVERT: H 228 TYR cc_start: 0.9404 (m-80) cc_final: 0.8606 (m-80) REVERT: H 273 ILE cc_start: 0.9468 (tt) cc_final: 0.9017 (tt) REVERT: H 277 TYR cc_start: 0.8088 (m-80) cc_final: 0.7065 (m-80) REVERT: H 280 PHE cc_start: 0.8297 (m-80) cc_final: 0.7711 (m-80) REVERT: H 302 MET cc_start: 0.9380 (ttm) cc_final: 0.8796 (ttp) REVERT: I 38 TYR cc_start: 0.8119 (m-80) cc_final: 0.7845 (m-10) REVERT: I 40 ASN cc_start: 0.8187 (t0) cc_final: 0.7860 (t0) REVERT: I 56 ASN cc_start: 0.8577 (t0) cc_final: 0.8094 (t0) REVERT: I 114 ILE cc_start: 0.9489 (pt) cc_final: 0.9157 (tp) REVERT: I 153 ILE cc_start: 0.9646 (pt) cc_final: 0.9250 (mm) REVERT: P 92 MET cc_start: 0.8795 (mmp) cc_final: 0.8193 (mmm) REVERT: P 96 LEU cc_start: 0.8968 (pt) cc_final: 0.8615 (pt) REVERT: P 97 MET cc_start: 0.8146 (mmm) cc_final: 0.7387 (mmp) REVERT: P 102 GLN cc_start: 0.8302 (mp10) cc_final: 0.7874 (mp10) REVERT: P 220 TYR cc_start: 0.8870 (m-80) cc_final: 0.8469 (m-80) REVERT: P 300 TRP cc_start: 0.7664 (m100) cc_final: 0.7232 (m-10) REVERT: Q 78 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7715 (ttp-170) REVERT: Q 84 ARG cc_start: 0.8417 (tmm160) cc_final: 0.8157 (tmm-80) REVERT: Q 88 GLN cc_start: 0.8745 (mt0) cc_final: 0.8029 (mm-40) REVERT: Q 96 LYS cc_start: 0.9355 (mptt) cc_final: 0.8892 (mtmt) REVERT: Q 117 THR cc_start: 0.7241 (t) cc_final: 0.5997 (m) REVERT: Q 121 LEU cc_start: 0.9247 (mt) cc_final: 0.9039 (mt) REVERT: R 76 ILE cc_start: 0.8606 (mt) cc_final: 0.8352 (mp) REVERT: S 44 LEU cc_start: 0.8848 (tp) cc_final: 0.8527 (pp) REVERT: T 113 LEU cc_start: 0.9364 (tp) cc_final: 0.9110 (tp) REVERT: T 130 ILE cc_start: 0.9352 (mm) cc_final: 0.7998 (mm) REVERT: T 138 LEU cc_start: 0.9300 (pt) cc_final: 0.9092 (pt) REVERT: T 147 TYR cc_start: 0.7861 (t80) cc_final: 0.7307 (t80) REVERT: V 24 LEU cc_start: 0.9614 (mt) cc_final: 0.8752 (mt) REVERT: V 28 TYR cc_start: 0.8676 (m-80) cc_final: 0.8189 (m-80) REVERT: V 58 MET cc_start: 0.9121 (mtm) cc_final: 0.8626 (mtm) REVERT: V 86 LYS cc_start: 0.9694 (mmtt) cc_final: 0.9484 (mmmm) REVERT: V 90 LEU cc_start: 0.9549 (tp) cc_final: 0.9294 (tt) REVERT: W 32 LYS cc_start: 0.9342 (ptpt) cc_final: 0.8990 (pttp) REVERT: W 42 TRP cc_start: 0.9113 (m100) cc_final: 0.8490 (m100) REVERT: W 43 TYR cc_start: 0.8859 (t80) cc_final: 0.7929 (t80) REVERT: W 66 VAL cc_start: 0.9490 (t) cc_final: 0.9180 (t) REVERT: W 73 ASN cc_start: 0.9556 (m110) cc_final: 0.9080 (m-40) REVERT: W 85 LEU cc_start: 0.9717 (mt) cc_final: 0.9480 (mt) REVERT: W 90 LYS cc_start: 0.9582 (tptp) cc_final: 0.9257 (tptp) REVERT: W 94 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8740 (tp-100) REVERT: W 98 LYS cc_start: 0.9484 (mmpt) cc_final: 0.9209 (mmmt) REVERT: W 105 HIS cc_start: 0.8947 (m-70) cc_final: 0.8605 (m-70) REVERT: W 129 HIS cc_start: 0.6644 (m-70) cc_final: 0.6348 (m-70) REVERT: Z 24 ASN cc_start: 0.8464 (m-40) cc_final: 0.8196 (m-40) REVERT: Z 43 LEU cc_start: 0.9397 (tp) cc_final: 0.8611 (tp) REVERT: Z 47 TYR cc_start: 0.9146 (m-10) cc_final: 0.8689 (m-80) REVERT: Z 84 LEU cc_start: 0.9401 (mt) cc_final: 0.9135 (mt) REVERT: a 15 CYS cc_start: 0.9255 (m) cc_final: 0.9024 (m) REVERT: a 48 MET cc_start: 0.8747 (ttm) cc_final: 0.8514 (mmm) REVERT: b 19 LEU cc_start: 0.9516 (mt) cc_final: 0.9224 (mt) REVERT: b 23 PHE cc_start: 0.8473 (m-80) cc_final: 0.8153 (m-80) REVERT: b 62 ASN cc_start: 0.8294 (p0) cc_final: 0.7570 (p0) REVERT: q 66 THR cc_start: 0.4501 (m) cc_final: 0.4122 (m) REVERT: q 87 HIS cc_start: 0.2460 (t70) cc_final: 0.1816 (t-170) REVERT: q 93 MET cc_start: 0.6316 (mtt) cc_final: 0.5781 (ttm) outliers start: 0 outliers final: 0 residues processed: 880 average time/residue: 0.1985 time to fit residues: 285.8980 Evaluate side-chains 692 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 114 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 302 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 321 optimal weight: 0.0370 chunk 142 optimal weight: 6.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 HIS ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN W 105 HIS ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.073573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058158 restraints weight = 173248.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.059966 restraints weight = 105531.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.061188 restraints weight = 73605.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062026 restraints weight = 56715.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062712 restraints weight = 48075.147| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34019 Z= 0.150 Angle : 0.991 70.565 46156 Z= 0.368 Chirality : 0.046 0.277 5059 Planarity : 0.005 0.073 5846 Dihedral : 8.089 161.286 4702 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.49 % 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: -0.89 (0.13), residues: 4054 helix: 0.16 (0.12), residues: 1853 sheet: -1.68 (0.26), residues: 379 loop : -1.05 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 153 TYR 0.025 0.002 TYR B 73 PHE 0.039 0.002 PHE D 204 TRP 0.049 0.002 TRP C 170 HIS 0.008 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00347 (33978) covalent geometry : angle 0.72197 (46064) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.71959 ( 8) hydrogen bonds : bond 0.04020 ( 1320) hydrogen bonds : angle 5.34019 ( 3759) metal coordination : bond 0.01630 ( 37) metal coordination : angle 15.91235 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 871 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 55 PHE cc_start: 0.9216 (m-80) cc_final: 0.8900 (m-80) REVERT: A 61 THR cc_start: 0.9595 (m) cc_final: 0.9266 (m) REVERT: A 63 LEU cc_start: 0.9253 (tp) cc_final: 0.9052 (tp) REVERT: B 76 THR cc_start: 0.9393 (p) cc_final: 0.9006 (p) REVERT: B 105 MET cc_start: 0.9127 (mmm) cc_final: 0.8918 (mmt) REVERT: B 117 PHE cc_start: 0.8789 (m-80) cc_final: 0.8460 (m-80) REVERT: B 152 MET cc_start: 0.8818 (ttm) cc_final: 0.8403 (ttm) REVERT: B 190 TYR cc_start: 0.8971 (m-80) cc_final: 0.8221 (m-80) REVERT: B 202 LEU cc_start: 0.9616 (tp) cc_final: 0.9411 (tp) REVERT: B 205 ILE cc_start: 0.9738 (mm) cc_final: 0.9507 (mm) REVERT: B 218 LEU cc_start: 0.9101 (mm) cc_final: 0.8721 (mp) REVERT: C 165 TYR cc_start: 0.9241 (m-80) cc_final: 0.8831 (m-80) REVERT: C 176 PHE cc_start: 0.8019 (t80) cc_final: 0.6888 (t80) REVERT: C 187 LEU cc_start: 0.8588 (pp) cc_final: 0.8288 (pp) REVERT: C 214 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8416 (mm-30) REVERT: C 230 ARG cc_start: 0.8434 (ptp90) cc_final: 0.7836 (ptt-90) REVERT: D 124 ILE cc_start: 0.9550 (mm) cc_final: 0.9260 (mm) REVERT: D 138 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8480 (mtt90) REVERT: D 185 MET cc_start: 0.8845 (tpt) cc_final: 0.8496 (tpt) REVERT: D 202 TRP cc_start: 0.8438 (m-10) cc_final: 0.7799 (m-90) REVERT: D 205 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 261 MET cc_start: 0.8505 (mmt) cc_final: 0.8242 (mtt) REVERT: E 46 ASN cc_start: 0.6233 (t0) cc_final: 0.5917 (t0) REVERT: E 65 ILE cc_start: 0.9038 (mm) cc_final: 0.8780 (mm) REVERT: E 165 ASP cc_start: 0.8742 (t70) cc_final: 0.8534 (p0) REVERT: F 102 MET cc_start: 0.7927 (mmt) cc_final: 0.7417 (mmt) REVERT: F 149 MET cc_start: 0.4408 (mmt) cc_final: 0.4155 (mmt) REVERT: F 191 TYR cc_start: 0.7491 (t80) cc_final: 0.7152 (t80) REVERT: F 204 TYR cc_start: 0.6733 (t80) cc_final: 0.6530 (t80) REVERT: F 292 MET cc_start: 0.7859 (ppp) cc_final: 0.7382 (ppp) REVERT: F 314 LEU cc_start: 0.9496 (mm) cc_final: 0.9246 (mt) REVERT: F 392 MET cc_start: 0.9562 (mmt) cc_final: 0.9096 (mmp) REVERT: F 442 PHE cc_start: 0.8841 (m-80) cc_final: 0.8562 (m-80) REVERT: G 74 ASN cc_start: 0.9492 (m110) cc_final: 0.9143 (t0) REVERT: G 118 GLU cc_start: 0.9285 (tt0) cc_final: 0.9063 (tm-30) REVERT: G 144 MET cc_start: 0.9027 (tpp) cc_final: 0.8769 (tpt) REVERT: G 173 MET cc_start: 0.8176 (tpt) cc_final: 0.7352 (tpt) REVERT: G 306 MET cc_start: 0.8321 (mtm) cc_final: 0.7659 (mpp) REVERT: G 426 ASP cc_start: 0.8512 (t0) cc_final: 0.8285 (p0) REVERT: G 544 MET cc_start: 0.6926 (ptt) cc_final: 0.6550 (ptt) REVERT: G 546 PHE cc_start: 0.8390 (m-80) cc_final: 0.7788 (m-10) REVERT: G 548 LEU cc_start: 0.8851 (tp) cc_final: 0.8632 (tp) REVERT: G 598 ASN cc_start: 0.8930 (p0) cc_final: 0.8412 (p0) REVERT: G 607 LYS cc_start: 0.9295 (mppt) cc_final: 0.8954 (mmtm) REVERT: G 639 LEU cc_start: 0.9261 (pt) cc_final: 0.9016 (tp) REVERT: G 693 ASP cc_start: 0.8442 (m-30) cc_final: 0.7818 (t0) REVERT: G 694 PHE cc_start: 0.8558 (t80) cc_final: 0.7724 (t80) REVERT: H 7 LEU cc_start: 0.9542 (mm) cc_final: 0.9040 (pp) REVERT: H 15 ILE cc_start: 0.9258 (mp) cc_final: 0.8847 (mp) REVERT: H 17 MET cc_start: 0.8956 (tmm) cc_final: 0.8321 (tmm) REVERT: H 24 GLU cc_start: 0.9283 (tt0) cc_final: 0.8954 (tt0) REVERT: H 31 MET cc_start: 0.9094 (mmt) cc_final: 0.8675 (mmt) REVERT: H 35 LYS cc_start: 0.8604 (mtmt) cc_final: 0.8082 (mtpp) REVERT: H 53 MET cc_start: 0.9455 (tpt) cc_final: 0.8770 (tpp) REVERT: H 57 MET cc_start: 0.9255 (mmp) cc_final: 0.8544 (mmp) REVERT: H 89 LEU cc_start: 0.9199 (tp) cc_final: 0.8985 (tp) REVERT: H 97 ASN cc_start: 0.8796 (t0) cc_final: 0.8354 (t0) REVERT: H 134 ARG cc_start: 0.9348 (mtp-110) cc_final: 0.9110 (mtt90) REVERT: H 139 THR cc_start: 0.9597 (p) cc_final: 0.9303 (p) REVERT: H 143 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8579 (mm-30) REVERT: H 146 MET cc_start: 0.9140 (ptp) cc_final: 0.8621 (ptp) REVERT: H 150 LEU cc_start: 0.9527 (tp) cc_final: 0.9102 (tp) REVERT: H 172 MET cc_start: 0.8155 (tpt) cc_final: 0.7822 (tpt) REVERT: H 174 LEU cc_start: 0.9562 (mt) cc_final: 0.9243 (mt) REVERT: H 179 TRP cc_start: 0.8269 (p-90) cc_final: 0.8058 (p-90) REVERT: H 214 GLU cc_start: 0.7702 (tt0) cc_final: 0.7326 (tt0) REVERT: H 273 ILE cc_start: 0.9425 (tt) cc_final: 0.9053 (tt) REVERT: H 277 TYR cc_start: 0.7690 (m-80) cc_final: 0.7470 (m-80) REVERT: H 280 PHE cc_start: 0.8203 (m-80) cc_final: 0.7599 (m-80) REVERT: H 302 MET cc_start: 0.9423 (ttm) cc_final: 0.8923 (ttp) REVERT: I 38 TYR cc_start: 0.8110 (m-80) cc_final: 0.7900 (m-10) REVERT: I 40 ASN cc_start: 0.8285 (t0) cc_final: 0.7922 (t0) REVERT: I 72 MET cc_start: 0.7930 (mpp) cc_final: 0.7466 (mpp) REVERT: I 114 ILE cc_start: 0.9533 (pt) cc_final: 0.9203 (tp) REVERT: P 92 MET cc_start: 0.8814 (mmp) cc_final: 0.8177 (mmm) REVERT: P 96 LEU cc_start: 0.8908 (pt) cc_final: 0.8605 (pt) REVERT: P 97 MET cc_start: 0.8014 (mmm) cc_final: 0.7801 (mmp) REVERT: P 220 TYR cc_start: 0.8792 (m-80) cc_final: 0.8319 (m-80) REVERT: P 300 TRP cc_start: 0.7532 (m100) cc_final: 0.7149 (m-10) REVERT: Q 78 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7923 (ttp-170) REVERT: Q 84 ARG cc_start: 0.8401 (tmm160) cc_final: 0.8074 (tmm-80) REVERT: Q 88 GLN cc_start: 0.8653 (mt0) cc_final: 0.7644 (mm-40) REVERT: Q 96 LYS cc_start: 0.9361 (mptt) cc_final: 0.8899 (mtmt) REVERT: Q 117 THR cc_start: 0.6859 (t) cc_final: 0.5737 (m) REVERT: Q 160 TYR cc_start: 0.8092 (t80) cc_final: 0.7808 (t80) REVERT: R 76 ILE cc_start: 0.8601 (mt) cc_final: 0.8358 (mp) REVERT: S 44 LEU cc_start: 0.8829 (tp) cc_final: 0.8511 (pp) REVERT: T 113 LEU cc_start: 0.9352 (tp) cc_final: 0.9060 (tp) REVERT: T 130 ILE cc_start: 0.9384 (mm) cc_final: 0.8012 (mm) REVERT: T 147 TYR cc_start: 0.7905 (t80) cc_final: 0.7359 (t80) REVERT: V 24 LEU cc_start: 0.9618 (mt) cc_final: 0.9251 (mt) REVERT: V 28 TYR cc_start: 0.8603 (m-80) cc_final: 0.8101 (m-10) REVERT: V 44 TYR cc_start: 0.8884 (t80) cc_final: 0.8680 (t80) REVERT: V 58 MET cc_start: 0.9110 (mtm) cc_final: 0.8837 (mtm) REVERT: V 90 LEU cc_start: 0.9657 (tp) cc_final: 0.9341 (tt) REVERT: V 93 LYS cc_start: 0.9307 (ptpp) cc_final: 0.8780 (ptpp) REVERT: V 94 MET cc_start: 0.8219 (mmp) cc_final: 0.7705 (mmm) REVERT: W 32 LYS cc_start: 0.9345 (ptpt) cc_final: 0.8992 (pttp) REVERT: W 73 ASN cc_start: 0.9545 (m110) cc_final: 0.9067 (m-40) REVERT: W 85 LEU cc_start: 0.9744 (mt) cc_final: 0.9514 (mt) REVERT: W 90 LYS cc_start: 0.9588 (tptp) cc_final: 0.9267 (tptp) REVERT: W 94 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8799 (tp-100) REVERT: W 95 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7476 (tm-30) REVERT: W 98 LYS cc_start: 0.9456 (mmpt) cc_final: 0.9173 (mmmt) REVERT: W 129 HIS cc_start: 0.6675 (m-70) cc_final: 0.6366 (m-70) REVERT: Z 84 LEU cc_start: 0.9433 (mt) cc_final: 0.9165 (mt) REVERT: Z 137 ASN cc_start: 0.8617 (p0) cc_final: 0.8046 (p0) REVERT: a 48 MET cc_start: 0.8750 (ttm) cc_final: 0.8521 (mmm) REVERT: b 19 LEU cc_start: 0.9553 (mt) cc_final: 0.9226 (mt) REVERT: b 23 PHE cc_start: 0.8537 (m-80) cc_final: 0.8179 (m-80) REVERT: b 62 ASN cc_start: 0.8184 (p0) cc_final: 0.7426 (p0) REVERT: q 66 THR cc_start: 0.4285 (m) cc_final: 0.3907 (m) REVERT: q 87 HIS cc_start: 0.2058 (t70) cc_final: 0.1493 (t-170) REVERT: q 93 MET cc_start: 0.6287 (mtt) cc_final: 0.5444 (ttm) REVERT: r 112 TYR cc_start: 0.8518 (m-80) cc_final: 0.8282 (m-80) outliers start: 1 outliers final: 1 residues processed: 872 average time/residue: 0.2006 time to fit residues: 286.5295 Evaluate side-chains 688 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 687 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 353 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 221 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.073424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058080 restraints weight = 173160.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.059894 restraints weight = 105140.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061128 restraints weight = 73520.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062036 restraints weight = 57348.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.062628 restraints weight = 47203.600| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34019 Z= 0.156 Angle : 1.002 69.520 46156 Z= 0.378 Chirality : 0.047 0.323 5059 Planarity : 0.005 0.064 5846 Dihedral : 8.153 164.238 4702 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.95 (0.13), residues: 4054 helix: 0.09 (0.12), residues: 1865 sheet: -1.70 (0.26), residues: 377 loop : -1.06 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 153 TYR 0.037 0.002 TYR D 135 PHE 0.036 0.002 PHE D 204 TRP 0.054 0.002 TRP C 170 HIS 0.008 0.001 HIS q 87 Details of bonding type rmsd covalent geometry : bond 0.00362 (33978) covalent geometry : angle 0.74294 (46064) SS BOND : bond 0.00340 ( 4) SS BOND : angle 2.46590 ( 8) hydrogen bonds : bond 0.04043 ( 1320) hydrogen bonds : angle 5.41516 ( 3759) metal coordination : bond 0.01567 ( 37) metal coordination : angle 15.77348 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 842 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9400 (mm) cc_final: 0.9030 (tt) REVERT: A 61 THR cc_start: 0.9588 (m) cc_final: 0.9265 (m) REVERT: B 76 THR cc_start: 0.9441 (p) cc_final: 0.9054 (p) REVERT: B 94 THR cc_start: 0.8868 (p) cc_final: 0.8447 (p) REVERT: B 105 MET cc_start: 0.9029 (mmm) cc_final: 0.8813 (mmt) REVERT: B 117 PHE cc_start: 0.8733 (m-80) cc_final: 0.8435 (m-80) REVERT: B 152 MET cc_start: 0.8525 (ttm) cc_final: 0.8220 (ttm) REVERT: B 190 TYR cc_start: 0.8867 (m-80) cc_final: 0.8090 (m-80) REVERT: B 202 LEU cc_start: 0.9578 (tp) cc_final: 0.9375 (tp) REVERT: B 218 LEU cc_start: 0.9032 (mm) cc_final: 0.8700 (mp) REVERT: C 165 TYR cc_start: 0.9268 (m-80) cc_final: 0.8912 (m-80) REVERT: C 176 PHE cc_start: 0.7953 (t80) cc_final: 0.6742 (t80) REVERT: C 187 LEU cc_start: 0.8757 (pp) cc_final: 0.8409 (pp) REVERT: C 192 PHE cc_start: 0.8954 (t80) cc_final: 0.8721 (t80) REVERT: C 225 LEU cc_start: 0.9041 (mm) cc_final: 0.8827 (mm) REVERT: D 145 MET cc_start: 0.9124 (tpp) cc_final: 0.8394 (tpt) REVERT: D 185 MET cc_start: 0.8878 (tpt) cc_final: 0.8514 (tpt) REVERT: D 202 TRP cc_start: 0.8476 (m-10) cc_final: 0.7950 (m-90) REVERT: E 46 ASN cc_start: 0.6265 (t0) cc_final: 0.6051 (t0) REVERT: E 65 ILE cc_start: 0.9038 (mm) cc_final: 0.8808 (mm) REVERT: E 83 ASP cc_start: 0.9176 (m-30) cc_final: 0.8932 (m-30) REVERT: E 165 ASP cc_start: 0.8743 (t70) cc_final: 0.8470 (p0) REVERT: F 275 LEU cc_start: 0.9273 (mm) cc_final: 0.8548 (tp) REVERT: F 292 MET cc_start: 0.7820 (ppp) cc_final: 0.7339 (ppp) REVERT: F 314 LEU cc_start: 0.9512 (mm) cc_final: 0.9273 (mt) REVERT: F 337 MET cc_start: 0.8807 (mtm) cc_final: 0.8434 (mtm) REVERT: F 392 MET cc_start: 0.9556 (mmt) cc_final: 0.9053 (mmp) REVERT: F 442 PHE cc_start: 0.8850 (m-80) cc_final: 0.8594 (m-80) REVERT: G 74 ASN cc_start: 0.9441 (m110) cc_final: 0.9176 (t0) REVERT: G 77 MET cc_start: 0.9000 (tpt) cc_final: 0.8774 (tpp) REVERT: G 144 MET cc_start: 0.9048 (tpp) cc_final: 0.8757 (tpt) REVERT: G 173 MET cc_start: 0.8192 (tpt) cc_final: 0.7418 (tpt) REVERT: G 306 MET cc_start: 0.8306 (mtm) cc_final: 0.7653 (mpp) REVERT: G 496 MET cc_start: 0.8533 (mpp) cc_final: 0.7814 (mtm) REVERT: G 544 MET cc_start: 0.6950 (ptt) cc_final: 0.6581 (ptt) REVERT: G 546 PHE cc_start: 0.8317 (m-80) cc_final: 0.7667 (m-10) REVERT: G 548 LEU cc_start: 0.8867 (tp) cc_final: 0.8665 (tp) REVERT: G 598 ASN cc_start: 0.8874 (p0) cc_final: 0.8337 (p0) REVERT: G 607 LYS cc_start: 0.9315 (mppt) cc_final: 0.9007 (mmtm) REVERT: G 693 ASP cc_start: 0.8466 (m-30) cc_final: 0.7863 (t0) REVERT: G 694 PHE cc_start: 0.8540 (t80) cc_final: 0.7748 (t80) REVERT: H 15 ILE cc_start: 0.9203 (mp) cc_final: 0.8880 (mp) REVERT: H 17 MET cc_start: 0.8916 (tmm) cc_final: 0.8296 (tmm) REVERT: H 31 MET cc_start: 0.9152 (mmt) cc_final: 0.8694 (mmt) REVERT: H 35 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8081 (mtpp) REVERT: H 53 MET cc_start: 0.9473 (tpt) cc_final: 0.8787 (tpp) REVERT: H 57 MET cc_start: 0.9256 (mmp) cc_final: 0.8468 (mmp) REVERT: H 97 ASN cc_start: 0.8932 (t0) cc_final: 0.8446 (t0) REVERT: H 106 LEU cc_start: 0.8817 (mm) cc_final: 0.8310 (tp) REVERT: H 150 LEU cc_start: 0.9530 (tp) cc_final: 0.9034 (tp) REVERT: H 154 LEU cc_start: 0.9508 (mt) cc_final: 0.9299 (mt) REVERT: H 179 TRP cc_start: 0.8267 (p-90) cc_final: 0.8067 (p-90) REVERT: H 184 MET cc_start: 0.9213 (mtt) cc_final: 0.8901 (mmm) REVERT: H 185 TRP cc_start: 0.9392 (t-100) cc_final: 0.9080 (t-100) REVERT: H 214 GLU cc_start: 0.7753 (tt0) cc_final: 0.7426 (tt0) REVERT: H 228 TYR cc_start: 0.9411 (m-80) cc_final: 0.8724 (m-80) REVERT: H 273 ILE cc_start: 0.9413 (tt) cc_final: 0.8995 (tt) REVERT: H 277 TYR cc_start: 0.7920 (m-80) cc_final: 0.7356 (m-80) REVERT: H 302 MET cc_start: 0.9382 (ttm) cc_final: 0.8965 (ttp) REVERT: I 38 TYR cc_start: 0.8151 (m-80) cc_final: 0.7945 (m-10) REVERT: I 40 ASN cc_start: 0.8276 (t0) cc_final: 0.7950 (t0) REVERT: I 72 MET cc_start: 0.7864 (mpp) cc_final: 0.7532 (mpp) REVERT: I 114 ILE cc_start: 0.9520 (pt) cc_final: 0.9212 (tp) REVERT: I 120 GLU cc_start: 0.7944 (tp30) cc_final: 0.7635 (tp30) REVERT: P 92 MET cc_start: 0.8790 (mmp) cc_final: 0.8156 (mmm) REVERT: P 220 TYR cc_start: 0.8818 (m-80) cc_final: 0.8344 (m-80) REVERT: P 300 TRP cc_start: 0.7537 (m100) cc_final: 0.7137 (m-10) REVERT: P 346 GLU cc_start: 0.7914 (mp0) cc_final: 0.7650 (mp0) REVERT: Q 84 ARG cc_start: 0.8317 (tmm160) cc_final: 0.8076 (tmm-80) REVERT: Q 88 GLN cc_start: 0.8730 (mt0) cc_final: 0.7726 (mm-40) REVERT: Q 96 LYS cc_start: 0.9358 (mptt) cc_final: 0.8894 (mtmt) REVERT: Q 151 LYS cc_start: 0.7975 (mmpt) cc_final: 0.6895 (mtpp) REVERT: Q 160 TYR cc_start: 0.8181 (t80) cc_final: 0.7842 (t80) REVERT: R 76 ILE cc_start: 0.8611 (mt) cc_final: 0.8371 (mp) REVERT: S 44 LEU cc_start: 0.8830 (tp) cc_final: 0.8525 (pp) REVERT: S 64 LYS cc_start: 0.8731 (pttm) cc_final: 0.7969 (ptpp) REVERT: S 80 ASN cc_start: 0.8796 (p0) cc_final: 0.8116 (p0) REVERT: T 113 LEU cc_start: 0.9376 (tp) cc_final: 0.9025 (tp) REVERT: V 24 LEU cc_start: 0.9595 (mt) cc_final: 0.9263 (mt) REVERT: V 28 TYR cc_start: 0.8591 (m-80) cc_final: 0.8101 (m-10) REVERT: V 44 TYR cc_start: 0.8855 (t80) cc_final: 0.8654 (t80) REVERT: V 90 LEU cc_start: 0.9633 (tp) cc_final: 0.9264 (tt) REVERT: V 93 LYS cc_start: 0.9302 (ptpp) cc_final: 0.8887 (pttt) REVERT: V 94 MET cc_start: 0.8172 (mmp) cc_final: 0.7719 (mmm) REVERT: W 32 LYS cc_start: 0.9359 (ptpt) cc_final: 0.9011 (pttp) REVERT: W 39 TYR cc_start: 0.7813 (t80) cc_final: 0.6693 (t80) REVERT: W 43 TYR cc_start: 0.8869 (t80) cc_final: 0.8241 (t80) REVERT: W 73 ASN cc_start: 0.9508 (m110) cc_final: 0.9033 (m-40) REVERT: W 85 LEU cc_start: 0.9722 (mt) cc_final: 0.9499 (mt) REVERT: W 90 LYS cc_start: 0.9585 (tptp) cc_final: 0.9209 (tptp) REVERT: W 93 LEU cc_start: 0.9338 (mt) cc_final: 0.9138 (mt) REVERT: W 94 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8814 (tp-100) REVERT: W 98 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9146 (mmmt) REVERT: W 110 PHE cc_start: 0.8168 (m-10) cc_final: 0.7324 (m-80) REVERT: W 129 HIS cc_start: 0.6618 (m-70) cc_final: 0.6292 (m-70) REVERT: Z 24 ASN cc_start: 0.8475 (m-40) cc_final: 0.8177 (m-40) REVERT: Z 36 PHE cc_start: 0.8933 (m-80) cc_final: 0.8434 (t80) REVERT: Z 84 LEU cc_start: 0.9435 (mt) cc_final: 0.9168 (mt) REVERT: Z 137 ASN cc_start: 0.8504 (p0) cc_final: 0.7871 (p0) REVERT: a 48 MET cc_start: 0.8730 (ttm) cc_final: 0.8511 (mmm) REVERT: b 19 LEU cc_start: 0.9552 (mt) cc_final: 0.9245 (mt) REVERT: b 23 PHE cc_start: 0.8571 (m-80) cc_final: 0.8188 (m-80) REVERT: b 62 ASN cc_start: 0.8119 (p0) cc_final: 0.7556 (p0) REVERT: q 66 THR cc_start: 0.4242 (m) cc_final: 0.3853 (m) REVERT: q 87 HIS cc_start: 0.2122 (t70) cc_final: 0.1562 (t-170) REVERT: q 93 MET cc_start: 0.6133 (mtt) cc_final: 0.5281 (ttm) REVERT: r 112 TYR cc_start: 0.8568 (m-80) cc_final: 0.8326 (m-80) outliers start: 0 outliers final: 0 residues processed: 842 average time/residue: 0.1983 time to fit residues: 274.1505 Evaluate side-chains 678 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 68 optimal weight: 0.9980 chunk 375 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 107 optimal weight: 40.0000 chunk 370 optimal weight: 0.3980 chunk 354 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.074202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058771 restraints weight = 172845.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.060646 restraints weight = 105355.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.061966 restraints weight = 73232.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.062813 restraints weight = 56259.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.063476 restraints weight = 46787.579| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34019 Z= 0.149 Angle : 0.983 67.042 46156 Z= 0.377 Chirality : 0.047 0.294 5059 Planarity : 0.005 0.064 5846 Dihedral : 8.089 167.741 4702 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % 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: -0.94 (0.13), residues: 4054 helix: 0.10 (0.12), residues: 1866 sheet: -1.72 (0.26), residues: 375 loop : -1.04 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 153 TYR 0.025 0.002 TYR B 73 PHE 0.027 0.002 PHE H 19 TRP 0.066 0.002 TRP C 170 HIS 0.008 0.001 HIS q 87 Details of bonding type rmsd covalent geometry : bond 0.00342 (33978) covalent geometry : angle 0.74143 (46064) SS BOND : bond 0.00366 ( 4) SS BOND : angle 2.40202 ( 8) hydrogen bonds : bond 0.04025 ( 1320) hydrogen bonds : angle 5.43330 ( 3759) metal coordination : bond 0.01312 ( 37) metal coordination : angle 15.14407 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8108 Ramachandran restraints generated. 4054 Oldfield, 0 Emsley, 4054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 854 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9430 (mm) cc_final: 0.9203 (tp) REVERT: A 56 PHE cc_start: 0.7280 (m-80) cc_final: 0.7036 (m-80) REVERT: A 61 THR cc_start: 0.9593 (m) cc_final: 0.9253 (m) REVERT: B 76 THR cc_start: 0.9429 (p) cc_final: 0.9035 (p) REVERT: B 105 MET cc_start: 0.8975 (mmm) cc_final: 0.8745 (mmt) REVERT: B 114 MET cc_start: 0.8135 (ptt) cc_final: 0.7848 (ptt) REVERT: B 117 PHE cc_start: 0.8770 (m-80) cc_final: 0.8486 (m-80) REVERT: B 138 THR cc_start: 0.9570 (p) cc_final: 0.8859 (p) REVERT: B 141 MET cc_start: 0.8319 (mmm) cc_final: 0.7779 (mmm) REVERT: B 152 MET cc_start: 0.8442 (ttm) cc_final: 0.8086 (ttt) REVERT: B 190 TYR cc_start: 0.8984 (m-80) cc_final: 0.8137 (m-80) REVERT: B 202 LEU cc_start: 0.9575 (tp) cc_final: 0.9297 (tp) REVERT: B 205 ILE cc_start: 0.9692 (mm) cc_final: 0.9457 (mm) REVERT: B 218 LEU cc_start: 0.9063 (mm) cc_final: 0.8685 (mp) REVERT: C 165 TYR cc_start: 0.9242 (m-80) cc_final: 0.8811 (m-80) REVERT: C 176 PHE cc_start: 0.7928 (t80) cc_final: 0.6473 (t80) REVERT: C 214 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8421 (mm-30) REVERT: D 124 ILE cc_start: 0.9564 (mm) cc_final: 0.9359 (mm) REVERT: D 145 MET cc_start: 0.9065 (tpp) cc_final: 0.7964 (tpt) REVERT: D 185 MET cc_start: 0.8849 (tpt) cc_final: 0.8486 (tpt) REVERT: E 46 ASN cc_start: 0.6442 (t0) cc_final: 0.6168 (t0) REVERT: E 65 ILE cc_start: 0.9025 (mm) cc_final: 0.8725 (mm) REVERT: E 165 ASP cc_start: 0.8701 (t70) cc_final: 0.8410 (p0) REVERT: F 204 TYR cc_start: 0.6808 (t80) cc_final: 0.6581 (t80) REVERT: F 275 LEU cc_start: 0.9299 (mm) cc_final: 0.8556 (tp) REVERT: F 292 MET cc_start: 0.7816 (ppp) cc_final: 0.7337 (ppp) REVERT: F 314 LEU cc_start: 0.9482 (mm) cc_final: 0.9251 (mt) REVERT: F 337 MET cc_start: 0.8710 (mtm) cc_final: 0.8312 (mtm) REVERT: F 392 MET cc_start: 0.9586 (mmt) cc_final: 0.9075 (mmp) REVERT: F 442 PHE cc_start: 0.8848 (m-80) cc_final: 0.8583 (m-80) REVERT: G 74 ASN cc_start: 0.9532 (m-40) cc_final: 0.9223 (t0) REVERT: G 173 MET cc_start: 0.8147 (tpt) cc_final: 0.7393 (tpt) REVERT: G 306 MET cc_start: 0.8295 (mtm) cc_final: 0.7648 (mpp) REVERT: G 544 MET cc_start: 0.6942 (ptt) cc_final: 0.6681 (ptt) REVERT: G 546 PHE cc_start: 0.8310 (m-80) cc_final: 0.7675 (m-10) REVERT: G 598 ASN cc_start: 0.9019 (p0) cc_final: 0.8407 (p0) REVERT: G 607 LYS cc_start: 0.9286 (mppt) cc_final: 0.8960 (mmtm) REVERT: G 694 PHE cc_start: 0.8562 (t80) cc_final: 0.7780 (t80) REVERT: H 15 ILE cc_start: 0.9204 (mp) cc_final: 0.8954 (mp) REVERT: H 17 MET cc_start: 0.8936 (tmm) cc_final: 0.8348 (tmm) REVERT: H 31 MET cc_start: 0.9173 (mmt) cc_final: 0.8390 (mmt) REVERT: H 35 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8082 (mtpp) REVERT: H 53 MET cc_start: 0.9467 (tpt) cc_final: 0.9214 (tpp) REVERT: H 76 THR cc_start: 0.7978 (p) cc_final: 0.7437 (t) REVERT: H 97 ASN cc_start: 0.9018 (t0) cc_final: 0.8593 (t0) REVERT: H 118 TRP cc_start: 0.8055 (m-10) cc_final: 0.7848 (m-10) REVERT: H 139 THR cc_start: 0.9575 (p) cc_final: 0.9284 (p) REVERT: H 143 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8605 (mm-30) REVERT: H 150 LEU cc_start: 0.9545 (tp) cc_final: 0.9063 (tp) REVERT: H 154 LEU cc_start: 0.9538 (mt) cc_final: 0.9273 (mt) REVERT: H 174 LEU cc_start: 0.9585 (mt) cc_final: 0.9293 (mt) REVERT: H 179 TRP cc_start: 0.8298 (p-90) cc_final: 0.8058 (p-90) REVERT: H 184 MET cc_start: 0.9211 (mtt) cc_final: 0.8902 (mmm) REVERT: H 185 TRP cc_start: 0.9412 (t-100) cc_final: 0.9081 (t-100) REVERT: H 214 GLU cc_start: 0.7807 (tt0) cc_final: 0.7495 (tt0) REVERT: H 273 ILE cc_start: 0.9387 (tt) cc_final: 0.9116 (tt) REVERT: H 277 TYR cc_start: 0.7624 (m-80) cc_final: 0.7215 (m-80) REVERT: H 291 LYS cc_start: 0.9410 (mttt) cc_final: 0.9092 (mtmt) REVERT: H 302 MET cc_start: 0.9355 (ttm) cc_final: 0.9043 (ttp) REVERT: I 38 TYR cc_start: 0.8142 (m-80) cc_final: 0.7892 (m-10) REVERT: I 40 ASN cc_start: 0.8496 (t0) cc_final: 0.8132 (t0) REVERT: I 72 MET cc_start: 0.7710 (mpp) cc_final: 0.7374 (mpp) REVERT: I 114 ILE cc_start: 0.9476 (pt) cc_final: 0.9175 (tp) REVERT: I 117 LYS cc_start: 0.9453 (mtmt) cc_final: 0.8760 (mtmt) REVERT: I 143 THR cc_start: 0.9389 (p) cc_final: 0.9083 (p) REVERT: P 92 MET cc_start: 0.8815 (mmp) cc_final: 0.8142 (mmm) REVERT: P 96 LEU cc_start: 0.8921 (pt) cc_final: 0.8557 (pt) REVERT: P 97 MET cc_start: 0.8023 (mmm) cc_final: 0.7467 (mmp) REVERT: P 220 TYR cc_start: 0.8595 (m-80) cc_final: 0.8155 (m-80) REVERT: P 300 TRP cc_start: 0.7575 (m100) cc_final: 0.7155 (m-10) REVERT: P 346 GLU cc_start: 0.7855 (mp0) cc_final: 0.7557 (mp0) REVERT: Q 84 ARG cc_start: 0.8319 (tmm160) cc_final: 0.8020 (tmm-80) REVERT: Q 88 GLN cc_start: 0.8828 (mt0) cc_final: 0.7842 (mm-40) REVERT: Q 96 LYS cc_start: 0.9346 (mptt) cc_final: 0.8876 (mtmt) REVERT: Q 151 LYS cc_start: 0.8023 (mmpt) cc_final: 0.6973 (mtpp) REVERT: S 44 LEU cc_start: 0.8813 (tp) cc_final: 0.8511 (pp) REVERT: S 62 GLN cc_start: 0.8346 (pp30) cc_final: 0.7996 (pp30) REVERT: S 80 ASN cc_start: 0.8269 (p0) cc_final: 0.7268 (p0) REVERT: T 113 LEU cc_start: 0.9377 (tp) cc_final: 0.9078 (tp) REVERT: T 123 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8523 (tm-30) REVERT: V 24 LEU cc_start: 0.9593 (mt) cc_final: 0.9200 (mt) REVERT: V 33 ASP cc_start: 0.8628 (m-30) cc_final: 0.8425 (m-30) REVERT: V 44 TYR cc_start: 0.8856 (t80) cc_final: 0.8619 (t80) REVERT: V 86 LYS cc_start: 0.9607 (mmtt) cc_final: 0.9389 (mmmm) REVERT: V 90 LEU cc_start: 0.9645 (tp) cc_final: 0.9268 (tt) REVERT: V 93 LYS cc_start: 0.9290 (ptpp) cc_final: 0.8908 (pttt) REVERT: V 94 MET cc_start: 0.8242 (mmp) cc_final: 0.7797 (mmm) REVERT: W 32 LYS cc_start: 0.9393 (ptpt) cc_final: 0.9042 (pttp) REVERT: W 73 ASN cc_start: 0.9499 (m110) cc_final: 0.9004 (m-40) REVERT: W 85 LEU cc_start: 0.9723 (mt) cc_final: 0.9484 (mt) REVERT: W 90 LYS cc_start: 0.9579 (tptp) cc_final: 0.9222 (tptp) REVERT: W 98 LYS cc_start: 0.9428 (mmpt) cc_final: 0.9198 (mmmt) REVERT: W 124 LYS cc_start: 0.9246 (pttp) cc_final: 0.8973 (ptpp) REVERT: Z 24 ASN cc_start: 0.8517 (m-40) cc_final: 0.8208 (m-40) REVERT: Z 36 PHE cc_start: 0.8897 (m-80) cc_final: 0.8435 (t80) REVERT: Z 84 LEU cc_start: 0.9425 (mt) cc_final: 0.9157 (mt) REVERT: Z 137 ASN cc_start: 0.8715 (p0) cc_final: 0.8095 (p0) REVERT: a 48 MET cc_start: 0.8831 (ttm) cc_final: 0.8539 (mmm) REVERT: b 19 LEU cc_start: 0.9583 (mt) cc_final: 0.9273 (mt) REVERT: b 23 PHE cc_start: 0.8622 (m-80) cc_final: 0.8197 (m-80) REVERT: b 62 ASN cc_start: 0.8116 (p0) cc_final: 0.7556 (p0) REVERT: q 66 THR cc_start: 0.4504 (m) cc_final: 0.4113 (m) REVERT: q 87 HIS cc_start: 0.2349 (t70) cc_final: 0.1791 (t-170) REVERT: q 93 MET cc_start: 0.6178 (mtt) cc_final: 0.5316 (ttm) outliers start: 1 outliers final: 0 residues processed: 854 average time/residue: 0.2031 time to fit residues: 283.0346 Evaluate side-chains 681 residues out of total 3566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 21 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 275 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 246 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 394 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN C 76 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 88 GLN ** R 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 HIS W 61 GLN ** X 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 64 ASN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.070345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055336 restraints weight = 178471.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057013 restraints weight = 106657.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058191 restraints weight = 74241.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059109 restraints weight = 57333.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.059646 restraints weight = 47604.005| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 34019 Z= 0.243 Angle : 1.085 68.326 46156 Z= 0.418 Chirality : 0.049 0.310 5059 Planarity : 0.006 0.106 5846 Dihedral : 8.218 170.819 4702 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.96 (0.13), residues: 4054 helix: 0.08 (0.12), residues: 1879 sheet: -1.63 (0.26), residues: 385 loop : -1.09 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 153 TYR 0.028 0.002 TYR C 71 PHE 0.036 0.003 PHE D 204 TRP 0.047 0.003 TRP C 170 HIS 0.016 0.002 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00525 (33978) covalent geometry : angle 0.80576 (46064) SS BOND : bond 0.00393 ( 4) SS BOND : angle 2.35419 ( 8) hydrogen bonds : bond 0.04345 ( 1320) hydrogen bonds : angle 5.66658 ( 3759) metal coordination : bond 0.02925 ( 37) metal coordination : angle 17.03295 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7339.08 seconds wall clock time: 127 minutes 20.33 seconds (7640.33 seconds total)