Starting phenix.real_space_refine on Tue May 5 22:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513.map" model { file = "/net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xns_38513/05_2026/8xns_38513_neut.cif" } resolution = 3.5 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= 0.083 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 8 5.49 5 S 245 5.16 5 C 21775 2.51 5 N 5802 2.21 5 O 6170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s 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: 34029 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2538 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 22, 'TRANS': 295} Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 8, 'TRANS': 111} Chain breaks: 1 Chain: "r" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 413 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 226 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-4': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 23 Chain: "I" Number of atoms: 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1178 SG CYS B 99 79.962 61.331 105.406 1.00 29.52 S ATOM 1681 SG CYS B 164 77.260 57.580 110.238 1.00 28.96 S ATOM 1911 SG CYS B 194 82.426 57.685 109.576 1.00 29.28 S ATOM 1184 SG CYS B 100 78.850 57.341 104.450 1.00 30.11 S ATOM 7691 SG CYS E 134 139.218 53.802 152.730 1.00 56.01 S ATOM 7725 SG CYS E 139 141.641 55.555 152.096 1.00 56.50 S ATOM 8009 SG CYS E 175 136.642 57.085 155.425 1.00 54.42 S ATOM 8032 SG CYS E 179 139.864 58.894 155.654 1.00 57.95 S ATOM 11562 SG CYS F 425 120.087 62.130 155.515 1.00 45.60 S ATOM 11240 SG CYS F 385 120.331 59.826 149.655 1.00 39.95 S ATOM 11220 SG CYS F 382 115.980 60.741 151.876 1.00 40.29 S ATOM 11201 SG CYS F 379 118.064 56.680 154.659 1.00 43.09 S ATOM 12610 SG CYS G 131 100.515 49.318 137.729 1.00 31.31 S ATOM 12589 SG CYS G 128 102.442 53.378 133.288 1.00 30.26 S ATOM 12650 SG CYS G 137 99.906 55.156 139.321 1.00 33.13 S ATOM 13335 SG CYS G 226 101.894 49.124 146.341 1.00 34.31 S ATOM 13006 SG CYS G 182 105.003 47.405 152.101 1.00 36.31 S ATOM 12982 SG CYS G 179 104.193 53.030 149.716 1.00 35.62 S ATOM 12959 SG CYS G 176 107.857 48.988 147.184 1.00 34.05 S ATOM 12096 SG CYS G 64 105.309 59.058 151.938 1.00 35.53 S ATOM 12182 SG CYS G 75 105.977 61.180 150.349 1.00 36.47 S ATOM 12207 SG CYS G 78 104.645 65.512 152.573 1.00 36.76 S ATOM 12308 SG CYS G 92 104.447 63.501 155.689 1.00 39.04 S ATOM 20336 SG CYS I 123 86.405 52.405 118.586 1.00 27.30 S ATOM 20562 SG CYS I 152 86.324 51.391 113.436 1.00 27.39 S ATOM 20609 SG CYS I 158 91.924 51.728 115.679 1.00 26.60 S ATOM 20588 SG CYS I 155 88.636 56.019 115.422 1.00 27.04 S ATOM 20285 SG CYS I 116 96.252 48.553 126.073 1.00 29.24 S ATOM 20308 SG CYS I 119 91.980 48.146 122.606 1.00 28.85 S ATOM 20266 SG CYS I 113 95.404 43.478 122.623 1.00 28.61 S ATOM 20638 SG CYS I 162 98.138 48.266 120.733 1.00 28.07 S ATOM 25147 SG CYS R 79 111.819 41.996 125.466 1.00 32.60 S ATOM 25323 SG CYS R 104 109.398 40.419 126.811 1.00 32.49 S ATOM 25345 SG CYS R 107 108.774 41.146 123.393 1.00 30.78 S Time building chain proxies: 8.07, per 1000 atoms: 0.24 Number of scatterers: 34029 At special positions: 0 Unit cell: (166.1, 129.8, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 245 16.00 P 8 15.00 O 6170 8.00 N 5802 7.00 C 21775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 158 " pdb="FE2 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 162 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 116 " pdb="FE2 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 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7880 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 31 sheets defined 49.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.503A pdb=" N ALA A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.314A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.584A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.250A pdb=" N PHE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 118' Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.589A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.602A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.321A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.298A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.772A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.765A 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 145 through 159 Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.707A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.669A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.530A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.525A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.682A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.558A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.294A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.553A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.921A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.516A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.636A 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: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.565A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.533A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.860A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.156A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.507A pdb=" N VAL F 343 " --> pdb=" O PHE F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.545A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.914A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.655A 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: 3.518A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.598A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.671A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.608A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 85 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.687A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.853A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.735A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 removed outlier: 4.348A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 242 removed outlier: 3.859A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.539A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.865A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.144A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.872A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.624A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.755A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 219 removed outlier: 4.082A pdb=" N PHE P 217 " --> pdb=" O PHE P 213 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 222 No H-bonds generated for 'chain 'P' and resid 220 through 222' Processing helix chain 'P' and resid 229 through 232 Processing helix chain 'P' and resid 242 through 254 Processing helix chain 'P' and resid 272 through 285 Processing helix chain 'P' and resid 294 through 308 removed outlier: 3.621A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.199A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 44 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.550A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 64' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.447A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.812A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.675A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.587A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.615A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 98 through 100 No H-bonds generated for 'chain 'W' and resid 98 through 100' Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.642A pdb=" N ARG W 108 " --> pdb=" O THR W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.529A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.625A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 51 Processing helix chain 'X' and resid 52 through 55 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.944A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 removed outlier: 4.463A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.905A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.758A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.845A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 removed outlier: 3.663A pdb=" N LEU q 23 " --> pdb=" O GLY q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.126A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 's' and resid 43 through 54 removed outlier: 4.203A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 removed outlier: 4.540A pdb=" N ILE B 132 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.523A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 83 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LYS C 143 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE C 85 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.149A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.107A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.352A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 401 removed outlier: 3.500A pdb=" N PHE D 407 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AB1, 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=AB2, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.152A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.868A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.313A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.454A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.408A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.360A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.360A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD1, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.507A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AD4, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.240A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 4125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 11596 1.37 - 1.59: 22792 1.59 - 1.80: 264 1.80 - 2.02: 122 2.02 - 2.23: 80 Bond restraints: 34854 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 1.398 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.180 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C VAL W 106 " pdb=" N MET W 107 " ideal model delta sigma weight residual 1.335 1.218 0.117 1.34e-02 5.57e+03 7.63e+01 bond pdb=" CA ASP R 39 " pdb=" C ASP R 39 " ideal model delta sigma weight residual 1.527 1.639 -0.112 1.41e-02 5.03e+03 6.30e+01 ... (remaining 34849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 46507 6.67 - 13.35: 583 13.35 - 20.02: 160 20.02 - 26.69: 1 26.69 - 33.37: 2 Bond angle restraints: 47253 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 89.01 25.63 1.52e+00 4.33e-01 2.84e+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 93.51 19.66 1.26e+00 6.30e-01 2.43e+02 angle pdb=" N VAL H 208 " pdb=" CA VAL H 208 " pdb=" C VAL H 208 " ideal model delta sigma weight residual 111.62 100.83 10.79 7.90e-01 1.60e+00 1.87e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.89 -18.72 1.40e+00 5.10e-01 1.79e+02 angle pdb=" N MET G 77 " pdb=" CA MET G 77 " pdb=" C MET G 77 " ideal model delta sigma weight residual 113.38 97.32 16.06 1.23e+00 6.61e-01 1.71e+02 ... (remaining 47248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 20610 35.18 - 70.35: 349 70.35 - 105.53: 30 105.53 - 140.71: 6 140.71 - 175.88: 2 Dihedral angle restraints: 20997 sinusoidal: 8771 harmonic: 12226 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.52 -68.52 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.66 -16.94 0 2.50e+00 1.60e-01 4.59e+01 dihedral pdb=" CB CYS S 24 " pdb=" SG CYS S 24 " pdb=" SG CYS S 58 " pdb=" CB CYS S 58 " ideal model delta sinusoidal sigma weight residual -86.00 -139.94 53.94 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 20994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4583 0.182 - 0.364: 511 0.364 - 0.547: 48 0.547 - 0.729: 4 0.729 - 0.911: 24 Chirality restraints: 5170 Sorted by residual: chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.07e+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 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 5167 not shown) Planarity restraints: 6013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " 0.131 2.00e-02 2.50e+03 2.84e-01 2.41e+03 pdb=" C1M UQ9 H 401 " 0.638 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " -0.102 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " -0.022 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " 0.042 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " 0.066 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " -0.102 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " -0.573 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " -0.361 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " -0.016 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " 0.080 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 B 302 " 0.034 2.00e-02 2.50e+03 2.02e-01 1.22e+03 pdb=" C1M UQ9 B 302 " 0.209 2.00e-02 2.50e+03 pdb=" C2 UQ9 B 302 " -0.133 2.00e-02 2.50e+03 pdb=" C3 UQ9 B 302 " 0.100 2.00e-02 2.50e+03 pdb=" C4 UQ9 B 302 " -0.006 2.00e-02 2.50e+03 pdb=" C5 UQ9 B 302 " -0.038 2.00e-02 2.50e+03 pdb=" C6 UQ9 B 302 " 0.025 2.00e-02 2.50e+03 pdb=" C7 UQ9 B 302 " 0.079 2.00e-02 2.50e+03 pdb=" O2 UQ9 B 302 " -0.463 2.00e-02 2.50e+03 pdb=" O3 UQ9 B 302 " 0.413 2.00e-02 2.50e+03 pdb=" O4 UQ9 B 302 " -0.106 2.00e-02 2.50e+03 pdb=" O5 UQ9 B 302 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ9 H 401 " 0.252 2.00e-02 2.50e+03 2.13e-01 5.70e+02 pdb=" C18 UQ9 H 401 " -0.359 2.00e-02 2.50e+03 pdb=" C19 UQ9 H 401 " -0.074 2.00e-02 2.50e+03 pdb=" C20 UQ9 H 401 " 0.008 2.00e-02 2.50e+03 pdb=" C21 UQ9 H 401 " 0.172 2.00e-02 2.50e+03 ... (remaining 6010 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 82 2.38 - 3.01: 23294 3.01 - 3.64: 53396 3.64 - 4.27: 84304 4.27 - 4.90: 135573 Nonbonded interactions: 296649 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.940 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.981 3.120 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.984 3.040 ... (remaining 296644 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: 3.650 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 1.142 34894 Z= 1.040 Angle : 2.236 52.609 47343 Z= 1.492 Chirality : 0.129 0.911 5170 Planarity : 0.010 0.284 6013 Dihedral : 13.284 175.885 13108 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 47.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 0.41 % Allowed : 7.61 % Favored : 91.98 % Cbeta Deviations : 1.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.12), residues: 4163 helix: -0.90 (0.11), residues: 1788 sheet: -1.25 (0.27), residues: 366 loop : -2.05 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.046 0.002 TYR B 112 PHE 0.032 0.002 PHE G 462 TRP 0.033 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01449 (34854) covalent geometry : angle 2.10861 (47253) SS BOND : bond 0.00733 ( 3) SS BOND : angle 2.19338 ( 6) hydrogen bonds : bond 0.24770 ( 1428) hydrogen bonds : angle 9.07168 ( 4125) metal coordination : bond 0.52542 ( 37) metal coordination : angle 17.76418 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1739 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 1724 time to evaluate : 1.447 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: A 30 TYR cc_start: 0.6306 (m-80) cc_final: 0.6028 (m-80) REVERT: A 104 TYR cc_start: 0.8412 (t80) cc_final: 0.8113 (t80) REVERT: B 124 SER cc_start: 0.8542 (p) cc_final: 0.8308 (p) REVERT: B 170 TYR cc_start: 0.8249 (t80) cc_final: 0.8018 (t80) REVERT: B 190 TYR cc_start: 0.8209 (m-80) cc_final: 0.7920 (m-80) REVERT: C 211 TYR cc_start: 0.8206 (t80) cc_final: 0.7946 (t80) REVERT: D 83 ASN cc_start: 0.8306 (p0) cc_final: 0.7808 (p0) REVERT: D 144 MET cc_start: 0.7037 (mpp) cc_final: 0.6829 (mpp) REVERT: D 182 ASN cc_start: 0.7507 (t0) cc_final: 0.7093 (t0) REVERT: D 232 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8636 (t) REVERT: D 286 TYR cc_start: 0.7277 (m-80) cc_final: 0.6946 (m-80) REVERT: D 298 ILE cc_start: 0.8153 (mt) cc_final: 0.7915 (mt) REVERT: D 438 MET cc_start: 0.7909 (mtp) cc_final: 0.7653 (mtp) REVERT: G 261 ILE cc_start: 0.8723 (pp) cc_final: 0.8456 (pt) REVERT: G 271 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7170 (mmp) REVERT: G 408 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7319 (ttt180) REVERT: G 698 ASP cc_start: 0.7179 (p0) cc_final: 0.6517 (p0) REVERT: H 264 LEU cc_start: 0.8420 (mt) cc_final: 0.8102 (mt) REVERT: H 283 ASP cc_start: 0.7898 (p0) cc_final: 0.7686 (p0) REVERT: I 144 ARG cc_start: 0.7466 (ttm170) cc_final: 0.7158 (tmm-80) REVERT: P 54 VAL cc_start: 0.7530 (t) cc_final: 0.7307 (t) REVERT: P 84 TYR cc_start: 0.8039 (p90) cc_final: 0.7696 (p90) REVERT: P 188 GLU cc_start: 0.6330 (pt0) cc_final: 0.5655 (pt0) REVERT: P 324 ILE cc_start: 0.8048 (mm) cc_final: 0.7335 (mm) REVERT: S 23 LEU cc_start: 0.7890 (pp) cc_final: 0.7675 (pp) REVERT: S 65 LEU cc_start: 0.8440 (tt) cc_final: 0.6733 (tt) REVERT: T 119 ILE cc_start: 0.9084 (mm) cc_final: 0.8873 (mp) REVERT: T 130 ILE cc_start: 0.8077 (mp) cc_final: 0.7571 (mm) REVERT: V 26 ILE cc_start: 0.9039 (mm) cc_final: 0.8260 (mm) REVERT: V 29 THR cc_start: 0.8305 (p) cc_final: 0.8102 (p) REVERT: V 51 ILE cc_start: 0.8476 (mt) cc_final: 0.8161 (mm) REVERT: W 43 TYR cc_start: 0.8333 (t80) cc_final: 0.7776 (t80) REVERT: a 43 TYR cc_start: 0.7407 (t80) cc_final: 0.7183 (m-80) REVERT: r 16 SER cc_start: 0.7215 (p) cc_final: 0.7010 (p) outliers start: 15 outliers final: 2 residues processed: 1733 average time/residue: 0.2451 time to fit residues: 661.5437 Evaluate side-chains 1034 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1030 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain G residue 271 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 179 ASN C 180 HIS C 227 GLN ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 117 HIS D 131 GLN D 147 ASN D 149 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 152 GLN E 190 ASN E 245 GLN F 44 ASN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 ASN F 455 GLN G 74 ASN G 164 ASN G 205 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN ** G 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 495 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 663 ASN H 32 GLN H 47 GLN H 97 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 235 ASN H 304 HIS I 193 ASN P 71 ASN ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 ASN ** P 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 356 HIS ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 HIS S 25 GLN V 41 HIS W 73 ASN W 105 HIS ** W 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN Z 8 GLN Z 54 ASN Z 85 GLN b 83 ASN q 12 GLN q 31 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 59 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088101 restraints weight = 88343.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091021 restraints weight = 39869.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092880 restraints weight = 23645.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094067 restraints weight = 16890.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094799 restraints weight = 13639.868| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 34894 Z= 0.217 Angle : 1.020 72.935 47343 Z= 0.440 Chirality : 0.050 0.251 5170 Planarity : 0.007 0.185 6013 Dihedral : 9.266 144.818 4817 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 4.16 % Allowed : 18.04 % Favored : 77.80 % 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: 4163 helix: 0.22 (0.12), residues: 1852 sheet: -0.84 (0.27), residues: 367 loop : -1.40 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 257 TYR 0.030 0.003 TYR F 177 PHE 0.038 0.003 PHE H 130 TRP 0.024 0.002 TRP G 285 HIS 0.010 0.002 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00499 (34854) covalent geometry : angle 0.84809 (47253) SS BOND : bond 0.00669 ( 3) SS BOND : angle 1.95900 ( 6) hydrogen bonds : bond 0.06124 ( 1428) hydrogen bonds : angle 5.79731 ( 4125) metal coordination : bond 0.02669 ( 37) metal coordination : angle 13.45398 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1093 time to evaluate : 1.183 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: A 5 THR cc_start: 0.8706 (m) cc_final: 0.8400 (p) REVERT: A 10 ASN cc_start: 0.8494 (t0) cc_final: 0.8248 (t0) REVERT: A 12 LEU cc_start: 0.8953 (mt) cc_final: 0.8719 (tp) REVERT: A 30 TYR cc_start: 0.6685 (m-80) cc_final: 0.6355 (m-80) REVERT: A 87 MET cc_start: 0.8880 (tmm) cc_final: 0.7945 (tmm) REVERT: B 141 MET cc_start: 0.8986 (tpt) cc_final: 0.8779 (tpt) REVERT: B 147 LYS cc_start: 0.9027 (tptm) cc_final: 0.8683 (tptm) REVERT: C 166 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 211 TYR cc_start: 0.8837 (t80) cc_final: 0.8336 (t80) REVERT: C 214 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 108 LYS cc_start: 0.8431 (mptt) cc_final: 0.8196 (mmtt) REVERT: D 144 MET cc_start: 0.7595 (mpp) cc_final: 0.7134 (mpp) REVERT: D 182 ASN cc_start: 0.8677 (t0) cc_final: 0.8334 (t0) REVERT: D 215 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 309 ASP cc_start: 0.8054 (m-30) cc_final: 0.7629 (m-30) REVERT: D 311 TYR cc_start: 0.8715 (m-80) cc_final: 0.8421 (m-80) REVERT: D 360 ASP cc_start: 0.8188 (m-30) cc_final: 0.7903 (t0) REVERT: D 404 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8205 (mmtt) REVERT: D 414 ASP cc_start: 0.8199 (t0) cc_final: 0.7944 (t0) REVERT: E 68 ASN cc_start: 0.6609 (m110) cc_final: 0.5722 (m110) REVERT: E 120 MET cc_start: 0.7770 (tpp) cc_final: 0.7281 (mtp) REVERT: E 140 MET cc_start: 0.8964 (tmm) cc_final: 0.8739 (tmm) REVERT: E 141 LEU cc_start: 0.8978 (mt) cc_final: 0.8701 (mt) REVERT: E 153 ARG cc_start: 0.8589 (mmp80) cc_final: 0.8382 (mmp80) REVERT: E 190 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6632 (t0) REVERT: E 244 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6251 (t) REVERT: F 61 ASP cc_start: 0.5803 (m-30) cc_final: 0.5376 (t0) REVERT: F 290 GLU cc_start: 0.7372 (tp30) cc_final: 0.6432 (tp30) REVERT: F 313 ASN cc_start: 0.8427 (m-40) cc_final: 0.7993 (t0) REVERT: F 337 MET cc_start: 0.8934 (mmm) cc_final: 0.8221 (mmp) REVERT: F 387 GLU cc_start: 0.8407 (mp0) cc_final: 0.7990 (mp0) REVERT: F 418 GLN cc_start: 0.8617 (mm-40) cc_final: 0.8056 (mt0) REVERT: G 97 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6097 (mtm) REVERT: G 117 MET cc_start: 0.8418 (tpp) cc_final: 0.7797 (mmm) REVERT: G 213 MET cc_start: 0.8253 (ptp) cc_final: 0.8001 (ptm) REVERT: G 271 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8295 (mmm) REVERT: G 527 ASP cc_start: 0.9101 (m-30) cc_final: 0.8813 (m-30) REVERT: H 181 MET cc_start: 0.8051 (mtm) cc_final: 0.7743 (mtm) REVERT: H 200 LEU cc_start: 0.7208 (tt) cc_final: 0.6899 (tt) REVERT: H 202 GLU cc_start: 0.7164 (tp30) cc_final: 0.6909 (tp30) REVERT: H 204 GLU cc_start: 0.8334 (tp30) cc_final: 0.8106 (tp30) REVERT: H 214 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8472 (mm-30) REVERT: H 224 PHE cc_start: 0.8022 (t80) cc_final: 0.7647 (t80) REVERT: H 264 LEU cc_start: 0.9040 (mt) cc_final: 0.8820 (mt) REVERT: H 284 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8295 (mp10) REVERT: H 286 MET cc_start: 0.8679 (ttp) cc_final: 0.8263 (ttp) REVERT: I 65 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: I 169 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6732 (mm-30) REVERT: I 208 ASP cc_start: 0.8509 (t0) cc_final: 0.8052 (t70) REVERT: P 293 LEU cc_start: 0.9063 (mt) cc_final: 0.8556 (mt) REVERT: P 324 ILE cc_start: 0.8698 (mm) cc_final: 0.8298 (mm) REVERT: P 335 LEU cc_start: 0.8686 (mt) cc_final: 0.8068 (mp) REVERT: P 349 SER cc_start: 0.9573 (p) cc_final: 0.9107 (m) REVERT: Q 88 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8099 (mm-40) REVERT: Q 100 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: Q 149 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7414 (pp20) REVERT: Q 157 SER cc_start: 0.8814 (m) cc_final: 0.8501 (p) REVERT: Q 160 TYR cc_start: 0.7778 (t80) cc_final: 0.6610 (t80) REVERT: Q 164 PHE cc_start: 0.7962 (m-80) cc_final: 0.7106 (m-80) REVERT: S 21 VAL cc_start: 0.9347 (t) cc_final: 0.9099 (p) REVERT: S 59 SER cc_start: 0.8082 (t) cc_final: 0.7628 (p) REVERT: S 64 LYS cc_start: 0.6761 (mtmt) cc_final: 0.6448 (mtmm) REVERT: S 91 MET cc_start: 0.8985 (mmm) cc_final: 0.8670 (mmm) REVERT: T 79 ILE cc_start: 0.8113 (mm) cc_final: 0.7515 (tt) REVERT: T 119 ILE cc_start: 0.9206 (mm) cc_final: 0.8872 (mm) REVERT: T 120 MET cc_start: 0.9173 (mtm) cc_final: 0.8760 (mtt) REVERT: T 123 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7274 (mp0) REVERT: T 134 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8623 (m-30) REVERT: V 19 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8454 (t) REVERT: V 28 TYR cc_start: 0.8567 (m-10) cc_final: 0.8194 (m-10) REVERT: W 43 TYR cc_start: 0.8816 (t80) cc_final: 0.8505 (t80) REVERT: W 53 MET cc_start: 0.8840 (mmm) cc_final: 0.8280 (mtt) REVERT: W 71 MET cc_start: 0.8681 (mtt) cc_final: 0.8470 (mtt) REVERT: W 98 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9137 (mtmt) REVERT: W 107 MET cc_start: 0.8799 (mmm) cc_final: 0.8495 (mmm) REVERT: W 119 LYS cc_start: 0.7686 (tppt) cc_final: 0.7180 (tppt) REVERT: W 120 ASP cc_start: 0.8051 (t0) cc_final: 0.7766 (m-30) REVERT: W 121 PHE cc_start: 0.8843 (t80) cc_final: 0.8431 (t80) REVERT: X 36 CYS cc_start: 0.7134 (m) cc_final: 0.6889 (t) REVERT: X 40 ASN cc_start: 0.8525 (m-40) cc_final: 0.8169 (m-40) REVERT: X 44 MET cc_start: 0.9042 (mmm) cc_final: 0.8792 (mmm) REVERT: Z 50 MET cc_start: 0.8856 (tpp) cc_final: 0.8323 (tpp) REVERT: a 5 ILE cc_start: 0.9382 (mt) cc_final: 0.9167 (mp) REVERT: a 43 TYR cc_start: 0.8334 (t80) cc_final: 0.6563 (m-80) REVERT: b 13 TRP cc_start: 0.8472 (t-100) cc_final: 0.7927 (t-100) REVERT: b 63 MET cc_start: 0.7323 (mtm) cc_final: 0.7009 (mtm) REVERT: q 12 GLN cc_start: 0.8112 (mm110) cc_final: 0.7734 (tm-30) REVERT: q 50 GLU cc_start: 0.7767 (pt0) cc_final: 0.7351 (pt0) REVERT: r 16 SER cc_start: 0.7439 (p) cc_final: 0.7138 (p) outliers start: 152 outliers final: 67 residues processed: 1177 average time/residue: 0.2199 time to fit residues: 423.9618 Evaluate side-chains 988 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 913 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 255 CYS Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain G residue 547 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 154 GLN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 134 ASP Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 53 ARG Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain q residue 63 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 133 optimal weight: 6.9990 chunk 408 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** B 106 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 87 GLN D 92 HIS ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS F 455 GLN G 205 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN H 287 HIS I 193 ASN I 204 ASN P 71 ASN P 166 HIS ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 275 HIS Q 51 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 ASN R 33 HIS R 56 ASN V 21 HIS V 111 GLN W 102 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN r 21 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086298 restraints weight = 88301.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089163 restraints weight = 38792.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.091002 restraints weight = 22771.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092183 restraints weight = 16164.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092905 restraints weight = 13025.151| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34894 Z= 0.190 Angle : 0.933 75.209 47343 Z= 0.384 Chirality : 0.047 0.285 5170 Planarity : 0.006 0.157 6013 Dihedral : 8.974 168.988 4816 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.32 % Rotamer: Outliers : 4.71 % Allowed : 19.44 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.59 (0.13), residues: 4163 helix: 0.52 (0.12), residues: 1842 sheet: -0.95 (0.26), residues: 385 loop : -1.12 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 48 TYR 0.041 0.002 TYR W 126 PHE 0.030 0.002 PHE A 62 TRP 0.035 0.002 TRP V 97 HIS 0.009 0.001 HIS D 380 Details of bonding type rmsd covalent geometry : bond 0.00440 (34854) covalent geometry : angle 0.75202 (47253) SS BOND : bond 0.00633 ( 3) SS BOND : angle 2.02105 ( 6) hydrogen bonds : bond 0.04994 ( 1428) hydrogen bonds : angle 5.37653 ( 4125) metal coordination : bond 0.02362 ( 37) metal coordination : angle 13.11163 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1007 time to evaluate : 1.306 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: A 5 THR cc_start: 0.8918 (m) cc_final: 0.8621 (p) REVERT: A 10 ASN cc_start: 0.8777 (t0) cc_final: 0.8496 (t0) REVERT: A 87 MET cc_start: 0.8941 (tmm) cc_final: 0.8053 (tmm) REVERT: B 72 GLU cc_start: 0.6389 (tt0) cc_final: 0.5788 (mt-10) REVERT: B 105 MET cc_start: 0.8784 (mmm) cc_final: 0.8458 (mmm) REVERT: B 147 LYS cc_start: 0.9049 (tptm) cc_final: 0.8839 (tptm) REVERT: C 166 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8237 (mt-10) REVERT: C 211 TYR cc_start: 0.8953 (t80) cc_final: 0.8519 (t80) REVERT: D 79 ASN cc_start: 0.8158 (m-40) cc_final: 0.7802 (t0) REVERT: D 130 LEU cc_start: 0.9412 (tp) cc_final: 0.9192 (tt) REVERT: D 182 ASN cc_start: 0.8655 (t0) cc_final: 0.8355 (t0) REVERT: D 212 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 254 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7981 (tpp80) REVERT: D 259 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8152 (mt-10) REVERT: D 311 TYR cc_start: 0.8686 (m-80) cc_final: 0.8469 (m-80) REVERT: D 437 LYS cc_start: 0.8547 (tptt) cc_final: 0.8332 (tptp) REVERT: D 455 ASP cc_start: 0.8489 (t0) cc_final: 0.8284 (t0) REVERT: E 129 TYR cc_start: 0.7462 (m-10) cc_final: 0.7081 (m-80) REVERT: E 140 MET cc_start: 0.8892 (tmm) cc_final: 0.8661 (tmm) REVERT: E 141 LEU cc_start: 0.8958 (mt) cc_final: 0.8007 (mt) REVERT: E 244 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6549 (t) REVERT: F 112 TYR cc_start: 0.8053 (m-80) cc_final: 0.7596 (m-80) REVERT: F 115 VAL cc_start: 0.9287 (t) cc_final: 0.8995 (p) REVERT: F 262 PHE cc_start: 0.7884 (t80) cc_final: 0.7472 (t80) REVERT: F 313 ASN cc_start: 0.8419 (m-40) cc_final: 0.8066 (t0) REVERT: F 337 MET cc_start: 0.8960 (mmm) cc_final: 0.8402 (mmp) REVERT: F 387 GLU cc_start: 0.8418 (mp0) cc_final: 0.8118 (mp0) REVERT: F 418 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: G 42 MET cc_start: 0.8271 (tpp) cc_final: 0.8022 (tpp) REVERT: G 213 MET cc_start: 0.8352 (ptp) cc_final: 0.8046 (ptm) REVERT: G 271 MET cc_start: 0.8532 (mmp) cc_final: 0.8261 (mmp) REVERT: G 431 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8422 (tp) REVERT: G 467 LYS cc_start: 0.8676 (mttp) cc_final: 0.8174 (mmtt) REVERT: H 181 MET cc_start: 0.8484 (mtm) cc_final: 0.8096 (mtm) REVERT: H 183 MET cc_start: 0.8085 (mtt) cc_final: 0.7833 (mtp) REVERT: H 214 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8486 (mm-30) REVERT: H 224 PHE cc_start: 0.8029 (t80) cc_final: 0.7804 (t80) REVERT: H 254 LEU cc_start: 0.7722 (mt) cc_final: 0.7147 (mm) REVERT: H 258 ASN cc_start: 0.7790 (m-40) cc_final: 0.7328 (m-40) REVERT: H 282 TYR cc_start: 0.7468 (t80) cc_final: 0.7172 (t80) REVERT: H 286 MET cc_start: 0.8674 (ttp) cc_final: 0.8384 (ttp) REVERT: I 151 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8944 (mtpt) REVERT: I 208 ASP cc_start: 0.8621 (t0) cc_final: 0.8229 (t70) REVERT: P 324 ILE cc_start: 0.8846 (mm) cc_final: 0.8528 (mm) REVERT: P 335 LEU cc_start: 0.8553 (mt) cc_final: 0.8151 (mp) REVERT: P 346 GLU cc_start: 0.8411 (pm20) cc_final: 0.8205 (mp0) REVERT: Q 100 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: Q 157 SER cc_start: 0.8679 (m) cc_final: 0.8441 (p) REVERT: Q 160 TYR cc_start: 0.7953 (t80) cc_final: 0.6724 (t80) REVERT: Q 164 PHE cc_start: 0.8184 (m-80) cc_final: 0.7584 (m-80) REVERT: S 59 SER cc_start: 0.8273 (t) cc_final: 0.7901 (p) REVERT: S 65 LEU cc_start: 0.9046 (tt) cc_final: 0.8525 (tt) REVERT: S 91 MET cc_start: 0.8911 (mmm) cc_final: 0.8584 (mmm) REVERT: T 79 ILE cc_start: 0.8140 (mm) cc_final: 0.7538 (tt) REVERT: V 47 TYR cc_start: 0.8476 (m-80) cc_final: 0.8080 (m-80) REVERT: V 76 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: V 85 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: W 45 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: W 58 THR cc_start: 0.8939 (m) cc_final: 0.8716 (p) REVERT: W 121 PHE cc_start: 0.9042 (t80) cc_final: 0.8792 (t80) REVERT: X 36 CYS cc_start: 0.7034 (m) cc_final: 0.6557 (t) REVERT: X 44 MET cc_start: 0.8960 (mmm) cc_final: 0.8732 (mmm) REVERT: Z 94 GLU cc_start: 0.8324 (tt0) cc_final: 0.8045 (tt0) REVERT: Z 133 MET cc_start: 0.7267 (tpp) cc_final: 0.6978 (tpp) REVERT: a 38 VAL cc_start: 0.9455 (t) cc_final: 0.9237 (m) REVERT: a 43 TYR cc_start: 0.8304 (t80) cc_final: 0.6352 (m-80) REVERT: b 63 MET cc_start: 0.7537 (mtm) cc_final: 0.7193 (mtt) REVERT: q 12 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7805 (tm-30) REVERT: q 39 VAL cc_start: 0.7317 (OUTLIER) cc_final: 0.7052 (m) REVERT: q 81 MET cc_start: 0.7378 (mmt) cc_final: 0.7056 (mmm) outliers start: 172 outliers final: 92 residues processed: 1095 average time/residue: 0.2091 time to fit residues: 380.4809 Evaluate side-chains 988 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 886 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 45 LYS Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 206 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 303 LYS Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 52 ASN Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain s residue 47 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 242 optimal weight: 0.5980 chunk 354 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 229 optimal weight: 0.1980 chunk 311 optimal weight: 4.9990 chunk 380 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN H 5 ASN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN I 126 GLN P 154 GLN P 171 ASN ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 GLN S 80 ASN V 21 HIS W 73 ASN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085789 restraints weight = 89250.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088691 restraints weight = 39034.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090568 restraints weight = 23024.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091749 restraints weight = 16422.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092389 restraints weight = 13298.340| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34894 Z= 0.158 Angle : 0.901 75.090 47343 Z= 0.363 Chirality : 0.045 0.235 5170 Planarity : 0.005 0.159 6013 Dihedral : 8.748 169.510 4813 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 4.65 % Allowed : 20.42 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4163 helix: 0.69 (0.12), residues: 1844 sheet: -0.89 (0.26), residues: 371 loop : -1.01 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 144 TYR 0.042 0.002 TYR W 126 PHE 0.033 0.002 PHE P 145 TRP 0.024 0.001 TRP F 62 HIS 0.007 0.001 HIS G 460 Details of bonding type rmsd covalent geometry : bond 0.00367 (34854) covalent geometry : angle 0.72270 (47253) SS BOND : bond 0.00566 ( 3) SS BOND : angle 2.02495 ( 6) hydrogen bonds : bond 0.04497 ( 1428) hydrogen bonds : angle 5.16701 ( 4125) metal coordination : bond 0.01649 ( 37) metal coordination : angle 12.78538 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 982 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 5 THR cc_start: 0.8932 (m) cc_final: 0.8656 (p) REVERT: A 8 PHE cc_start: 0.7802 (m-80) cc_final: 0.7373 (m-10) REVERT: A 87 MET cc_start: 0.8891 (tmm) cc_final: 0.8584 (tmm) REVERT: B 72 GLU cc_start: 0.6354 (tt0) cc_final: 0.5892 (mt-10) REVERT: B 105 MET cc_start: 0.8698 (mmm) cc_final: 0.8484 (mmm) REVERT: B 174 SER cc_start: 0.9524 (t) cc_final: 0.9213 (t) REVERT: B 182 ASP cc_start: 0.8628 (p0) cc_final: 0.8308 (p0) REVERT: B 216 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6941 (pm20) REVERT: C 166 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 168 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8886 (tm-30) REVERT: C 211 TYR cc_start: 0.8988 (t80) cc_final: 0.8496 (t80) REVERT: C 212 ASP cc_start: 0.7894 (t70) cc_final: 0.7101 (t70) REVERT: D 79 ASN cc_start: 0.8316 (m-40) cc_final: 0.8005 (t0) REVERT: D 80 MET cc_start: 0.8542 (tmm) cc_final: 0.7280 (tmm) REVERT: D 144 MET cc_start: 0.7298 (mpp) cc_final: 0.6859 (mpp) REVERT: D 212 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7298 (tm-30) REVERT: D 254 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7903 (tpp80) REVERT: D 259 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8288 (mt-10) REVERT: D 356 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8842 (pp) REVERT: E 129 TYR cc_start: 0.7424 (m-10) cc_final: 0.6566 (m-10) REVERT: E 170 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7028 (pt) REVERT: E 244 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6642 (t) REVERT: F 112 TYR cc_start: 0.7883 (m-80) cc_final: 0.7430 (m-80) REVERT: F 191 TYR cc_start: 0.6273 (t80) cc_final: 0.5332 (t80) REVERT: F 262 PHE cc_start: 0.8178 (t80) cc_final: 0.7711 (t80) REVERT: F 313 ASN cc_start: 0.8356 (m-40) cc_final: 0.7962 (t0) REVERT: F 337 MET cc_start: 0.8967 (mmm) cc_final: 0.8476 (mmp) REVERT: F 376 HIS cc_start: 0.7790 (m90) cc_final: 0.7462 (m90) REVERT: F 387 GLU cc_start: 0.8402 (mp0) cc_final: 0.8154 (mp0) REVERT: F 418 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: G 117 MET cc_start: 0.8675 (mmm) cc_final: 0.8094 (mmm) REVERT: G 126 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8585 (pp) REVERT: G 213 MET cc_start: 0.8362 (ptp) cc_final: 0.8105 (ptm) REVERT: G 271 MET cc_start: 0.8486 (mmp) cc_final: 0.8149 (mmp) REVERT: G 431 LEU cc_start: 0.8659 (tp) cc_final: 0.8412 (tp) REVERT: G 467 LYS cc_start: 0.8682 (mttp) cc_final: 0.8402 (mtmm) REVERT: G 482 GLN cc_start: 0.8090 (mm110) cc_final: 0.7637 (mm110) REVERT: H 92 PRO cc_start: 0.8809 (Cg_endo) cc_final: 0.8548 (Cg_endo) REVERT: H 181 MET cc_start: 0.8582 (mtm) cc_final: 0.8346 (mtt) REVERT: H 183 MET cc_start: 0.8055 (mtt) cc_final: 0.7789 (mtp) REVERT: H 214 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8519 (mm-30) REVERT: H 254 LEU cc_start: 0.7873 (mt) cc_final: 0.7217 (mt) REVERT: H 258 ASN cc_start: 0.7780 (m-40) cc_final: 0.7349 (m-40) REVERT: H 284 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7490 (mt0) REVERT: H 286 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: H 318 MET cc_start: 0.7264 (tpt) cc_final: 0.6274 (tpt) REVERT: I 40 ASN cc_start: 0.8990 (t0) cc_final: 0.8291 (t0) REVERT: I 149 MET cc_start: 0.8917 (mmm) cc_final: 0.8460 (mmm) REVERT: I 208 ASP cc_start: 0.8636 (t0) cc_final: 0.8262 (t70) REVERT: P 324 ILE cc_start: 0.8830 (mm) cc_final: 0.8570 (mm) REVERT: Q 100 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: Q 160 TYR cc_start: 0.7951 (t80) cc_final: 0.6720 (t80) REVERT: Q 164 PHE cc_start: 0.8187 (m-80) cc_final: 0.7724 (m-80) REVERT: R 95 LEU cc_start: 0.8141 (mt) cc_final: 0.7646 (pp) REVERT: S 59 SER cc_start: 0.8031 (t) cc_final: 0.7604 (p) REVERT: S 65 LEU cc_start: 0.9043 (tt) cc_final: 0.8439 (tt) REVERT: S 80 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: S 91 MET cc_start: 0.8927 (mmm) cc_final: 0.8626 (mmm) REVERT: S 92 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8724 (pp30) REVERT: T 79 ILE cc_start: 0.8176 (mm) cc_final: 0.7638 (tt) REVERT: T 140 CYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4747 (m) REVERT: V 47 TYR cc_start: 0.8506 (m-80) cc_final: 0.8158 (m-80) REVERT: V 85 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: W 43 TYR cc_start: 0.9035 (t80) cc_final: 0.8615 (t80) REVERT: W 107 MET cc_start: 0.8936 (mmm) cc_final: 0.8313 (tpt) REVERT: W 122 LEU cc_start: 0.9185 (tp) cc_final: 0.8907 (mt) REVERT: W 125 PHE cc_start: 0.8918 (t80) cc_final: 0.8534 (t80) REVERT: X 36 CYS cc_start: 0.7019 (m) cc_final: 0.5907 (t) REVERT: X 40 ASN cc_start: 0.8677 (m-40) cc_final: 0.7883 (m-40) REVERT: X 44 MET cc_start: 0.9048 (mmm) cc_final: 0.8846 (mmm) REVERT: Z 94 GLU cc_start: 0.8450 (tt0) cc_final: 0.8198 (tt0) REVERT: Z 133 MET cc_start: 0.7285 (tpp) cc_final: 0.6936 (tpp) REVERT: a 43 TYR cc_start: 0.8267 (t80) cc_final: 0.6291 (m-80) REVERT: a 47 LEU cc_start: 0.9615 (mp) cc_final: 0.9340 (mp) REVERT: b 13 TRP cc_start: 0.8616 (t-100) cc_final: 0.7971 (t-100) REVERT: b 30 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8718 (mt) REVERT: b 31 ILE cc_start: 0.9051 (tt) cc_final: 0.8823 (mm) REVERT: b 63 MET cc_start: 0.7612 (mtm) cc_final: 0.7160 (mtt) REVERT: b 66 VAL cc_start: 0.8484 (t) cc_final: 0.8280 (m) REVERT: q 12 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7807 (tm-30) REVERT: q 81 MET cc_start: 0.7350 (mmt) cc_final: 0.7061 (mmm) REVERT: s 49 ASN cc_start: 0.9075 (t0) cc_final: 0.8801 (t0) REVERT: s 56 ARG cc_start: 0.6363 (mmp80) cc_final: 0.6138 (mmp-170) outliers start: 170 outliers final: 93 residues processed: 1073 average time/residue: 0.2021 time to fit residues: 360.6743 Evaluate side-chains 984 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 877 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 310 GLU Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 303 LYS Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 80 ASN Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 140 CYS Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 304 optimal weight: 0.7980 chunk 339 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 369 optimal weight: 1.9990 chunk 238 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 374 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 188 ASN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 663 ASN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN W 51 HIS ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086242 restraints weight = 88798.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.089060 restraints weight = 38847.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.090891 restraints weight = 22756.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092056 restraints weight = 16105.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092798 restraints weight = 12975.266| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34894 Z= 0.154 Angle : 0.891 75.900 47343 Z= 0.356 Chirality : 0.045 0.239 5170 Planarity : 0.005 0.141 6013 Dihedral : 8.533 144.592 4813 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 4.13 % Allowed : 21.93 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4163 helix: 0.82 (0.12), residues: 1838 sheet: -0.96 (0.27), residues: 359 loop : -0.89 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 279 TYR 0.045 0.002 TYR W 126 PHE 0.036 0.002 PHE W 121 TRP 0.023 0.001 TRP F 62 HIS 0.010 0.001 HIS W 51 Details of bonding type rmsd covalent geometry : bond 0.00360 (34854) covalent geometry : angle 0.70960 (47253) SS BOND : bond 0.00525 ( 3) SS BOND : angle 1.98510 ( 6) hydrogen bonds : bond 0.04286 ( 1428) hydrogen bonds : angle 5.04221 ( 4125) metal coordination : bond 0.01688 ( 37) metal coordination : angle 12.79970 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 964 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: A 5 THR cc_start: 0.8970 (m) cc_final: 0.8756 (p) REVERT: A 8 PHE cc_start: 0.7740 (m-80) cc_final: 0.7339 (m-10) REVERT: A 10 ASN cc_start: 0.8561 (t0) cc_final: 0.8292 (t0) REVERT: A 26 GLN cc_start: 0.8187 (tt0) cc_final: 0.7210 (tm-30) REVERT: A 55 PHE cc_start: 0.7491 (p90) cc_final: 0.7214 (p90) REVERT: A 87 MET cc_start: 0.8819 (tmm) cc_final: 0.8490 (tmm) REVERT: B 72 GLU cc_start: 0.6354 (tt0) cc_final: 0.5938 (mt-10) REVERT: B 127 GLN cc_start: 0.8898 (mt0) cc_final: 0.8595 (mt0) REVERT: B 147 LYS cc_start: 0.9000 (tptm) cc_final: 0.8741 (tptm) REVERT: B 174 SER cc_start: 0.9568 (t) cc_final: 0.9280 (t) REVERT: B 216 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: C 112 ASP cc_start: 0.8362 (t0) cc_final: 0.8017 (t70) REVERT: C 157 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 166 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 168 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8948 (tm-30) REVERT: C 211 TYR cc_start: 0.9034 (t80) cc_final: 0.8540 (t80) REVERT: C 212 ASP cc_start: 0.7877 (t70) cc_final: 0.7141 (t70) REVERT: D 80 MET cc_start: 0.8633 (tmm) cc_final: 0.7548 (tmm) REVERT: D 82 LEU cc_start: 0.8364 (tp) cc_final: 0.8161 (tt) REVERT: D 140 ASP cc_start: 0.8620 (t0) cc_final: 0.8372 (t70) REVERT: D 144 MET cc_start: 0.7779 (mpp) cc_final: 0.7236 (mpp) REVERT: D 145 MET cc_start: 0.7800 (mtt) cc_final: 0.7594 (mtt) REVERT: D 182 ASN cc_start: 0.8549 (t0) cc_final: 0.8229 (t0) REVERT: D 212 GLU cc_start: 0.7648 (tm-30) cc_final: 0.6863 (tm-30) REVERT: D 254 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7973 (tpp80) REVERT: D 259 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8346 (mt-10) REVERT: D 311 TYR cc_start: 0.8725 (m-80) cc_final: 0.8516 (m-80) REVERT: D 356 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8948 (pp) REVERT: E 86 GLN cc_start: 0.8681 (tt0) cc_final: 0.8458 (tt0) REVERT: E 129 TYR cc_start: 0.7763 (m-10) cc_final: 0.7094 (m-10) REVERT: E 132 GLN cc_start: 0.9242 (pt0) cc_final: 0.8949 (pt0) REVERT: E 140 MET cc_start: 0.8809 (tmm) cc_final: 0.8358 (tmm) REVERT: E 141 LEU cc_start: 0.8853 (mt) cc_final: 0.8589 (mt) REVERT: E 170 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7058 (pt) REVERT: E 194 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: E 244 VAL cc_start: 0.7189 (OUTLIER) cc_final: 0.6885 (t) REVERT: F 112 TYR cc_start: 0.7887 (m-80) cc_final: 0.7419 (m-80) REVERT: F 191 TYR cc_start: 0.6242 (t80) cc_final: 0.5291 (t80) REVERT: F 219 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7993 (mtpt) REVERT: F 262 PHE cc_start: 0.8086 (t80) cc_final: 0.7878 (t80) REVERT: F 290 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6717 (tp30) REVERT: F 313 ASN cc_start: 0.8289 (m-40) cc_final: 0.8072 (t0) REVERT: F 376 HIS cc_start: 0.7886 (m90) cc_final: 0.7522 (m90) REVERT: G 117 MET cc_start: 0.8809 (mmm) cc_final: 0.8245 (mmm) REVERT: G 126 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8540 (pp) REVERT: G 205 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: G 213 MET cc_start: 0.8334 (ptp) cc_final: 0.8090 (ptm) REVERT: G 225 ILE cc_start: 0.9080 (tt) cc_final: 0.8838 (tt) REVERT: G 271 MET cc_start: 0.8448 (mmp) cc_final: 0.8107 (mmp) REVERT: G 431 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8395 (tp) REVERT: G 579 MET cc_start: 0.8151 (ptm) cc_final: 0.7939 (ptm) REVERT: H 51 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8631 (m-30) REVERT: H 58 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8127 (ttmt) REVERT: H 68 MET cc_start: 0.8320 (mmm) cc_final: 0.7662 (ptt) REVERT: H 183 MET cc_start: 0.8129 (mtt) cc_final: 0.7829 (mtp) REVERT: H 214 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8381 (mm-30) REVERT: H 253 GLU cc_start: 0.7812 (mp0) cc_final: 0.7570 (tt0) REVERT: H 254 LEU cc_start: 0.7984 (mt) cc_final: 0.7326 (mt) REVERT: H 258 ASN cc_start: 0.7858 (m-40) cc_final: 0.7362 (m-40) REVERT: H 282 TYR cc_start: 0.7448 (t80) cc_final: 0.7095 (t80) REVERT: H 286 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8401 (ttp) REVERT: H 291 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7897 (tttt) REVERT: H 318 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6326 (tpt) REVERT: I 55 ASP cc_start: 0.8645 (m-30) cc_final: 0.8333 (m-30) REVERT: I 149 MET cc_start: 0.8942 (mmm) cc_final: 0.8439 (mmm) REVERT: I 151 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8994 (mtpt) REVERT: I 208 ASP cc_start: 0.8635 (t0) cc_final: 0.8297 (t70) REVERT: P 207 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7604 (t80) REVERT: P 217 PHE cc_start: 0.9236 (m-80) cc_final: 0.8883 (m-80) REVERT: P 346 GLU cc_start: 0.8267 (pm20) cc_final: 0.7906 (mp0) REVERT: Q 100 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: Q 160 TYR cc_start: 0.7966 (t80) cc_final: 0.6731 (t80) REVERT: Q 164 PHE cc_start: 0.8117 (m-80) cc_final: 0.7674 (m-80) REVERT: S 59 SER cc_start: 0.8111 (t) cc_final: 0.7729 (p) REVERT: S 65 LEU cc_start: 0.9030 (tt) cc_final: 0.8557 (tt) REVERT: S 69 TYR cc_start: 0.7441 (m-80) cc_final: 0.6986 (m-80) REVERT: S 91 MET cc_start: 0.8905 (mmm) cc_final: 0.8661 (mmm) REVERT: T 79 ILE cc_start: 0.8103 (mm) cc_final: 0.7564 (tt) REVERT: V 47 TYR cc_start: 0.8617 (m-80) cc_final: 0.8405 (m-80) REVERT: V 85 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: W 125 PHE cc_start: 0.8988 (t80) cc_final: 0.8692 (t80) REVERT: X 36 CYS cc_start: 0.6924 (m) cc_final: 0.5998 (t) REVERT: X 40 ASN cc_start: 0.8643 (m-40) cc_final: 0.7932 (m-40) REVERT: X 55 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8352 (mmp80) REVERT: X 109 GLN cc_start: 0.8840 (tt0) cc_final: 0.8447 (tm-30) REVERT: Z 35 MET cc_start: 0.8933 (mtp) cc_final: 0.8669 (mtp) REVERT: Z 94 GLU cc_start: 0.8219 (tt0) cc_final: 0.8001 (tt0) REVERT: Z 133 MET cc_start: 0.7357 (tpp) cc_final: 0.6918 (tpp) REVERT: a 43 TYR cc_start: 0.8241 (t80) cc_final: 0.6286 (m-80) REVERT: b 13 TRP cc_start: 0.8731 (t-100) cc_final: 0.8134 (t-100) REVERT: b 22 SER cc_start: 0.9089 (t) cc_final: 0.8820 (p) REVERT: b 30 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8709 (mt) REVERT: b 31 ILE cc_start: 0.9058 (tt) cc_final: 0.8854 (mm) REVERT: b 63 MET cc_start: 0.7636 (mtm) cc_final: 0.7204 (mtt) REVERT: b 66 VAL cc_start: 0.8535 (t) cc_final: 0.8319 (m) REVERT: q 12 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7919 (tm-30) REVERT: q 50 GLU cc_start: 0.7970 (pt0) cc_final: 0.7476 (pt0) REVERT: q 81 MET cc_start: 0.7368 (mmt) cc_final: 0.7159 (mmm) outliers start: 151 outliers final: 93 residues processed: 1042 average time/residue: 0.2022 time to fit residues: 350.1493 Evaluate side-chains 977 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 866 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 453 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 51 HIS Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 193 optimal weight: 0.0970 chunk 130 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 351 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 GLN F 455 GLN ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 ASN I 40 ASN ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085173 restraints weight = 88253.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087974 restraints weight = 38905.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089816 restraints weight = 23019.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090967 restraints weight = 16351.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.091703 restraints weight = 13229.612| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34894 Z= 0.147 Angle : 0.893 76.438 47343 Z= 0.353 Chirality : 0.045 0.212 5170 Planarity : 0.005 0.149 6013 Dihedral : 8.468 145.988 4813 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 4.27 % Allowed : 22.61 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.15 (0.13), residues: 4163 helix: 0.87 (0.12), residues: 1849 sheet: -1.01 (0.27), residues: 358 loop : -0.82 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 279 TYR 0.047 0.002 TYR W 126 PHE 0.032 0.002 PHE W 121 TRP 0.043 0.002 TRP V 97 HIS 0.033 0.001 HIS W 51 Details of bonding type rmsd covalent geometry : bond 0.00343 (34854) covalent geometry : angle 0.71142 (47253) SS BOND : bond 0.00507 ( 3) SS BOND : angle 1.91287 ( 6) hydrogen bonds : bond 0.04126 ( 1428) hydrogen bonds : angle 4.97872 ( 4125) metal coordination : bond 0.01554 ( 37) metal coordination : angle 12.80908 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 932 time to evaluate : 1.523 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: A 5 THR cc_start: 0.8994 (m) cc_final: 0.8742 (p) REVERT: A 8 PHE cc_start: 0.7797 (m-80) cc_final: 0.7390 (m-10) REVERT: A 10 ASN cc_start: 0.8664 (t0) cc_final: 0.8328 (t0) REVERT: A 26 GLN cc_start: 0.8221 (tt0) cc_final: 0.7373 (tm-30) REVERT: A 87 MET cc_start: 0.8829 (tmm) cc_final: 0.8519 (tmm) REVERT: B 72 GLU cc_start: 0.6312 (tt0) cc_final: 0.5972 (mt-10) REVERT: B 80 ASP cc_start: 0.8213 (t0) cc_final: 0.8004 (t0) REVERT: B 216 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: C 56 GLN cc_start: 0.8357 (mt0) cc_final: 0.8157 (mt0) REVERT: C 112 ASP cc_start: 0.8369 (t0) cc_final: 0.8042 (t70) REVERT: C 113 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (tt) REVERT: C 145 TYR cc_start: 0.9014 (p90) cc_final: 0.8698 (p90) REVERT: C 166 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 168 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8987 (tm-30) REVERT: C 190 TYR cc_start: 0.8617 (m-80) cc_final: 0.8368 (m-80) REVERT: C 211 TYR cc_start: 0.9055 (t80) cc_final: 0.8403 (t80) REVERT: C 212 ASP cc_start: 0.7856 (t70) cc_final: 0.7088 (t70) REVERT: D 80 MET cc_start: 0.8738 (tmm) cc_final: 0.7735 (tmm) REVERT: D 82 LEU cc_start: 0.8353 (tp) cc_final: 0.7997 (tt) REVERT: D 144 MET cc_start: 0.7897 (mpp) cc_final: 0.7174 (mpp) REVERT: D 182 ASN cc_start: 0.8582 (t0) cc_final: 0.8226 (t0) REVERT: D 212 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6787 (tm-30) REVERT: D 254 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7875 (tpp80) REVERT: D 311 TYR cc_start: 0.8774 (m-80) cc_final: 0.8563 (m-80) REVERT: D 356 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8987 (pp) REVERT: E 86 GLN cc_start: 0.8719 (tt0) cc_final: 0.8432 (tt0) REVERT: E 132 GLN cc_start: 0.9292 (pt0) cc_final: 0.8874 (pt0) REVERT: E 140 MET cc_start: 0.8861 (tmm) cc_final: 0.8269 (tmm) REVERT: E 141 LEU cc_start: 0.8894 (mt) cc_final: 0.8567 (mt) REVERT: E 148 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9028 (mp) REVERT: E 170 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.6928 (pt) REVERT: E 222 PHE cc_start: 0.6888 (m-10) cc_final: 0.6487 (t80) REVERT: E 244 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6934 (t) REVERT: F 112 TYR cc_start: 0.7792 (m-80) cc_final: 0.7259 (m-80) REVERT: F 131 MET cc_start: 0.8714 (tpt) cc_final: 0.8257 (mmm) REVERT: F 191 TYR cc_start: 0.6160 (t80) cc_final: 0.5354 (t80) REVERT: F 219 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8094 (mtpt) REVERT: F 290 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6712 (tp30) REVERT: F 292 MET cc_start: 0.6177 (mtm) cc_final: 0.5955 (mtm) REVERT: F 337 MET cc_start: 0.8570 (mmm) cc_final: 0.8116 (mmp) REVERT: F 372 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: F 376 HIS cc_start: 0.7934 (m90) cc_final: 0.7669 (m90) REVERT: F 387 GLU cc_start: 0.8393 (mp0) cc_final: 0.7809 (mp0) REVERT: G 126 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8497 (pp) REVERT: G 213 MET cc_start: 0.8338 (ptp) cc_final: 0.8108 (ptm) REVERT: G 225 ILE cc_start: 0.9164 (tt) cc_final: 0.8933 (tt) REVERT: G 271 MET cc_start: 0.8404 (mmp) cc_final: 0.8111 (mmp) REVERT: G 431 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8291 (tp) REVERT: G 684 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6713 (pp) REVERT: H 68 MET cc_start: 0.8348 (mmm) cc_final: 0.7802 (ptt) REVERT: H 85 LEU cc_start: 0.8809 (mt) cc_final: 0.8548 (mt) REVERT: H 111 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8683 (tt) REVERT: H 172 MET cc_start: 0.7963 (ppp) cc_final: 0.7713 (ppp) REVERT: H 183 MET cc_start: 0.8187 (mtt) cc_final: 0.7915 (mtp) REVERT: H 214 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8555 (mm-30) REVERT: H 254 LEU cc_start: 0.8057 (mt) cc_final: 0.7494 (mt) REVERT: H 258 ASN cc_start: 0.7839 (m-40) cc_final: 0.7405 (m-40) REVERT: H 261 MET cc_start: 0.8108 (mmt) cc_final: 0.7787 (ttt) REVERT: H 291 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7949 (tttt) REVERT: H 318 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6177 (tpt) REVERT: I 50 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5734 (tpp) REVERT: I 55 ASP cc_start: 0.8652 (m-30) cc_final: 0.8369 (m-30) REVERT: I 208 ASP cc_start: 0.8654 (t0) cc_final: 0.8428 (t70) REVERT: P 207 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7511 (t80) REVERT: P 217 PHE cc_start: 0.9251 (m-80) cc_final: 0.8966 (m-80) REVERT: P 336 GLU cc_start: 0.7628 (mp0) cc_final: 0.7294 (mp0) REVERT: P 346 GLU cc_start: 0.8284 (pm20) cc_final: 0.7951 (mp0) REVERT: Q 160 TYR cc_start: 0.7960 (t80) cc_final: 0.6869 (t80) REVERT: Q 164 PHE cc_start: 0.8066 (m-80) cc_final: 0.7674 (m-80) REVERT: Q 166 TRP cc_start: 0.7702 (t-100) cc_final: 0.6834 (t-100) REVERT: S 62 GLN cc_start: 0.8816 (pt0) cc_final: 0.8555 (mt0) REVERT: S 65 LEU cc_start: 0.9055 (tt) cc_final: 0.8564 (tt) REVERT: S 69 TYR cc_start: 0.7443 (m-80) cc_final: 0.7064 (m-80) REVERT: S 91 MET cc_start: 0.8912 (mmm) cc_final: 0.8684 (mmm) REVERT: T 79 ILE cc_start: 0.8133 (mm) cc_final: 0.7585 (tt) REVERT: T 132 ASP cc_start: 0.7204 (p0) cc_final: 0.6861 (p0) REVERT: V 31 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8754 (p) REVERT: V 47 TYR cc_start: 0.8661 (m-80) cc_final: 0.8378 (m-80) REVERT: V 85 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: W 125 PHE cc_start: 0.8970 (t80) cc_final: 0.8713 (t80) REVERT: X 36 CYS cc_start: 0.6835 (m) cc_final: 0.5883 (t) REVERT: X 40 ASN cc_start: 0.8681 (m-40) cc_final: 0.8067 (m-40) REVERT: Z 133 MET cc_start: 0.7421 (tpp) cc_final: 0.7007 (tpp) REVERT: a 35 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8161 (mp0) REVERT: a 43 TYR cc_start: 0.8394 (t80) cc_final: 0.6580 (m-80) REVERT: a 47 LEU cc_start: 0.9526 (mp) cc_final: 0.9131 (mp) REVERT: b 13 TRP cc_start: 0.8768 (t-100) cc_final: 0.8161 (t-100) REVERT: b 22 SER cc_start: 0.9095 (t) cc_final: 0.8825 (p) REVERT: b 30 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8677 (mt) REVERT: b 52 ASN cc_start: 0.7417 (m-40) cc_final: 0.7128 (t0) REVERT: b 63 MET cc_start: 0.7657 (mtm) cc_final: 0.7235 (mtt) REVERT: b 66 VAL cc_start: 0.8551 (t) cc_final: 0.8335 (m) REVERT: q 81 MET cc_start: 0.7458 (mmt) cc_final: 0.7252 (mmm) REVERT: s 46 LEU cc_start: 0.9020 (tp) cc_final: 0.8644 (tt) outliers start: 156 outliers final: 90 residues processed: 1015 average time/residue: 0.2120 time to fit residues: 357.4458 Evaluate side-chains 978 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 870 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 392 MET Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 145 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 chunk 269 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 241 optimal weight: 0.9990 chunk 359 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 397 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN T 103 HIS ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085591 restraints weight = 88899.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088428 restraints weight = 39140.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.090267 restraints weight = 23031.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091436 restraints weight = 16339.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092157 restraints weight = 13174.395| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34894 Z= 0.141 Angle : 0.884 76.012 47343 Z= 0.350 Chirality : 0.044 0.230 5170 Planarity : 0.005 0.158 6013 Dihedral : 8.344 147.870 4813 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 3.78 % Allowed : 23.51 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4163 helix: 0.89 (0.12), residues: 1854 sheet: -0.97 (0.27), residues: 365 loop : -0.79 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 221 TYR 0.041 0.002 TYR W 126 PHE 0.030 0.001 PHE W 121 TRP 0.031 0.001 TRP V 97 HIS 0.006 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00332 (34854) covalent geometry : angle 0.70245 (47253) SS BOND : bond 0.00461 ( 3) SS BOND : angle 1.87981 ( 6) hydrogen bonds : bond 0.04015 ( 1428) hydrogen bonds : angle 4.91021 ( 4125) metal coordination : bond 0.01494 ( 37) metal coordination : angle 12.77076 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 918 time to evaluate : 1.347 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: A 5 THR cc_start: 0.9049 (m) cc_final: 0.8803 (p) REVERT: A 8 PHE cc_start: 0.7866 (m-80) cc_final: 0.7490 (m-10) REVERT: A 10 ASN cc_start: 0.8693 (t0) cc_final: 0.8294 (t0) REVERT: A 18 ILE cc_start: 0.9468 (tp) cc_final: 0.9224 (tp) REVERT: A 26 GLN cc_start: 0.8204 (tt0) cc_final: 0.7395 (tm-30) REVERT: A 87 MET cc_start: 0.8768 (tmm) cc_final: 0.8562 (tmm) REVERT: B 72 GLU cc_start: 0.6351 (tt0) cc_final: 0.6012 (mt-10) REVERT: B 127 GLN cc_start: 0.8819 (mt0) cc_final: 0.8590 (mt0) REVERT: C 145 TYR cc_start: 0.9022 (p90) cc_final: 0.8707 (p90) REVERT: C 168 GLU cc_start: 0.9242 (tm-30) cc_final: 0.9012 (tm-30) REVERT: C 209 LEU cc_start: 0.9321 (mt) cc_final: 0.9091 (mt) REVERT: C 211 TYR cc_start: 0.9016 (t80) cc_final: 0.8412 (t80) REVERT: C 212 ASP cc_start: 0.7729 (t70) cc_final: 0.7038 (t70) REVERT: D 80 MET cc_start: 0.8793 (tmm) cc_final: 0.8000 (tmm) REVERT: D 144 MET cc_start: 0.8128 (mpp) cc_final: 0.7328 (mpp) REVERT: D 182 ASN cc_start: 0.8598 (t0) cc_final: 0.8315 (t0) REVERT: D 212 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7292 (tm-30) REVERT: D 254 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7896 (tpp80) REVERT: D 270 ASN cc_start: 0.8677 (t0) cc_final: 0.8001 (t0) REVERT: D 356 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9066 (pp) REVERT: D 371 MET cc_start: 0.8988 (ttp) cc_final: 0.8726 (ttp) REVERT: E 86 GLN cc_start: 0.8710 (tt0) cc_final: 0.8401 (tt0) REVERT: E 132 GLN cc_start: 0.9318 (pt0) cc_final: 0.8908 (pt0) REVERT: E 140 MET cc_start: 0.8845 (tmm) cc_final: 0.8308 (ppp) REVERT: E 141 LEU cc_start: 0.8878 (mt) cc_final: 0.8568 (mt) REVERT: E 222 PHE cc_start: 0.6870 (m-10) cc_final: 0.6445 (t80) REVERT: E 244 VAL cc_start: 0.7151 (OUTLIER) cc_final: 0.6898 (t) REVERT: F 149 MET cc_start: 0.8065 (mtm) cc_final: 0.7812 (mpp) REVERT: F 191 TYR cc_start: 0.6188 (t80) cc_final: 0.5394 (t80) REVERT: F 219 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8129 (mtpt) REVERT: F 290 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6539 (tp30) REVERT: F 337 MET cc_start: 0.8696 (mmm) cc_final: 0.8099 (mmp) REVERT: F 372 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: F 376 HIS cc_start: 0.7889 (m90) cc_final: 0.7626 (m90) REVERT: G 42 MET cc_start: 0.8350 (tpp) cc_final: 0.7941 (tpp) REVERT: G 126 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8558 (pp) REVERT: G 205 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: G 213 MET cc_start: 0.8325 (ptp) cc_final: 0.8098 (ptm) REVERT: G 225 ILE cc_start: 0.9171 (tt) cc_final: 0.8936 (tt) REVERT: G 431 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8230 (tp) REVERT: G 591 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7341 (mt-10) REVERT: G 684 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6752 (pp) REVERT: H 68 MET cc_start: 0.8372 (mmm) cc_final: 0.7771 (ptt) REVERT: H 111 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8780 (tt) REVERT: H 172 MET cc_start: 0.8012 (ppp) cc_final: 0.7775 (ppp) REVERT: H 183 MET cc_start: 0.8162 (mtt) cc_final: 0.7922 (mtp) REVERT: H 184 MET cc_start: 0.8952 (mmm) cc_final: 0.8622 (mtp) REVERT: H 214 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8619 (mm-30) REVERT: H 247 TYR cc_start: 0.8044 (t80) cc_final: 0.7787 (t80) REVERT: H 254 LEU cc_start: 0.8152 (mt) cc_final: 0.7553 (mt) REVERT: H 258 ASN cc_start: 0.7849 (m-40) cc_final: 0.7416 (m-40) REVERT: H 261 MET cc_start: 0.8029 (mmt) cc_final: 0.7739 (ttt) REVERT: H 291 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7990 (tttt) REVERT: H 318 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6146 (tpt) REVERT: I 50 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5749 (tpp) REVERT: I 55 ASP cc_start: 0.8668 (m-30) cc_final: 0.8403 (m-30) REVERT: I 149 MET cc_start: 0.8892 (mmm) cc_final: 0.8331 (mmm) REVERT: I 151 LYS cc_start: 0.9286 (ttpt) cc_final: 0.9018 (mtpt) REVERT: I 208 ASP cc_start: 0.8757 (t0) cc_final: 0.8484 (t70) REVERT: P 207 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7377 (t80) REVERT: P 211 ASP cc_start: 0.7061 (p0) cc_final: 0.6855 (p0) REVERT: P 217 PHE cc_start: 0.9277 (m-80) cc_final: 0.9040 (m-80) REVERT: P 336 GLU cc_start: 0.7520 (mp0) cc_final: 0.7198 (mp0) REVERT: P 346 GLU cc_start: 0.8221 (pm20) cc_final: 0.7906 (mp0) REVERT: Q 139 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8523 (mm-30) REVERT: Q 160 TYR cc_start: 0.7853 (t80) cc_final: 0.6777 (t80) REVERT: Q 164 PHE cc_start: 0.8001 (m-80) cc_final: 0.7627 (m-80) REVERT: Q 166 TRP cc_start: 0.7767 (t-100) cc_final: 0.6988 (t-100) REVERT: R 51 ARG cc_start: 0.6543 (mtm110) cc_final: 0.6128 (mtm110) REVERT: S 64 LYS cc_start: 0.6539 (mtmt) cc_final: 0.6141 (mtmm) REVERT: S 65 LEU cc_start: 0.9065 (tt) cc_final: 0.8564 (tt) REVERT: S 69 TYR cc_start: 0.7543 (m-80) cc_final: 0.7256 (m-80) REVERT: S 91 MET cc_start: 0.8906 (mmm) cc_final: 0.8642 (mmm) REVERT: T 132 ASP cc_start: 0.7152 (p0) cc_final: 0.6841 (p0) REVERT: V 44 TYR cc_start: 0.8690 (t80) cc_final: 0.8458 (t80) REVERT: V 47 TYR cc_start: 0.8567 (m-80) cc_final: 0.8354 (m-80) REVERT: V 85 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8476 (tm-30) REVERT: W 71 MET cc_start: 0.8760 (mpp) cc_final: 0.8210 (mpp) REVERT: W 125 PHE cc_start: 0.8953 (t80) cc_final: 0.8717 (t80) REVERT: X 36 CYS cc_start: 0.6785 (m) cc_final: 0.5913 (t) REVERT: X 40 ASN cc_start: 0.8723 (m-40) cc_final: 0.8169 (m-40) REVERT: X 85 TYR cc_start: 0.8276 (t80) cc_final: 0.7732 (t80) REVERT: Z 51 MET cc_start: 0.8130 (tmt) cc_final: 0.7825 (tmt) REVERT: Z 133 MET cc_start: 0.7477 (tpp) cc_final: 0.7077 (tpp) REVERT: a 35 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8172 (mp0) REVERT: a 43 TYR cc_start: 0.8471 (t80) cc_final: 0.6559 (m-80) REVERT: b 13 TRP cc_start: 0.8768 (t-100) cc_final: 0.8165 (t-100) REVERT: b 22 SER cc_start: 0.9089 (t) cc_final: 0.8835 (p) REVERT: b 30 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8707 (mt) REVERT: b 38 TYR cc_start: 0.8442 (m-80) cc_final: 0.8125 (m-10) REVERT: b 63 MET cc_start: 0.7639 (mtm) cc_final: 0.7212 (mtt) REVERT: s 46 LEU cc_start: 0.8903 (tp) cc_final: 0.8660 (tt) outliers start: 138 outliers final: 94 residues processed: 985 average time/residue: 0.2066 time to fit residues: 336.5035 Evaluate side-chains 972 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 864 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 448 SER Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 72 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 49 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 63 optimal weight: 3.9990 chunk 350 optimal weight: 0.0030 chunk 272 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** R 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN W 102 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.106482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085911 restraints weight = 88714.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088746 restraints weight = 39355.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090580 restraints weight = 23258.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091751 restraints weight = 16518.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092491 restraints weight = 13315.720| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34894 Z= 0.141 Angle : 0.896 76.874 47343 Z= 0.356 Chirality : 0.045 0.299 5170 Planarity : 0.005 0.161 6013 Dihedral : 8.317 149.443 4813 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 3.72 % Allowed : 23.95 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.14 (0.13), residues: 4163 helix: 0.88 (0.12), residues: 1844 sheet: -1.00 (0.27), residues: 364 loop : -0.81 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 279 TYR 0.039 0.002 TYR W 126 PHE 0.039 0.002 PHE F 262 TRP 0.031 0.001 TRP V 97 HIS 0.008 0.001 HIS W 111 Details of bonding type rmsd covalent geometry : bond 0.00327 (34854) covalent geometry : angle 0.71633 (47253) SS BOND : bond 0.00447 ( 3) SS BOND : angle 1.77796 ( 6) hydrogen bonds : bond 0.04007 ( 1428) hydrogen bonds : angle 4.89615 ( 4125) metal coordination : bond 0.01410 ( 37) metal coordination : angle 12.77408 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 930 time to evaluate : 1.489 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: A 5 THR cc_start: 0.9109 (m) cc_final: 0.8851 (p) REVERT: A 8 PHE cc_start: 0.7923 (m-80) cc_final: 0.7592 (m-10) REVERT: A 10 ASN cc_start: 0.8594 (t0) cc_final: 0.8143 (t0) REVERT: A 12 LEU cc_start: 0.8945 (mm) cc_final: 0.8095 (tp) REVERT: A 18 ILE cc_start: 0.9461 (tp) cc_final: 0.9203 (tp) REVERT: A 26 GLN cc_start: 0.8247 (tt0) cc_final: 0.7517 (tm-30) REVERT: A 109 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8039 (tppt) REVERT: B 127 GLN cc_start: 0.8836 (mt0) cc_final: 0.8417 (mt0) REVERT: B 147 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8654 (tptm) REVERT: B 182 ASP cc_start: 0.8454 (p0) cc_final: 0.7885 (t0) REVERT: B 216 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: C 145 TYR cc_start: 0.9032 (p90) cc_final: 0.8710 (p90) REVERT: C 168 GLU cc_start: 0.9249 (tm-30) cc_final: 0.9038 (tm-30) REVERT: C 209 LEU cc_start: 0.9332 (mt) cc_final: 0.9104 (mt) REVERT: C 211 TYR cc_start: 0.9049 (t80) cc_final: 0.8451 (t80) REVERT: C 212 ASP cc_start: 0.7715 (t70) cc_final: 0.7015 (t70) REVERT: C 238 TRP cc_start: 0.8533 (m100) cc_final: 0.8113 (m100) REVERT: D 80 MET cc_start: 0.8904 (tmm) cc_final: 0.8360 (tmm) REVERT: D 107 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8219 (mmm160) REVERT: D 144 MET cc_start: 0.8136 (mpp) cc_final: 0.7677 (mpp) REVERT: D 182 ASN cc_start: 0.8624 (t0) cc_final: 0.8267 (t0) REVERT: D 212 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7330 (tm-30) REVERT: D 254 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7885 (tpp80) REVERT: D 270 ASN cc_start: 0.8741 (t0) cc_final: 0.8343 (t0) REVERT: D 294 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: D 356 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9070 (pp) REVERT: D 360 ASP cc_start: 0.8308 (t0) cc_final: 0.8046 (t0) REVERT: E 86 GLN cc_start: 0.8697 (tt0) cc_final: 0.8370 (tt0) REVERT: E 120 MET cc_start: 0.8375 (tpp) cc_final: 0.7852 (ttm) REVERT: E 132 GLN cc_start: 0.9352 (pt0) cc_final: 0.8928 (pt0) REVERT: E 140 MET cc_start: 0.8827 (tmm) cc_final: 0.8303 (ppp) REVERT: E 141 LEU cc_start: 0.8912 (mt) cc_final: 0.8591 (mt) REVERT: E 170 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.6816 (pt) REVERT: E 222 PHE cc_start: 0.6951 (m-10) cc_final: 0.6551 (t80) REVERT: E 244 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6925 (t) REVERT: F 42 PHE cc_start: 0.8672 (m-80) cc_final: 0.8458 (m-10) REVERT: F 131 MET cc_start: 0.8696 (tpt) cc_final: 0.8270 (mmm) REVERT: F 191 TYR cc_start: 0.6083 (t80) cc_final: 0.5278 (t80) REVERT: F 219 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8106 (mtpt) REVERT: F 290 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6566 (tp30) REVERT: F 372 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: F 376 HIS cc_start: 0.7934 (m90) cc_final: 0.7688 (m-70) REVERT: F 377 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7641 (tm-30) REVERT: G 117 MET cc_start: 0.8369 (mmm) cc_final: 0.7978 (mmm) REVERT: G 126 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8566 (pp) REVERT: G 205 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: G 213 MET cc_start: 0.8306 (ptp) cc_final: 0.7968 (ptm) REVERT: G 225 ILE cc_start: 0.9170 (tt) cc_final: 0.8923 (tt) REVERT: G 431 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8188 (tp) REVERT: G 591 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7341 (mt-10) REVERT: G 684 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6870 (pp) REVERT: H 68 MET cc_start: 0.8462 (mmm) cc_final: 0.7832 (ptt) REVERT: H 111 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8784 (tt) REVERT: H 172 MET cc_start: 0.8128 (ppp) cc_final: 0.7910 (ppp) REVERT: H 174 LEU cc_start: 0.9125 (mt) cc_final: 0.8911 (mt) REVERT: H 183 MET cc_start: 0.8169 (mtt) cc_final: 0.7928 (mtp) REVERT: H 184 MET cc_start: 0.8886 (mmm) cc_final: 0.8627 (mtp) REVERT: H 214 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8411 (mm-30) REVERT: H 247 TYR cc_start: 0.8052 (t80) cc_final: 0.7822 (t80) REVERT: H 254 LEU cc_start: 0.8240 (mt) cc_final: 0.7195 (mt) REVERT: H 258 ASN cc_start: 0.7871 (m-40) cc_final: 0.7442 (m110) REVERT: H 261 MET cc_start: 0.8028 (mmt) cc_final: 0.7775 (ttt) REVERT: H 279 ARG cc_start: 0.7892 (mtm110) cc_final: 0.7580 (mtm180) REVERT: H 318 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6165 (tpt) REVERT: I 50 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.5768 (tpp) REVERT: I 55 ASP cc_start: 0.8669 (m-30) cc_final: 0.8389 (m-30) REVERT: I 149 MET cc_start: 0.8886 (mmm) cc_final: 0.8308 (mmm) REVERT: I 151 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9006 (mtpt) REVERT: I 200 GLU cc_start: 0.7759 (tt0) cc_final: 0.7530 (pt0) REVERT: I 208 ASP cc_start: 0.8752 (t0) cc_final: 0.8480 (t70) REVERT: P 207 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7454 (t80) REVERT: P 217 PHE cc_start: 0.9302 (m-80) cc_final: 0.9003 (m-80) REVERT: P 336 GLU cc_start: 0.7547 (mp0) cc_final: 0.7227 (mp0) REVERT: Q 139 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8513 (mm-30) REVERT: Q 145 TYR cc_start: 0.9064 (p90) cc_final: 0.8841 (p90) REVERT: Q 166 TRP cc_start: 0.7732 (t-100) cc_final: 0.6979 (t-100) REVERT: R 51 ARG cc_start: 0.6636 (mtm110) cc_final: 0.6200 (mtm110) REVERT: S 62 GLN cc_start: 0.8878 (mt0) cc_final: 0.8543 (mt0) REVERT: S 64 LYS cc_start: 0.6426 (mtmt) cc_final: 0.6012 (mtmm) REVERT: S 69 TYR cc_start: 0.7555 (m-80) cc_final: 0.7302 (m-80) REVERT: S 74 GLU cc_start: 0.7430 (tt0) cc_final: 0.6866 (tt0) REVERT: T 132 ASP cc_start: 0.7176 (p0) cc_final: 0.6857 (p0) REVERT: V 47 TYR cc_start: 0.8557 (m-80) cc_final: 0.8305 (m-80) REVERT: V 85 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: W 61 GLN cc_start: 0.8756 (tt0) cc_final: 0.8371 (pt0) REVERT: W 71 MET cc_start: 0.8795 (mpp) cc_final: 0.8162 (mpp) REVERT: W 107 MET cc_start: 0.8777 (mmm) cc_final: 0.8441 (mmm) REVERT: W 125 PHE cc_start: 0.8984 (t80) cc_final: 0.8712 (t80) REVERT: X 36 CYS cc_start: 0.6792 (m) cc_final: 0.5956 (t) REVERT: X 40 ASN cc_start: 0.8673 (m-40) cc_final: 0.8069 (m-40) REVERT: X 44 MET cc_start: 0.9031 (mmm) cc_final: 0.8700 (mmm) REVERT: X 55 ARG cc_start: 0.8841 (tpp-160) cc_final: 0.8484 (mmp80) REVERT: Z 120 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8367 (tt) REVERT: Z 133 MET cc_start: 0.7454 (tpp) cc_final: 0.6983 (tpp) REVERT: a 35 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8194 (mp0) REVERT: a 43 TYR cc_start: 0.8458 (t80) cc_final: 0.6433 (m-80) REVERT: b 13 TRP cc_start: 0.8767 (t-100) cc_final: 0.8091 (t-100) REVERT: b 22 SER cc_start: 0.9079 (t) cc_final: 0.8847 (p) REVERT: b 30 ILE cc_start: 0.9112 (tp) cc_final: 0.8808 (mt) REVERT: b 63 MET cc_start: 0.7637 (mtm) cc_final: 0.7141 (mtt) REVERT: s 46 LEU cc_start: 0.8921 (tp) cc_final: 0.8596 (tt) outliers start: 136 outliers final: 92 residues processed: 999 average time/residue: 0.2061 time to fit residues: 342.6698 Evaluate side-chains 976 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 866 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 351 GLU Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 16 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 71 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 173 optimal weight: 0.0870 chunk 174 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 79 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** R 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN W 73 ASN X 99 HIS ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.085383 restraints weight = 89025.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088162 restraints weight = 39561.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089972 restraints weight = 23490.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091142 restraints weight = 16742.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091867 restraints weight = 13497.004| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34894 Z= 0.148 Angle : 0.918 77.702 47343 Z= 0.365 Chirality : 0.045 0.286 5170 Planarity : 0.005 0.163 6013 Dihedral : 8.284 151.637 4813 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 3.50 % Allowed : 25.02 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.15 (0.13), residues: 4163 helix: 0.85 (0.12), residues: 1858 sheet: -1.00 (0.27), residues: 368 loop : -0.79 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.038 0.002 TYR W 126 PHE 0.029 0.002 PHE F 262 TRP 0.035 0.001 TRP V 97 HIS 0.005 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00350 (34854) covalent geometry : angle 0.73923 (47253) SS BOND : bond 0.00449 ( 3) SS BOND : angle 1.82942 ( 6) hydrogen bonds : bond 0.04046 ( 1428) hydrogen bonds : angle 4.92024 ( 4125) metal coordination : bond 0.01535 ( 37) metal coordination : angle 12.92500 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 894 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.9107 (m) cc_final: 0.8865 (p) REVERT: A 8 PHE cc_start: 0.7949 (m-80) cc_final: 0.7618 (m-10) REVERT: A 10 ASN cc_start: 0.8564 (t0) cc_final: 0.8077 (t0) REVERT: A 12 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8047 (tp) REVERT: A 26 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: A 109 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7984 (tppt) REVERT: B 127 GLN cc_start: 0.8815 (mt0) cc_final: 0.8412 (mt0) REVERT: B 147 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8652 (tptm) REVERT: B 182 ASP cc_start: 0.8463 (p0) cc_final: 0.7916 (t0) REVERT: B 216 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: C 133 SER cc_start: 0.8988 (t) cc_final: 0.8271 (p) REVERT: C 145 TYR cc_start: 0.9044 (p90) cc_final: 0.8712 (p90) REVERT: C 209 LEU cc_start: 0.9337 (mt) cc_final: 0.9113 (mt) REVERT: C 211 TYR cc_start: 0.9077 (t80) cc_final: 0.8419 (t80) REVERT: C 212 ASP cc_start: 0.7709 (t70) cc_final: 0.7021 (t70) REVERT: D 80 MET cc_start: 0.8901 (tmm) cc_final: 0.8372 (tmm) REVERT: D 182 ASN cc_start: 0.8585 (t0) cc_final: 0.8219 (t0) REVERT: D 212 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7198 (tm-30) REVERT: D 270 ASN cc_start: 0.8753 (t0) cc_final: 0.8286 (t0) REVERT: D 294 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7673 (mtm-85) REVERT: D 323 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7427 (ttt90) REVERT: D 356 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9111 (pp) REVERT: D 360 ASP cc_start: 0.8319 (t0) cc_final: 0.8048 (t0) REVERT: E 86 GLN cc_start: 0.8720 (tt0) cc_final: 0.8395 (tt0) REVERT: E 120 MET cc_start: 0.8195 (tpp) cc_final: 0.7765 (ttm) REVERT: E 132 GLN cc_start: 0.9349 (pt0) cc_final: 0.8998 (pt0) REVERT: E 140 MET cc_start: 0.8795 (tmm) cc_final: 0.8267 (ppp) REVERT: E 141 LEU cc_start: 0.8897 (mt) cc_final: 0.8550 (mt) REVERT: E 170 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.6768 (pt) REVERT: E 222 PHE cc_start: 0.6918 (m-10) cc_final: 0.6525 (t80) REVERT: F 42 PHE cc_start: 0.8665 (m-80) cc_final: 0.8464 (m-10) REVERT: F 191 TYR cc_start: 0.5792 (t80) cc_final: 0.5077 (t80) REVERT: F 219 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8136 (mtpt) REVERT: F 290 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6635 (tp30) REVERT: F 337 MET cc_start: 0.8742 (mmm) cc_final: 0.8066 (mmp) REVERT: F 372 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: F 376 HIS cc_start: 0.8013 (m90) cc_final: 0.7724 (m90) REVERT: F 377 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7635 (tm-30) REVERT: G 59 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8407 (tp-100) REVERT: G 117 MET cc_start: 0.8368 (mmm) cc_final: 0.8071 (mmm) REVERT: G 126 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8504 (pp) REVERT: G 158 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8091 (ttp-170) REVERT: G 205 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: G 213 MET cc_start: 0.8278 (ptp) cc_final: 0.7945 (ptm) REVERT: G 225 ILE cc_start: 0.9192 (tt) cc_final: 0.8947 (tt) REVERT: G 431 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8193 (tp) REVERT: G 548 LEU cc_start: 0.8823 (mt) cc_final: 0.8288 (mt) REVERT: G 591 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7365 (mt-10) REVERT: G 684 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6904 (pp) REVERT: H 68 MET cc_start: 0.8491 (mmm) cc_final: 0.7858 (ptt) REVERT: H 111 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8854 (tt) REVERT: H 172 MET cc_start: 0.8178 (ppp) cc_final: 0.7961 (ppp) REVERT: H 183 MET cc_start: 0.8013 (mtt) cc_final: 0.7763 (mtp) REVERT: H 184 MET cc_start: 0.8929 (mmm) cc_final: 0.8717 (mtp) REVERT: H 214 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8431 (mm-30) REVERT: H 254 LEU cc_start: 0.8283 (mt) cc_final: 0.7188 (mt) REVERT: H 255 TYR cc_start: 0.6861 (t80) cc_final: 0.6437 (t80) REVERT: H 258 ASN cc_start: 0.7893 (m-40) cc_final: 0.7431 (m110) REVERT: H 261 MET cc_start: 0.7985 (mmt) cc_final: 0.7753 (ttt) REVERT: H 318 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6206 (tpt) REVERT: I 38 TYR cc_start: 0.8286 (m-80) cc_final: 0.7947 (m-80) REVERT: I 50 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5793 (tpp) REVERT: I 55 ASP cc_start: 0.8636 (m-30) cc_final: 0.8378 (m-30) REVERT: I 149 MET cc_start: 0.8885 (mmm) cc_final: 0.8318 (mmm) REVERT: I 151 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9028 (mtpt) REVERT: I 208 ASP cc_start: 0.8755 (t0) cc_final: 0.8518 (t70) REVERT: P 217 PHE cc_start: 0.9325 (m-80) cc_final: 0.9012 (m-80) REVERT: P 336 GLU cc_start: 0.7550 (mp0) cc_final: 0.7070 (mp0) REVERT: Q 139 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8394 (mm-30) REVERT: Q 145 TYR cc_start: 0.9084 (p90) cc_final: 0.8754 (p90) REVERT: Q 160 TYR cc_start: 0.8231 (t80) cc_final: 0.8021 (t80) REVERT: Q 166 TRP cc_start: 0.7650 (t-100) cc_final: 0.6984 (t-100) REVERT: S 64 LYS cc_start: 0.6611 (mtmt) cc_final: 0.6229 (mtmm) REVERT: S 65 LEU cc_start: 0.9220 (tt) cc_final: 0.8889 (tt) REVERT: S 69 TYR cc_start: 0.7601 (m-80) cc_final: 0.7299 (m-80) REVERT: S 74 GLU cc_start: 0.7412 (tt0) cc_final: 0.6748 (tt0) REVERT: S 92 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8190 (pp30) REVERT: T 79 ILE cc_start: 0.7088 (mp) cc_final: 0.6582 (tt) REVERT: T 132 ASP cc_start: 0.7093 (p0) cc_final: 0.6784 (p0) REVERT: V 47 TYR cc_start: 0.8571 (m-80) cc_final: 0.8299 (m-80) REVERT: V 85 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: W 61 GLN cc_start: 0.8756 (tt0) cc_final: 0.8389 (pt0) REVERT: W 71 MET cc_start: 0.8782 (mpp) cc_final: 0.8149 (mpp) REVERT: W 125 PHE cc_start: 0.9023 (t80) cc_final: 0.8783 (t80) REVERT: X 36 CYS cc_start: 0.6735 (m) cc_final: 0.5953 (t) REVERT: X 40 ASN cc_start: 0.8614 (m-40) cc_final: 0.7919 (m-40) REVERT: X 44 MET cc_start: 0.9016 (mmm) cc_final: 0.8675 (mmm) REVERT: Z 64 ASP cc_start: 0.9035 (t70) cc_final: 0.8690 (t0) REVERT: Z 120 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8413 (tt) REVERT: Z 133 MET cc_start: 0.7498 (tpp) cc_final: 0.7098 (tpp) REVERT: a 43 TYR cc_start: 0.8471 (t80) cc_final: 0.6579 (m-80) REVERT: b 13 TRP cc_start: 0.8753 (t-100) cc_final: 0.8429 (t-100) REVERT: b 22 SER cc_start: 0.9083 (t) cc_final: 0.8868 (p) REVERT: b 30 ILE cc_start: 0.9125 (tp) cc_final: 0.8829 (mt) REVERT: b 63 MET cc_start: 0.7651 (mtm) cc_final: 0.7205 (mtt) REVERT: q 49 TYR cc_start: 0.7219 (m-80) cc_final: 0.6938 (m-80) REVERT: s 46 LEU cc_start: 0.8890 (tp) cc_final: 0.8536 (tt) outliers start: 128 outliers final: 93 residues processed: 958 average time/residue: 0.2073 time to fit residues: 330.7001 Evaluate side-chains 975 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 863 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 419 ILE Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 370 LYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain T residue 150 ASP Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 18 ASP Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 24 LEU Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 16 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 0 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 336 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 313 optimal weight: 0.4980 chunk 382 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 127 GLN C 235 ASN D 83 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** R 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN q 12 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.085892 restraints weight = 89362.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088692 restraints weight = 39603.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090511 restraints weight = 23425.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091675 restraints weight = 16673.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092413 restraints weight = 13430.025| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34894 Z= 0.144 Angle : 0.922 77.660 47343 Z= 0.368 Chirality : 0.045 0.279 5170 Planarity : 0.005 0.163 6013 Dihedral : 8.267 152.882 4812 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 3.12 % Allowed : 25.54 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4163 helix: 0.86 (0.12), residues: 1853 sheet: -0.86 (0.27), residues: 370 loop : -0.81 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 122 TYR 0.038 0.002 TYR W 126 PHE 0.025 0.001 PHE Q 164 TRP 0.037 0.001 TRP V 97 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00338 (34854) covalent geometry : angle 0.74628 (47253) SS BOND : bond 0.00408 ( 3) SS BOND : angle 1.77404 ( 6) hydrogen bonds : bond 0.03995 ( 1428) hydrogen bonds : angle 4.92521 ( 4125) metal coordination : bond 0.01497 ( 37) metal coordination : angle 12.88221 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8326 Ramachandran restraints generated. 4163 Oldfield, 0 Emsley, 4163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 897 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.9099 (m) cc_final: 0.8879 (p) REVERT: A 8 PHE cc_start: 0.7939 (m-80) cc_final: 0.7591 (m-10) REVERT: A 10 ASN cc_start: 0.8539 (t0) cc_final: 0.8058 (t0) REVERT: A 12 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 26 GLN cc_start: 0.8198 (tt0) cc_final: 0.7009 (mm-40) REVERT: A 109 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7995 (tppt) REVERT: B 127 GLN cc_start: 0.8790 (mt0) cc_final: 0.8364 (mt0) REVERT: B 140 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8747 (mttp) REVERT: B 147 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8644 (tptm) REVERT: B 149 TYR cc_start: 0.9395 (t80) cc_final: 0.8955 (t80) REVERT: B 182 ASP cc_start: 0.8463 (p0) cc_final: 0.7949 (t0) REVERT: B 216 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: C 133 SER cc_start: 0.8779 (t) cc_final: 0.8029 (p) REVERT: C 145 TYR cc_start: 0.9048 (p90) cc_final: 0.8713 (p90) REVERT: C 211 TYR cc_start: 0.9057 (t80) cc_final: 0.8428 (t80) REVERT: C 212 ASP cc_start: 0.7773 (t70) cc_final: 0.7124 (t70) REVERT: C 238 TRP cc_start: 0.8516 (m100) cc_final: 0.8115 (m100) REVERT: D 80 MET cc_start: 0.8931 (tmm) cc_final: 0.8465 (tmm) REVERT: D 182 ASN cc_start: 0.8606 (t0) cc_final: 0.8271 (t0) REVERT: D 212 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7230 (tm-30) REVERT: D 254 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7913 (tpp80) REVERT: D 256 ASP cc_start: 0.8820 (m-30) cc_final: 0.8544 (m-30) REVERT: D 270 ASN cc_start: 0.8755 (t0) cc_final: 0.8356 (t0) REVERT: D 294 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: D 323 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7498 (ttt90) REVERT: D 356 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9114 (pp) REVERT: D 360 ASP cc_start: 0.8333 (t0) cc_final: 0.8099 (t0) REVERT: E 86 GLN cc_start: 0.8738 (tt0) cc_final: 0.8437 (tt0) REVERT: E 120 MET cc_start: 0.8124 (tpp) cc_final: 0.7649 (ttm) REVERT: E 132 GLN cc_start: 0.9345 (pt0) cc_final: 0.9042 (pt0) REVERT: E 140 MET cc_start: 0.8769 (tmm) cc_final: 0.8243 (ppp) REVERT: E 141 LEU cc_start: 0.8875 (mt) cc_final: 0.8553 (mt) REVERT: E 170 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.6784 (pt) REVERT: E 222 PHE cc_start: 0.6944 (m-10) cc_final: 0.6571 (t80) REVERT: F 42 PHE cc_start: 0.8635 (m-80) cc_final: 0.8433 (m-10) REVERT: F 191 TYR cc_start: 0.5740 (t80) cc_final: 0.5005 (t80) REVERT: F 219 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8141 (mtpt) REVERT: F 290 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6887 (tp30) REVERT: F 337 MET cc_start: 0.8767 (mmm) cc_final: 0.8082 (mmp) REVERT: F 377 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7708 (tm-30) REVERT: G 59 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8417 (tp40) REVERT: G 158 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.8147 (ttp-170) REVERT: G 205 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: G 213 MET cc_start: 0.8272 (ptp) cc_final: 0.7931 (ptm) REVERT: G 225 ILE cc_start: 0.9189 (tt) cc_final: 0.8941 (tt) REVERT: G 329 MET cc_start: 0.7955 (mmt) cc_final: 0.7740 (mmt) REVERT: G 370 GLU cc_start: 0.6906 (tp30) cc_final: 0.6603 (tp30) REVERT: G 431 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8180 (tp) REVERT: G 591 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7358 (mt-10) REVERT: G 684 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6928 (pp) REVERT: H 68 MET cc_start: 0.8515 (mmm) cc_final: 0.7900 (ptt) REVERT: H 111 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8880 (tt) REVERT: H 183 MET cc_start: 0.8042 (mtt) cc_final: 0.7807 (mtp) REVERT: H 184 MET cc_start: 0.8898 (mmm) cc_final: 0.8524 (mtt) REVERT: H 214 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8412 (mm-30) REVERT: H 224 PHE cc_start: 0.8048 (t80) cc_final: 0.7464 (t80) REVERT: H 254 LEU cc_start: 0.8452 (mt) cc_final: 0.7905 (mt) REVERT: H 258 ASN cc_start: 0.7885 (m-40) cc_final: 0.7573 (m110) REVERT: H 261 MET cc_start: 0.7968 (mmt) cc_final: 0.7732 (ttt) REVERT: H 279 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7434 (mtm180) REVERT: H 302 MET cc_start: 0.8785 (mtp) cc_final: 0.8525 (mtt) REVERT: H 318 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6281 (tpt) REVERT: I 38 TYR cc_start: 0.8268 (m-80) cc_final: 0.7930 (m-80) REVERT: I 42 LYS cc_start: 0.7562 (mmmm) cc_final: 0.5718 (tmtt) REVERT: I 50 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5784 (tpp) REVERT: I 55 ASP cc_start: 0.8658 (m-30) cc_final: 0.8402 (m-30) REVERT: I 137 ASP cc_start: 0.8293 (p0) cc_final: 0.7891 (p0) REVERT: I 149 MET cc_start: 0.8807 (mmm) cc_final: 0.8259 (mmm) REVERT: I 151 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9060 (mtpt) REVERT: I 200 GLU cc_start: 0.7857 (pt0) cc_final: 0.7373 (pt0) REVERT: I 208 ASP cc_start: 0.8758 (t0) cc_final: 0.8528 (t70) REVERT: Q 99 MET cc_start: 0.8517 (ttm) cc_final: 0.8043 (ttm) REVERT: Q 139 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8424 (mm-30) REVERT: Q 145 TYR cc_start: 0.9024 (p90) cc_final: 0.8744 (p90) REVERT: Q 160 TYR cc_start: 0.8265 (t80) cc_final: 0.8000 (t80) REVERT: Q 166 TRP cc_start: 0.7544 (t-100) cc_final: 0.6870 (t-100) REVERT: S 64 LYS cc_start: 0.6731 (mtmt) cc_final: 0.6315 (mtmm) REVERT: S 69 TYR cc_start: 0.7595 (m-80) cc_final: 0.7293 (m-80) REVERT: V 47 TYR cc_start: 0.8521 (m-80) cc_final: 0.8272 (m-80) REVERT: V 76 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: W 61 GLN cc_start: 0.8764 (tt0) cc_final: 0.8412 (pt0) REVERT: W 71 MET cc_start: 0.8786 (mpp) cc_final: 0.8135 (mpp) REVERT: W 125 PHE cc_start: 0.8976 (t80) cc_final: 0.8739 (t80) REVERT: X 36 CYS cc_start: 0.6717 (m) cc_final: 0.5995 (t) REVERT: X 40 ASN cc_start: 0.8583 (m-40) cc_final: 0.7987 (m-40) REVERT: X 44 MET cc_start: 0.9058 (mmm) cc_final: 0.8738 (mmm) REVERT: X 55 ARG cc_start: 0.8857 (tpp-160) cc_final: 0.8564 (mmp80) REVERT: Z 51 MET cc_start: 0.8095 (tmt) cc_final: 0.7698 (tmm) REVERT: Z 64 ASP cc_start: 0.9018 (t70) cc_final: 0.8690 (t0) REVERT: Z 98 MET cc_start: 0.4756 (mtt) cc_final: 0.3887 (mtm) REVERT: Z 120 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8430 (tt) REVERT: Z 133 MET cc_start: 0.7541 (tpp) cc_final: 0.7147 (tpp) REVERT: a 43 TYR cc_start: 0.8477 (t80) cc_final: 0.6542 (m-80) REVERT: b 13 TRP cc_start: 0.8758 (t-100) cc_final: 0.8420 (t-100) REVERT: b 22 SER cc_start: 0.9084 (t) cc_final: 0.8873 (p) REVERT: b 30 ILE cc_start: 0.9162 (tp) cc_final: 0.8848 (mt) REVERT: b 38 TYR cc_start: 0.8283 (m-10) cc_final: 0.8030 (m-10) REVERT: b 63 MET cc_start: 0.7565 (mtm) cc_final: 0.7150 (mtt) REVERT: q 49 TYR cc_start: 0.7219 (m-80) cc_final: 0.6923 (m-80) REVERT: q 81 MET cc_start: 0.6886 (mmt) cc_final: 0.6338 (mmm) REVERT: s 46 LEU cc_start: 0.8813 (tp) cc_final: 0.8538 (tt) outliers start: 114 outliers final: 83 residues processed: 952 average time/residue: 0.2166 time to fit residues: 343.6197 Evaluate side-chains 959 residues out of total 3653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 860 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 254 ARG Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 674 LEU Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain G residue 696 MET Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 209 SER Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 LYS Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 307 LEU Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 22 GLU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 114 GLU Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 109 SER Chi-restraints excluded: chain Z residue 113 THR Chi-restraints excluded: chain Z residue 120 LEU Chi-restraints excluded: chain Z residue 134 SER Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain q residue 12 GLN Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 130 THR Chi-restraints excluded: chain r residue 7 VAL Chi-restraints excluded: chain r residue 16 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 373 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 182 optimal weight: 0.0020 chunk 135 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 26 optimal weight: 0.0040 chunk 12 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 HIS ** S 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086055 restraints weight = 88749.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.089442 restraints weight = 39324.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091180 restraints weight = 21219.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091693 restraints weight = 15455.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092082 restraints weight = 13040.429| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.202 34894 Z= 0.234 Angle : 1.039 77.649 47343 Z= 0.471 Chirality : 0.047 0.580 5170 Planarity : 0.006 0.172 6013 Dihedral : 8.261 152.879 4812 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 3.09 % Allowed : 25.87 % Favored : 71.04 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.14 (0.13), residues: 4163 helix: 0.86 (0.12), residues: 1853 sheet: -0.85 (0.27), residues: 370 loop : -0.82 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 122 TYR 0.035 0.002 TYR W 126 PHE 0.065 0.002 PHE B 121 TRP 0.033 0.001 TRP V 97 HIS 0.018 0.001 HIS F 376 Details of bonding type rmsd covalent geometry : bond 0.00524 (34854) covalent geometry : angle 0.88640 (47253) SS BOND : bond 0.00412 ( 3) SS BOND : angle 1.78233 ( 6) hydrogen bonds : bond 0.04007 ( 1428) hydrogen bonds : angle 4.92568 ( 4125) metal coordination : bond 0.01557 ( 37) metal coordination : angle 12.87487 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8691.08 seconds wall clock time: 150 minutes 6.71 seconds (9006.71 seconds total)