Starting phenix.real_space_refine on Tue May 5 22:25:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332.map" model { file = "/net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib5_35332/05_2026/8ib5_35332_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.087 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 13 5.49 5 S 244 5.16 5 C 21740 2.51 5 N 5760 2.21 5 O 6157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33943 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 754 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3095 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 21, 'TRANS': 364} 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: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2510 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 22, 'TRANS': 291} Chain breaks: 2 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: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "q" Number of atoms: 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: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 418 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain breaks: 1 Chain: "s" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 115 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'PC1': 1, 'SF4': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 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: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "a" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1017 SG CYS B 99 80.656 60.015 106.239 1.00 29.52 S ATOM 1520 SG CYS B 164 77.870 56.523 111.216 1.00 28.96 S ATOM 1750 SG CYS B 194 83.026 56.385 110.477 1.00 29.28 S ATOM 1023 SG CYS B 100 79.358 56.051 105.414 1.00 30.11 S ATOM 7537 SG CYS E 134 140.219 51.263 152.981 1.00 56.01 S ATOM 7571 SG CYS E 139 142.703 52.891 152.257 1.00 56.50 S ATOM 7855 SG CYS E 175 137.829 54.729 155.618 1.00 54.42 S ATOM 7878 SG CYS E 179 141.128 56.405 155.741 1.00 57.95 S ATOM 11408 SG CYS F 425 121.558 60.476 155.714 1.00 45.60 S ATOM 11086 SG CYS F 385 121.611 58.000 149.921 1.00 39.95 S ATOM 11066 SG CYS F 382 117.338 59.164 152.177 1.00 40.29 S ATOM 11047 SG CYS F 379 119.290 55.097 155.044 1.00 43.09 S ATOM 12456 SG CYS G 131 101.176 48.030 138.589 1.00 31.31 S ATOM 12435 SG CYS G 128 103.205 51.877 134.006 1.00 30.26 S ATOM 12496 SG CYS G 137 100.844 53.932 140.023 1.00 33.13 S ATOM 13181 SG CYS G 226 102.680 48.018 147.181 1.00 34.31 S ATOM 12852 SG CYS G 182 105.805 46.328 152.942 1.00 36.31 S ATOM 12828 SG CYS G 179 105.198 51.913 150.410 1.00 35.62 S ATOM 12805 SG CYS G 176 108.646 47.649 147.942 1.00 34.05 S ATOM 11942 SG CYS G 64 106.607 57.948 152.441 1.00 35.53 S ATOM 12028 SG CYS G 75 107.341 59.994 150.783 1.00 36.47 S ATOM 12053 SG CYS G 78 106.229 64.441 152.900 1.00 36.76 S ATOM 12154 SG CYS G 92 105.997 62.527 156.078 1.00 39.04 S ATOM 20154 SG CYS I 123 86.912 51.190 119.573 1.00 27.30 S ATOM 20380 SG CYS I 152 86.706 50.037 114.456 1.00 27.39 S ATOM 20427 SG CYS I 158 92.350 50.194 116.606 1.00 26.60 S ATOM 20406 SG CYS I 155 89.244 54.614 116.274 1.00 27.04 S ATOM 20103 SG CYS I 116 96.701 47.126 127.022 1.00 29.24 S ATOM 20126 SG CYS I 119 92.361 46.808 123.632 1.00 28.85 S ATOM 20084 SG CYS I 113 95.582 41.998 123.733 1.00 28.61 S ATOM 20456 SG CYS I 162 98.489 46.608 121.666 1.00 28.07 S ATOM 24965 SG CYS R 79 111.961 39.886 126.378 1.00 32.60 S ATOM 25141 SG CYS R 104 109.496 38.453 127.802 1.00 32.49 S ATOM 25163 SG CYS R 107 108.850 39.111 124.374 1.00 30.78 S Time building chain proxies: 7.19, per 1000 atoms: 0.21 Number of scatterers: 33943 At special positions: 0 Unit cell: (168.3, 128.7, 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 244 16.00 P 13 15.00 O 6157 8.00 N 5760 7.00 C 21740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS X 36 " - pdb=" SG CYS X 66 " distance=2.00 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.09 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: 3.09 Conformation dependent library (CDL) restraints added in 1.3 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 303 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 303 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 304 " pdb="FE3 SF4 I 304 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 304 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 304 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 304 " - 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 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7816 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 36 sheets defined 49.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.314A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 106 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.586A 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 114 through 118 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: 3.590A 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: 3.603A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.967A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.297A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.772A 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: 3.726A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.861A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.707A 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: 3.702A 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: 3.743A 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: 3.670A 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: 3.531A 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 73 through 76 removed outlier: 3.638A pdb=" N ALA E 76 " --> pdb=" O HIS E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.526A 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: 3.684A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 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: 3.554A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.922A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.515A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 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: 3.601A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.532A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.872A 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 296 through 303 removed outlier: 3.862A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 4.061A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.660A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.644A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.349A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.519A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.599A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.775A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.713A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 204 " --> pdb=" O GLY G 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 200 through 204' Processing helix chain 'G' and resid 220 through 226 removed outlier: 3.820A 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: 3.670A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A 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: 3.635A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.522A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.641A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.749A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.574A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.740A pdb=" N THR H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 124 removed outlier: 3.688A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.001A 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: 3.554A 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 217 through 242 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: 3.864A 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: 5.990A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.873A 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: 4.027A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.275A 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 Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.594A pdb=" N LYS P 189 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 3.660A 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 323 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.034A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.200A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 45 through 49 Processing helix chain 'R' and resid 59 through 64 removed outlier: 3.650A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.513A pdb=" N TYR S 41 " --> pdb=" O ILE S 37 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.810A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.677A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.856A pdb=" N ARG W 33 " --> pdb=" O ASN W 29 " (cutoff:3.500A) removed outlier: 4.461A 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: 3.517A 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 107 Processing helix chain 'W' and resid 120 through 127 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.528A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 35 removed outlier: 4.624A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 27 removed outlier: 4.499A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 6 through 15 removed outlier: 4.398A pdb=" N ALA b 12 " --> pdb=" O PHE b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.759A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.601A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 78 through 82 removed outlier: 3.538A pdb=" N VAL q 82 " --> pdb=" O GLY q 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.126A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 7 through 17 Processing helix chain 's' and resid 78 through 89 removed outlier: 3.519A pdb=" N LEU s 85 " --> pdb=" O LEU s 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.277A pdb=" N MET B 93 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 134 " --> pdb=" O MET B 93 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.919A 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: 6.798A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.568A pdb=" N CYS C 86 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.831A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.981A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.564A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 84 removed outlier: 3.525A pdb=" N LEU D 97 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA9, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.356A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, 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=AB2, first strand: chain 'E' and resid 131 through 133 removed outlier: 3.515A pdb=" N TYR E 192 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.442A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.151A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.487A 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=AB5, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.808A pdb=" N VAL F 294 " --> pdb=" O MET F 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 Processing sheet with id=AB7, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.867A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB9, 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=AC1, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AC2, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A 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=AC7, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.359A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC9, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.359A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'P' and resid 263 through 264 Processing sheet with id=AD2, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AD3, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AD4, first strand: chain 'R' and resid 52 through 53 removed outlier: 7.650A pdb=" N GLN R 52 " --> pdb=" O VAL q 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'R' and resid 76 through 79 removed outlier: 4.032A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.508A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD7, 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=AD8, first strand: chain 'X' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'q' and resid 37 through 42 removed outlier: 6.239A pdb=" N LEU q 38 " --> pdb=" O GLU q 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU q 50 " --> pdb=" O LEU q 38 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY q 40 " --> pdb=" O TYR q 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN q 46 " --> pdb=" O ASP q 42 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 4122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 3.93 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: 11493 1.37 - 1.59: 22769 1.59 - 1.80: 274 1.80 - 2.02: 134 2.02 - 2.23: 80 Bond restraints: 34750 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 1.33e+03 bond pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 1.473 1.262 0.211 1.40e-02 5.10e+03 2.26e+02 bond pdb=" N PRO q 139 " pdb=" CD PRO q 139 " ideal model delta sigma weight residual 1.473 1.285 0.188 1.40e-02 5.10e+03 1.81e+02 bond pdb=" N PRO P 371 " pdb=" CD PRO P 371 " ideal model delta sigma weight residual 1.473 1.654 -0.181 1.40e-02 5.10e+03 1.67e+02 bond pdb=" N PRO G 532 " pdb=" CD PRO G 532 " ideal model delta sigma weight residual 1.473 1.298 0.175 1.40e-02 5.10e+03 1.57e+02 ... (remaining 34745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 46228 6.66 - 13.33: 667 13.33 - 19.99: 171 19.99 - 26.65: 3 26.65 - 33.32: 2 Bond angle restraints: 47071 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.39 -21.74 1.13e+00 7.83e-01 3.70e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.53 17.89 9.40e-01 1.13e+00 3.62e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.09 25.55 1.52e+00 4.33e-01 2.83e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.46 19.71 1.26e+00 6.30e-01 2.45e+02 angle pdb=" N CYS F 332 " pdb=" CA CYS F 332 " pdb=" C CYS F 332 " ideal model delta sigma weight residual 111.02 130.09 -19.07 1.22e+00 6.72e-01 2.44e+02 ... (remaining 47066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.45: 20224 27.45 - 54.90: 662 54.90 - 82.35: 99 82.35 - 109.81: 9 109.81 - 137.26: 3 Dihedral angle restraints: 20997 sinusoidal: 8874 harmonic: 12123 Sorted by residual: dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.22 -21.38 0 2.50e+00 1.60e-01 7.31e+01 dihedral pdb=" C PHE a 3 " pdb=" N PHE a 3 " pdb=" CA PHE a 3 " pdb=" CB PHE a 3 " ideal model delta harmonic sigma weight residual -122.60 -101.67 -20.93 0 2.50e+00 1.60e-01 7.01e+01 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 93.00 161.49 -68.49 1 1.00e+01 1.00e-02 6.08e+01 ... (remaining 20994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4468 0.183 - 0.365: 586 0.365 - 0.548: 54 0.548 - 0.731: 6 0.731 - 0.913: 24 Chirality restraints: 5138 Sorted by residual: chirality pdb="FE3 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S4 SF4 I 304 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb="FE2 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S3 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb="FE4 SF4 I 304 " pdb=" S1 SF4 I 304 " pdb=" S2 SF4 I 304 " pdb=" S3 SF4 I 304 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 5135 not shown) Planarity restraints: 5966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 H 401 " -0.016 2.00e-02 2.50e+03 2.20e-01 1.46e+03 pdb=" C1M UQ9 H 401 " -0.109 2.00e-02 2.50e+03 pdb=" C2 UQ9 H 401 " 0.027 2.00e-02 2.50e+03 pdb=" C3 UQ9 H 401 " -0.050 2.00e-02 2.50e+03 pdb=" C4 UQ9 H 401 " 0.088 2.00e-02 2.50e+03 pdb=" C5 UQ9 H 401 " -0.122 2.00e-02 2.50e+03 pdb=" C6 UQ9 H 401 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.271 2.00e-02 2.50e+03 pdb=" O2 UQ9 H 401 " 0.135 2.00e-02 2.50e+03 pdb=" O3 UQ9 H 401 " -0.257 2.00e-02 2.50e+03 pdb=" O4 UQ9 H 401 " 0.438 2.00e-02 2.50e+03 pdb=" O5 UQ9 H 401 " -0.441 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 302 " -0.041 2.00e-02 2.50e+03 1.73e-01 8.94e+02 pdb=" C2 UQ1 B 302 " 0.025 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 302 " 0.053 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 302 " -0.112 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 302 " 0.063 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 302 " 0.001 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 302 " -0.037 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 302 " 0.305 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 302 " -0.132 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 302 " 0.060 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 302 " 0.227 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 302 " -0.411 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 H 401 " 0.190 2.00e-02 2.50e+03 2.57e-01 8.26e+02 pdb=" C11 UQ9 H 401 " 0.037 2.00e-02 2.50e+03 pdb=" C7 UQ9 H 401 " 0.303 2.00e-02 2.50e+03 pdb=" C8 UQ9 H 401 " -0.438 2.00e-02 2.50e+03 pdb=" C9 UQ9 H 401 " -0.092 2.00e-02 2.50e+03 ... (remaining 5963 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 76 2.38 - 3.01: 22427 3.01 - 3.64: 53048 3.64 - 4.27: 83105 4.27 - 4.90: 134973 Nonbonded interactions: 293629 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASP q 76 " pdb=" OD1 ASP q 76 " model vdw 1.904 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 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 1.980 3.120 ... (remaining 293624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 39.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.023 1.141 34791 Z= 1.088 Angle : 2.323 52.571 47163 Z= 1.563 Chirality : 0.136 0.913 5138 Planarity : 0.010 0.257 5966 Dihedral : 13.544 137.257 13169 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 44.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 0.28 % Allowed : 7.73 % Favored : 91.99 % Cbeta Deviations : 2.28 % 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: -2.04 (0.12), residues: 4124 helix: -0.71 (0.11), residues: 1807 sheet: -1.11 (0.27), residues: 365 loop : -2.01 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.046 0.003 TYR B 112 PHE 0.071 0.002 PHE B 121 TRP 0.034 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01516 (34750) covalent geometry : angle 2.20029 (47071) SS BOND : bond 0.03573 ( 4) SS BOND : angle 5.79692 ( 8) hydrogen bonds : bond 0.24410 ( 1414) hydrogen bonds : angle 8.83201 ( 4122) metal coordination : bond 0.52816 ( 37) metal coordination : angle 17.72255 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1457 time to evaluate : 1.792 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: B 166 ASN cc_start: 0.7999 (m-40) cc_final: 0.7794 (m110) REVERT: B 201 LEU cc_start: 0.8973 (tp) cc_final: 0.8409 (tp) REVERT: D 197 MET cc_start: 0.6846 (ptp) cc_final: 0.6601 (ptm) REVERT: E 47 ASN cc_start: 0.7920 (p0) cc_final: 0.7698 (p0) REVERT: E 167 LEU cc_start: 0.7456 (tp) cc_final: 0.7134 (tp) REVERT: F 287 THR cc_start: 0.7799 (m) cc_final: 0.5935 (m) REVERT: G 329 MET cc_start: 0.7188 (mmm) cc_final: 0.6657 (mmt) REVERT: G 519 ILE cc_start: 0.8955 (mt) cc_final: 0.8662 (mt) REVERT: G 634 LEU cc_start: 0.8672 (mt) cc_final: 0.8378 (mt) REVERT: H 1 MET cc_start: 0.6897 (mmt) cc_final: 0.6645 (mmt) REVERT: H 72 ILE cc_start: 0.8469 (pp) cc_final: 0.8242 (pt) REVERT: H 134 ARG cc_start: 0.7300 (mtm180) cc_final: 0.6215 (mtm180) REVERT: H 193 THR cc_start: 0.8220 (p) cc_final: 0.8014 (p) REVERT: H 282 TYR cc_start: 0.7306 (t80) cc_final: 0.6789 (t80) REVERT: H 285 LEU cc_start: 0.8481 (tt) cc_final: 0.8175 (tt) REVERT: P 271 TYR cc_start: 0.7485 (m-80) cc_final: 0.6727 (m-80) REVERT: Q 63 THR cc_start: 0.9098 (p) cc_final: 0.8887 (p) REVERT: S 64 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8324 (mttp) REVERT: S 80 ASN cc_start: 0.8051 (t0) cc_final: 0.7713 (t0) REVERT: W 65 LYS cc_start: 0.8526 (tptt) cc_final: 0.8241 (tttt) REVERT: X 32 TYR cc_start: 0.8046 (t80) cc_final: 0.7758 (t80) REVERT: Z 133 MET cc_start: 0.8151 (ttp) cc_final: 0.7831 (ttt) outliers start: 10 outliers final: 1 residues processed: 1460 average time/residue: 0.2393 time to fit residues: 542.4084 Evaluate side-chains 908 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 907 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 103 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN C 56 GLN C 123 ASN C 130 ASN C 195 HIS ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 HIS D 346 GLN D 381 HIS ** E 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 245 GLN F 136 HIS F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 HIS F 393 ASN G 59 GLN G 74 ASN G 140 GLN G 164 ASN G 331 GLN G 495 ASN ** G 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 571 HIS G 605 GLN ** G 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 99 ASN H 163 GLN ** H 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 169 HIS P 251 ASN Q 88 GLN S 73 GLN W 29 ASN W 105 HIS X 35 GLN X 64 ASN ** X 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 104 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 GLN a 58 ASN b 69 HIS q 13 GLN q 31 ASN q 54 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 21 GLN ** r 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 84 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111627 restraints weight = 54069.966| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.65 r_work: 0.3311 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 34791 Z= 0.203 Angle : 0.977 67.540 47163 Z= 0.415 Chirality : 0.049 0.371 5138 Planarity : 0.006 0.122 5966 Dihedral : 10.093 150.201 4941 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.62 % Favored : 97.36 % Rotamer: Outliers : 3.01 % Allowed : 15.10 % Favored : 81.89 % 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: -0.88 (0.13), residues: 4124 helix: 0.35 (0.12), residues: 1870 sheet: -1.02 (0.25), residues: 372 loop : -1.42 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 67 TYR 0.026 0.002 TYR T 90 PHE 0.030 0.002 PHE T 126 TRP 0.021 0.002 TRP q 86 HIS 0.017 0.002 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00461 (34750) covalent geometry : angle 0.79391 (47071) SS BOND : bond 0.00903 ( 4) SS BOND : angle 4.25088 ( 8) hydrogen bonds : bond 0.06005 ( 1414) hydrogen bonds : angle 5.62921 ( 4122) metal coordination : bond 0.02729 ( 37) metal coordination : angle 13.46850 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 929 time to evaluate : 1.460 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: B 122 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7790 (mmt90) REVERT: B 199 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 178 PHE cc_start: 0.8573 (m-80) cc_final: 0.8186 (m-10) REVERT: D 142 VAL cc_start: 0.8824 (t) cc_final: 0.8412 (m) REVERT: D 185 MET cc_start: 0.8873 (tpt) cc_final: 0.8599 (tpt) REVERT: D 359 ASP cc_start: 0.7306 (p0) cc_final: 0.6995 (p0) REVERT: E 68 ASN cc_start: 0.8618 (t0) cc_final: 0.8327 (t0) REVERT: E 91 TRP cc_start: 0.7582 (t60) cc_final: 0.7173 (t60) REVERT: E 120 MET cc_start: 0.8436 (tpp) cc_final: 0.7641 (mmt) REVERT: E 129 TYR cc_start: 0.6881 (m-80) cc_final: 0.6531 (m-10) REVERT: F 51 TRP cc_start: 0.7616 (p-90) cc_final: 0.7015 (p-90) REVERT: F 149 MET cc_start: 0.7708 (mtt) cc_final: 0.7200 (mtt) REVERT: F 209 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: F 357 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8465 (mmm) REVERT: F 447 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8004 (mt-10) REVERT: G 58 MET cc_start: 0.6929 (mmp) cc_final: 0.6628 (mmp) REVERT: G 280 ASP cc_start: 0.8343 (m-30) cc_final: 0.8105 (m-30) REVERT: G 329 MET cc_start: 0.8209 (mmm) cc_final: 0.7428 (mmt) REVERT: G 380 ASP cc_start: 0.7983 (m-30) cc_final: 0.7620 (m-30) REVERT: G 455 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7272 (mp) REVERT: G 519 ILE cc_start: 0.8961 (mt) cc_final: 0.8748 (mm) REVERT: G 544 MET cc_start: 0.8347 (ttp) cc_final: 0.8086 (ttt) REVERT: G 712 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8556 (mtpp) REVERT: H 31 MET cc_start: 0.9313 (mtp) cc_final: 0.9090 (mtp) REVERT: H 134 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7993 (mtp-110) REVERT: H 166 ILE cc_start: 0.8474 (mm) cc_final: 0.8214 (mm) REVERT: H 193 THR cc_start: 0.8444 (p) cc_final: 0.8139 (p) REVERT: H 260 MET cc_start: 0.8782 (tmm) cc_final: 0.8175 (tmm) REVERT: H 261 MET cc_start: 0.8616 (mmt) cc_final: 0.8193 (mtt) REVERT: I 51 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7394 (mmmt) REVERT: I 94 SER cc_start: 0.9151 (p) cc_final: 0.8704 (p) REVERT: P 91 ILE cc_start: 0.9110 (tp) cc_final: 0.8798 (tp) REVERT: P 266 THR cc_start: 0.7456 (p) cc_final: 0.7192 (t) REVERT: P 269 ASN cc_start: 0.7934 (p0) cc_final: 0.7366 (p0) REVERT: P 271 TYR cc_start: 0.8024 (m-80) cc_final: 0.7166 (m-80) REVERT: P 283 MET cc_start: 0.8230 (tpp) cc_final: 0.7652 (tpp) REVERT: P 324 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8364 (tt) REVERT: Q 63 THR cc_start: 0.8962 (p) cc_final: 0.8563 (p) REVERT: Q 128 PHE cc_start: 0.8797 (m-80) cc_final: 0.8546 (m-80) REVERT: Q 165 SER cc_start: 0.8133 (t) cc_final: 0.7734 (p) REVERT: S 58 CYS cc_start: 0.7377 (t) cc_final: 0.6177 (m) REVERT: S 80 ASN cc_start: 0.8483 (t0) cc_final: 0.8147 (t0) REVERT: T 115 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7825 (tm-30) REVERT: T 137 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7934 (tmtt) REVERT: W 39 TYR cc_start: 0.8896 (t80) cc_final: 0.8366 (t80) REVERT: W 43 TYR cc_start: 0.8296 (t80) cc_final: 0.7553 (t80) REVERT: W 123 SER cc_start: 0.8922 (m) cc_final: 0.8552 (p) REVERT: X 6 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7055 (tm-30) REVERT: X 32 TYR cc_start: 0.9057 (t80) cc_final: 0.8583 (t80) REVERT: X 104 GLN cc_start: 0.8678 (tt0) cc_final: 0.8020 (tt0) REVERT: X 129 THR cc_start: 0.8208 (p) cc_final: 0.7986 (m) REVERT: Z 50 MET cc_start: 0.8258 (tpp) cc_final: 0.8026 (tpp) REVERT: Z 74 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8532 (tt) REVERT: Z 85 GLN cc_start: 0.8357 (tt0) cc_final: 0.8055 (tt0) REVERT: Z 98 MET cc_start: 0.6435 (ttm) cc_final: 0.6134 (ttm) REVERT: Z 133 MET cc_start: 0.8745 (ttp) cc_final: 0.8215 (ttt) REVERT: a 64 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7374 (tttp) REVERT: b 23 PHE cc_start: 0.8561 (m-80) cc_final: 0.8095 (m-80) REVERT: b 58 ARG cc_start: 0.6557 (mtp-110) cc_final: 0.6109 (mtp180) REVERT: q 58 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7214 (mtp180) REVERT: q 77 VAL cc_start: 0.6899 (t) cc_final: 0.6427 (p) REVERT: r 27 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6938 (ttp-110) REVERT: r 92 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7756 (mtpt) REVERT: s 78 TYR cc_start: 0.6730 (m-80) cc_final: 0.6348 (m-80) outliers start: 109 outliers final: 50 residues processed: 985 average time/residue: 0.2238 time to fit residues: 353.9116 Evaluate side-chains 856 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 800 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 455 ILE Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain G residue 712 LYS Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 71 PHE Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 8 THR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 126 SER Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 168 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 218 optimal weight: 0.0030 chunk 324 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN C 180 HIS ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 147 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 ASN G 663 ASN I 85 ASN P 238 GLN Q 51 GLN S 48 HIS V 50 GLN W 29 ASN a 44 GLN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 9 GLN r 110 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111941 restraints weight = 53786.415| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.44 r_work: 0.3317 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 34791 Z= 0.151 Angle : 0.861 70.046 47163 Z= 0.346 Chirality : 0.045 0.228 5138 Planarity : 0.005 0.125 5966 Dihedral : 9.685 156.580 4939 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 3.18 % Allowed : 16.29 % Favored : 80.54 % 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: -0.34 (0.13), residues: 4124 helix: 0.82 (0.12), residues: 1850 sheet: -0.98 (0.26), residues: 369 loop : -1.10 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 269 TYR 0.026 0.002 TYR C 63 PHE 0.022 0.002 PHE G 462 TRP 0.020 0.001 TRP b 80 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00344 (34750) covalent geometry : angle 0.67526 (47071) SS BOND : bond 0.00637 ( 4) SS BOND : angle 3.52736 ( 8) hydrogen bonds : bond 0.04710 ( 1414) hydrogen bonds : angle 5.07390 ( 4122) metal coordination : bond 0.01881 ( 37) metal coordination : angle 12.61913 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 878 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8137 (tmm) cc_final: 0.7706 (tmm) REVERT: A 100 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8715 (mm) REVERT: A 105 GLU cc_start: 0.9010 (tp30) cc_final: 0.8437 (tp30) REVERT: B 122 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7968 (mmt90) REVERT: B 141 MET cc_start: 0.9249 (tpt) cc_final: 0.8890 (tpt) REVERT: B 219 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8663 (ttmm) REVERT: C 58 SER cc_start: 0.9148 (t) cc_final: 0.8736 (p) REVERT: C 78 SER cc_start: 0.9138 (t) cc_final: 0.8829 (p) REVERT: C 150 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 178 PHE cc_start: 0.8655 (m-80) cc_final: 0.8289 (m-10) REVERT: D 107 ARG cc_start: 0.8054 (mmp-170) cc_final: 0.7807 (mmm160) REVERT: D 142 VAL cc_start: 0.8837 (t) cc_final: 0.8578 (m) REVERT: D 144 MET cc_start: 0.8139 (mpp) cc_final: 0.7838 (mpp) REVERT: E 69 TYR cc_start: 0.6902 (m-80) cc_final: 0.6555 (m-80) REVERT: E 74 GLN cc_start: 0.7912 (mp10) cc_final: 0.7457 (mp10) REVERT: E 142 ARG cc_start: 0.7465 (tpp80) cc_final: 0.6750 (mmt90) REVERT: F 51 TRP cc_start: 0.7744 (p-90) cc_final: 0.7021 (p-90) REVERT: F 102 MET cc_start: 0.8206 (ppp) cc_final: 0.7976 (ppp) REVERT: F 149 MET cc_start: 0.7975 (mtt) cc_final: 0.7677 (mpp) REVERT: F 209 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: G 39 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8210 (tm-30) REVERT: G 42 MET cc_start: 0.8573 (mmm) cc_final: 0.7911 (mmm) REVERT: G 58 MET cc_start: 0.7043 (mmp) cc_final: 0.6748 (mmt) REVERT: G 87 LYS cc_start: 0.8989 (ptpt) cc_final: 0.8769 (ptmt) REVERT: G 329 MET cc_start: 0.8381 (mmm) cc_final: 0.7690 (mmt) REVERT: G 380 ASP cc_start: 0.8025 (m-30) cc_final: 0.7732 (m-30) REVERT: G 479 SER cc_start: 0.8805 (p) cc_final: 0.8581 (m) REVERT: H 31 MET cc_start: 0.9429 (mtp) cc_final: 0.9150 (mtp) REVERT: H 134 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7425 (mtp-110) REVERT: H 166 ILE cc_start: 0.8355 (mm) cc_final: 0.8117 (mm) REVERT: H 193 THR cc_start: 0.8430 (p) cc_final: 0.8123 (p) REVERT: H 200 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.6660 (pp) REVERT: H 260 MET cc_start: 0.8977 (tmm) cc_final: 0.8348 (tmm) REVERT: H 261 MET cc_start: 0.8703 (mmt) cc_final: 0.8388 (mtt) REVERT: H 282 TYR cc_start: 0.8301 (t80) cc_final: 0.7650 (t80) REVERT: H 284 GLN cc_start: 0.8593 (mt0) cc_final: 0.7800 (mt0) REVERT: I 51 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7323 (mmmt) REVERT: I 73 THR cc_start: 0.8326 (p) cc_final: 0.7993 (p) REVERT: I 94 SER cc_start: 0.9310 (p) cc_final: 0.8751 (p) REVERT: P 91 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8884 (tp) REVERT: P 266 THR cc_start: 0.7432 (p) cc_final: 0.7104 (p) REVERT: P 271 TYR cc_start: 0.8122 (m-80) cc_final: 0.7263 (m-10) REVERT: P 283 MET cc_start: 0.8295 (tpp) cc_final: 0.7877 (mmm) REVERT: P 324 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8266 (tt) REVERT: Q 51 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5755 (pm20) REVERT: Q 164 PHE cc_start: 0.8768 (m-10) cc_final: 0.8383 (m-10) REVERT: Q 165 SER cc_start: 0.7931 (t) cc_final: 0.7590 (p) REVERT: R 94 ASN cc_start: 0.9034 (t0) cc_final: 0.8787 (t0) REVERT: S 57 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7723 (mm-30) REVERT: S 80 ASN cc_start: 0.8541 (t0) cc_final: 0.8306 (t0) REVERT: T 117 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8074 (mt-10) REVERT: T 142 GLN cc_start: 0.8356 (pt0) cc_final: 0.7971 (mt0) REVERT: W 39 TYR cc_start: 0.9033 (t80) cc_final: 0.8688 (t80) REVERT: W 45 GLU cc_start: 0.9143 (tp30) cc_final: 0.8767 (tp30) REVERT: W 123 SER cc_start: 0.8936 (m) cc_final: 0.8573 (p) REVERT: X 6 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7101 (tm-30) REVERT: X 32 TYR cc_start: 0.9100 (t80) cc_final: 0.8688 (t80) REVERT: X 47 ARG cc_start: 0.7778 (tpt90) cc_final: 0.5897 (tpt90) REVERT: X 104 GLN cc_start: 0.8616 (tt0) cc_final: 0.8334 (tt0) REVERT: X 129 THR cc_start: 0.8344 (p) cc_final: 0.8086 (m) REVERT: Z 50 MET cc_start: 0.8311 (tpp) cc_final: 0.7831 (tpp) REVERT: Z 69 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8235 (mp) REVERT: Z 80 ASP cc_start: 0.8363 (m-30) cc_final: 0.8018 (m-30) REVERT: Z 98 MET cc_start: 0.6494 (ttm) cc_final: 0.6068 (ttm) REVERT: Z 133 MET cc_start: 0.8701 (ttp) cc_final: 0.8360 (ttt) REVERT: Z 138 PHE cc_start: 0.8459 (m-80) cc_final: 0.8202 (m-80) REVERT: b 23 PHE cc_start: 0.8607 (m-80) cc_final: 0.8112 (m-80) REVERT: b 47 LYS cc_start: 0.9092 (ttpt) cc_final: 0.8662 (ttpp) REVERT: b 58 ARG cc_start: 0.7008 (mtp-110) cc_final: 0.6566 (mtp180) REVERT: b 82 LYS cc_start: 0.8640 (tttp) cc_final: 0.8309 (mtmm) REVERT: q 58 ARG cc_start: 0.7822 (mtm180) cc_final: 0.7480 (mtp180) REVERT: q 77 VAL cc_start: 0.6945 (t) cc_final: 0.6599 (p) REVERT: r 14 TRP cc_start: 0.6189 (t60) cc_final: 0.5937 (t-100) REVERT: r 92 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7926 (ttpt) REVERT: s 78 TYR cc_start: 0.6670 (m-80) cc_final: 0.6342 (m-80) outliers start: 115 outliers final: 60 residues processed: 935 average time/residue: 0.2274 time to fit residues: 345.0528 Evaluate side-chains 838 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 770 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 652 ASN Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 71 PHE Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 77 THR Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 100 ASP Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 226 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 320 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 330 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 384 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 356 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN C 88 HIS D 79 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 ASN G 663 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 171 ASN ** P 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN V 50 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112777 restraints weight = 53858.558| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.42 r_work: 0.3305 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 34791 Z= 0.139 Angle : 0.827 71.506 47163 Z= 0.325 Chirality : 0.043 0.198 5138 Planarity : 0.005 0.126 5966 Dihedral : 9.438 158.195 4939 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 3.73 % Allowed : 17.26 % Favored : 79.02 % 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: -0.21 (0.13), residues: 4124 helix: 0.94 (0.12), residues: 1860 sheet: -0.97 (0.26), residues: 367 loop : -1.04 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 184 TYR 0.018 0.001 TYR T 85 PHE 0.017 0.001 PHE H 310 TRP 0.020 0.001 TRP G 100 HIS 0.005 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00322 (34750) covalent geometry : angle 0.63453 (47071) SS BOND : bond 0.01201 ( 4) SS BOND : angle 3.93898 ( 8) hydrogen bonds : bond 0.04244 ( 1414) hydrogen bonds : angle 4.88632 ( 4122) metal coordination : bond 0.01536 ( 37) metal coordination : angle 12.52431 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 844 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8162 (tmm) cc_final: 0.7735 (tmm) REVERT: A 105 GLU cc_start: 0.9088 (tp30) cc_final: 0.8693 (tp30) REVERT: B 141 MET cc_start: 0.9217 (tpt) cc_final: 0.8863 (tpt) REVERT: B 219 LYS cc_start: 0.8961 (ttpt) cc_final: 0.8709 (ttmm) REVERT: C 58 SER cc_start: 0.9143 (t) cc_final: 0.8758 (p) REVERT: C 78 SER cc_start: 0.9182 (t) cc_final: 0.8887 (p) REVERT: C 148 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 150 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8904 (p) REVERT: C 178 PHE cc_start: 0.8655 (m-80) cc_final: 0.8276 (m-10) REVERT: D 83 ASN cc_start: 0.8190 (p0) cc_final: 0.7886 (p0) REVERT: D 142 VAL cc_start: 0.8770 (t) cc_final: 0.8533 (m) REVERT: D 144 MET cc_start: 0.8147 (mpp) cc_final: 0.7625 (mpp) REVERT: D 294 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8161 (ttm-80) REVERT: E 69 TYR cc_start: 0.7243 (m-80) cc_final: 0.7040 (m-80) REVERT: E 74 GLN cc_start: 0.7938 (mp10) cc_final: 0.7427 (mp10) REVERT: E 91 TRP cc_start: 0.7760 (t60) cc_final: 0.7308 (t60) REVERT: E 142 ARG cc_start: 0.7537 (tpp80) cc_final: 0.6740 (mmt90) REVERT: F 51 TRP cc_start: 0.7620 (p-90) cc_final: 0.6946 (p-90) REVERT: F 140 GLU cc_start: 0.7115 (pt0) cc_final: 0.6905 (tt0) REVERT: F 149 MET cc_start: 0.7965 (mtt) cc_final: 0.7674 (mpp) REVERT: F 209 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: F 217 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8649 (mt-10) REVERT: G 32 ILE cc_start: 0.7984 (mm) cc_final: 0.7646 (mt) REVERT: G 39 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8142 (tm-30) REVERT: G 42 MET cc_start: 0.8525 (mmm) cc_final: 0.7871 (mmm) REVERT: G 58 MET cc_start: 0.7067 (mmp) cc_final: 0.6778 (mmt) REVERT: G 87 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8727 (ptmt) REVERT: G 97 MET cc_start: 0.8091 (ptp) cc_final: 0.7324 (ptp) REVERT: G 165 ILE cc_start: 0.8678 (tt) cc_final: 0.8406 (tt) REVERT: G 329 MET cc_start: 0.8306 (mmm) cc_final: 0.7560 (mmt) REVERT: G 380 ASP cc_start: 0.8037 (m-30) cc_final: 0.7788 (m-30) REVERT: H 1 MET cc_start: 0.7872 (mmt) cc_final: 0.7596 (tpp) REVERT: H 111 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9154 (tt) REVERT: H 134 ARG cc_start: 0.8454 (mtm180) cc_final: 0.7410 (mtp-110) REVERT: H 172 MET cc_start: 0.8721 (ppp) cc_final: 0.8480 (ppp) REVERT: H 193 THR cc_start: 0.8499 (p) cc_final: 0.8206 (p) REVERT: H 260 MET cc_start: 0.9083 (tmm) cc_final: 0.8733 (tmm) REVERT: H 261 MET cc_start: 0.8674 (mmt) cc_final: 0.8359 (mpp) REVERT: H 282 TYR cc_start: 0.8412 (t80) cc_final: 0.7785 (t80) REVERT: H 284 GLN cc_start: 0.8510 (mt0) cc_final: 0.7738 (mt0) REVERT: I 41 LYS cc_start: 0.8226 (tptp) cc_final: 0.7795 (tptp) REVERT: I 94 SER cc_start: 0.9338 (p) cc_final: 0.8882 (p) REVERT: P 91 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8948 (tp) REVERT: P 102 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: P 219 ASN cc_start: 0.8508 (m-40) cc_final: 0.8228 (m-40) REVERT: P 269 ASN cc_start: 0.7908 (p0) cc_final: 0.7346 (p0) REVERT: P 271 TYR cc_start: 0.8070 (m-80) cc_final: 0.7308 (m-80) REVERT: P 283 MET cc_start: 0.8256 (tpp) cc_final: 0.7812 (mmm) REVERT: P 310 PHE cc_start: 0.5525 (t80) cc_final: 0.5019 (t80) REVERT: P 324 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8221 (tt) REVERT: Q 165 SER cc_start: 0.7742 (t) cc_final: 0.7451 (p) REVERT: R 94 ASN cc_start: 0.9007 (t0) cc_final: 0.8780 (t0) REVERT: S 57 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7680 (mm-30) REVERT: S 69 TYR cc_start: 0.8565 (m-80) cc_final: 0.8007 (m-80) REVERT: S 80 ASN cc_start: 0.8272 (t0) cc_final: 0.8040 (t0) REVERT: T 80 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7771 (tptp) REVERT: T 117 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8026 (mt-10) REVERT: V 35 LEU cc_start: 0.9097 (mm) cc_final: 0.8820 (mt) REVERT: W 45 GLU cc_start: 0.9069 (tp30) cc_final: 0.8630 (tp30) REVERT: W 98 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8454 (mttt) REVERT: W 123 SER cc_start: 0.8910 (m) cc_final: 0.8586 (p) REVERT: X 32 TYR cc_start: 0.9092 (t80) cc_final: 0.8670 (t80) REVERT: X 47 ARG cc_start: 0.7818 (tpt90) cc_final: 0.6002 (tpt90) REVERT: X 135 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6814 (ttp80) REVERT: Z 28 ARG cc_start: 0.6808 (ptt90) cc_final: 0.6442 (tmm-80) REVERT: Z 45 PHE cc_start: 0.8794 (t80) cc_final: 0.8518 (t80) REVERT: Z 51 MET cc_start: 0.8443 (tmm) cc_final: 0.8119 (tmm) REVERT: Z 69 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8313 (mp) REVERT: Z 74 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8659 (tt) REVERT: Z 98 MET cc_start: 0.6444 (ttm) cc_final: 0.5930 (ttm) REVERT: Z 133 MET cc_start: 0.8648 (ttp) cc_final: 0.8385 (ttt) REVERT: a 1 MET cc_start: 0.7036 (mmt) cc_final: 0.6822 (mpp) REVERT: a 25 TYR cc_start: 0.8117 (m-80) cc_final: 0.7894 (m-80) REVERT: a 29 PHE cc_start: 0.7770 (m-80) cc_final: 0.7541 (m-10) REVERT: a 35 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7943 (mm-30) REVERT: b 10 LYS cc_start: 0.7481 (mtmt) cc_final: 0.7061 (tttt) REVERT: b 23 PHE cc_start: 0.8596 (m-80) cc_final: 0.8125 (m-80) REVERT: b 47 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8726 (ttpp) REVERT: b 58 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6753 (mtp180) REVERT: q 58 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7446 (mtp180) REVERT: r 92 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7972 (ttpt) REVERT: s 78 TYR cc_start: 0.6579 (m-80) cc_final: 0.6253 (m-80) outliers start: 135 outliers final: 72 residues processed: 912 average time/residue: 0.2206 time to fit residues: 324.6585 Evaluate side-chains 858 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 777 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 148 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 496 MET Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 102 GLN Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 144 SER Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 198 optimal weight: 7.9990 chunk 133 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 251 optimal weight: 0.0370 chunk 366 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 227 optimal weight: 0.9980 chunk 371 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 74 ASN G 663 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN P 238 GLN P 356 HIS Q 51 GLN V 50 GLN X 95 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112780 restraints weight = 54154.633| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.53 r_work: 0.3314 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 34791 Z= 0.128 Angle : 0.805 73.116 47163 Z= 0.312 Chirality : 0.043 0.198 5138 Planarity : 0.005 0.126 5966 Dihedral : 9.212 159.558 4939 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 3.67 % Allowed : 18.44 % Favored : 77.89 % 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: -0.08 (0.13), residues: 4124 helix: 1.09 (0.12), residues: 1864 sheet: -0.86 (0.27), residues: 356 loop : -1.02 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 184 TYR 0.024 0.001 TYR H 247 PHE 0.025 0.001 PHE P 263 TRP 0.020 0.001 TRP G 100 HIS 0.005 0.001 HIS b 69 Details of bonding type rmsd covalent geometry : bond 0.00290 (34750) covalent geometry : angle 0.61356 (47071) SS BOND : bond 0.00390 ( 4) SS BOND : angle 3.75264 ( 8) hydrogen bonds : bond 0.03933 ( 1414) hydrogen bonds : angle 4.73418 ( 4122) metal coordination : bond 0.01499 ( 37) metal coordination : angle 12.30991 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 819 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8096 (tmm) cc_final: 0.7685 (tmm) REVERT: B 219 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8646 (ttmm) REVERT: C 58 SER cc_start: 0.9100 (t) cc_final: 0.8722 (p) REVERT: C 78 SER cc_start: 0.9122 (t) cc_final: 0.8847 (p) REVERT: C 118 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8795 (p) REVERT: C 150 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8862 (p) REVERT: C 178 PHE cc_start: 0.8564 (m-80) cc_final: 0.8205 (m-10) REVERT: D 83 ASN cc_start: 0.8110 (p0) cc_final: 0.7765 (p0) REVERT: D 144 MET cc_start: 0.7788 (mpp) cc_final: 0.7267 (mpp) REVERT: E 91 TRP cc_start: 0.7709 (t60) cc_final: 0.7259 (t60) REVERT: E 142 ARG cc_start: 0.7554 (tpp80) cc_final: 0.6748 (mmt90) REVERT: E 168 PHE cc_start: 0.8274 (m-80) cc_final: 0.7990 (m-10) REVERT: F 51 TRP cc_start: 0.7615 (p-90) cc_final: 0.7119 (p-90) REVERT: F 140 GLU cc_start: 0.6963 (pt0) cc_final: 0.6747 (tt0) REVERT: F 193 PHE cc_start: 0.6821 (t80) cc_final: 0.6596 (t80) REVERT: F 209 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: F 226 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.6804 (ptmm) REVERT: F 450 MET cc_start: 0.8511 (mmt) cc_final: 0.7947 (mmt) REVERT: G 39 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7992 (tm-30) REVERT: G 58 MET cc_start: 0.7064 (mmp) cc_final: 0.6776 (mmt) REVERT: G 87 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8644 (ptmt) REVERT: G 97 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7774 (ptp) REVERT: G 181 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8137 (mtm180) REVERT: G 329 MET cc_start: 0.8148 (mmm) cc_final: 0.7447 (mmt) REVERT: H 1 MET cc_start: 0.7767 (mmt) cc_final: 0.7545 (tpp) REVERT: H 85 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8858 (mt) REVERT: H 108 THR cc_start: 0.9442 (m) cc_final: 0.9101 (p) REVERT: H 111 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9152 (tt) REVERT: H 134 ARG cc_start: 0.8342 (mtm180) cc_final: 0.7351 (mtp-110) REVERT: H 193 THR cc_start: 0.8442 (p) cc_final: 0.8150 (p) REVERT: H 250 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8016 (p0) REVERT: H 282 TYR cc_start: 0.8313 (t80) cc_final: 0.7803 (t80) REVERT: H 284 GLN cc_start: 0.8303 (mt0) cc_final: 0.8011 (mt0) REVERT: I 41 LYS cc_start: 0.8216 (tptp) cc_final: 0.7781 (tptp) REVERT: I 94 SER cc_start: 0.9152 (p) cc_final: 0.8636 (p) REVERT: P 91 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8938 (tp) REVERT: P 271 TYR cc_start: 0.8036 (m-80) cc_final: 0.7677 (m-80) REVERT: P 283 MET cc_start: 0.8244 (tpp) cc_final: 0.7947 (mmm) REVERT: P 324 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8104 (tt) REVERT: Q 78 ARG cc_start: 0.8132 (ptm-80) cc_final: 0.7887 (ptm-80) REVERT: Q 165 SER cc_start: 0.7868 (t) cc_final: 0.7623 (p) REVERT: R 33 HIS cc_start: 0.1344 (OUTLIER) cc_final: 0.0962 (t-90) REVERT: R 94 ASN cc_start: 0.8923 (t0) cc_final: 0.8693 (t0) REVERT: S 57 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7355 (mm-30) REVERT: S 69 TYR cc_start: 0.8313 (m-80) cc_final: 0.7907 (m-80) REVERT: S 75 LYS cc_start: 0.8346 (pttt) cc_final: 0.8002 (pttt) REVERT: S 80 ASN cc_start: 0.8188 (t0) cc_final: 0.7850 (t0) REVERT: T 80 LYS cc_start: 0.7985 (tmmt) cc_final: 0.7598 (tptp) REVERT: T 115 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7941 (tm-30) REVERT: W 45 GLU cc_start: 0.9032 (tp30) cc_final: 0.8541 (tp30) REVERT: W 123 SER cc_start: 0.8915 (m) cc_final: 0.8602 (p) REVERT: X 32 TYR cc_start: 0.9017 (t80) cc_final: 0.8365 (t80) REVERT: X 47 ARG cc_start: 0.7627 (tpt90) cc_final: 0.5949 (tpt90) REVERT: X 88 CYS cc_start: 0.6099 (OUTLIER) cc_final: 0.5866 (t) REVERT: X 91 TYR cc_start: 0.8648 (t80) cc_final: 0.8439 (t80) REVERT: Z 45 PHE cc_start: 0.8723 (t80) cc_final: 0.8433 (t80) REVERT: Z 50 MET cc_start: 0.8170 (tpp) cc_final: 0.7684 (mpp) REVERT: Z 69 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8186 (mp) REVERT: Z 80 ASP cc_start: 0.8558 (m-30) cc_final: 0.8234 (m-30) REVERT: Z 98 MET cc_start: 0.6420 (ttm) cc_final: 0.5917 (ttm) REVERT: a 25 TYR cc_start: 0.7878 (m-80) cc_final: 0.7658 (m-80) REVERT: a 29 PHE cc_start: 0.7515 (m-80) cc_final: 0.7232 (m-10) REVERT: a 38 VAL cc_start: 0.9153 (t) cc_final: 0.8913 (p) REVERT: a 50 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8304 (ttp80) REVERT: b 5 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6137 (pp) REVERT: b 10 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7296 (tttt) REVERT: b 23 PHE cc_start: 0.8491 (m-80) cc_final: 0.8032 (m-80) REVERT: b 47 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8694 (ttpp) REVERT: b 82 LYS cc_start: 0.8647 (tttp) cc_final: 0.8420 (mtmm) REVERT: q 58 ARG cc_start: 0.7815 (mtm180) cc_final: 0.7500 (mtp180) REVERT: r 92 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7805 (ttpt) REVERT: s 78 TYR cc_start: 0.6536 (m-80) cc_final: 0.6274 (m-80) outliers start: 133 outliers final: 71 residues processed: 881 average time/residue: 0.2166 time to fit residues: 307.0769 Evaluate side-chains 839 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 753 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 306 MET Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 250 ASN Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 220 TYR Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 5 ILE Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 121 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 358 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 348 optimal weight: 0.0040 chunk 133 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 396 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN B 172 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 74 ASN G 605 GLN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN W 54 GLN X 31 HIS ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** r 18 GLN ** 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 = 0.3945 r_free = 0.3945 target = 0.148625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111802 restraints weight = 53771.452| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.53 r_work: 0.3276 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34791 Z= 0.154 Angle : 0.819 74.765 47163 Z= 0.318 Chirality : 0.043 0.201 5138 Planarity : 0.005 0.128 5966 Dihedral : 9.160 161.149 4939 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 3.48 % Allowed : 18.80 % Favored : 77.72 % 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: -0.06 (0.13), residues: 4124 helix: 1.13 (0.12), residues: 1867 sheet: -0.92 (0.26), residues: 372 loop : -1.02 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 643 TYR 0.020 0.002 TYR H 247 PHE 0.016 0.001 PHE Z 138 TRP 0.023 0.001 TRP G 100 HIS 0.008 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00366 (34750) covalent geometry : angle 0.62735 (47071) SS BOND : bond 0.00412 ( 4) SS BOND : angle 3.81467 ( 8) hydrogen bonds : bond 0.03954 ( 1414) hydrogen bonds : angle 4.69139 ( 4122) metal coordination : bond 0.01880 ( 37) metal coordination : angle 12.45394 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 798 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8175 (tmm) cc_final: 0.7717 (tmm) REVERT: A 98 LEU cc_start: 0.8738 (mm) cc_final: 0.8478 (mm) REVERT: B 80 ASP cc_start: 0.8392 (m-30) cc_final: 0.8190 (m-30) REVERT: B 219 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8744 (ttmm) REVERT: C 58 SER cc_start: 0.9138 (t) cc_final: 0.8765 (p) REVERT: C 78 SER cc_start: 0.9191 (t) cc_final: 0.8882 (p) REVERT: C 150 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8925 (p) REVERT: C 216 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8796 (mmtm) REVERT: D 80 MET cc_start: 0.6769 (ttm) cc_final: 0.6436 (ttm) REVERT: D 83 ASN cc_start: 0.8151 (p0) cc_final: 0.7792 (p0) REVERT: E 91 TRP cc_start: 0.7822 (t60) cc_final: 0.7396 (t60) REVERT: E 142 ARG cc_start: 0.7445 (tpp80) cc_final: 0.6703 (mmt90) REVERT: E 168 PHE cc_start: 0.8033 (m-80) cc_final: 0.7769 (m-10) REVERT: E 184 MET cc_start: 0.6828 (tmm) cc_final: 0.6597 (tmm) REVERT: F 51 TRP cc_start: 0.7579 (p-90) cc_final: 0.7001 (p-90) REVERT: F 74 ASP cc_start: 0.8765 (m-30) cc_final: 0.8085 (p0) REVERT: F 140 GLU cc_start: 0.6992 (pt0) cc_final: 0.6791 (tt0) REVERT: F 149 MET cc_start: 0.7673 (mmm) cc_final: 0.6550 (mmm) REVERT: F 157 TYR cc_start: 0.7940 (t80) cc_final: 0.7731 (t80) REVERT: F 182 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6688 (pt) REVERT: F 209 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: F 226 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.6997 (ptpt) REVERT: F 450 MET cc_start: 0.8490 (mmt) cc_final: 0.7931 (mmt) REVERT: G 39 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8071 (tm-30) REVERT: G 54 GLU cc_start: 0.8882 (tt0) cc_final: 0.8284 (tm-30) REVERT: G 58 MET cc_start: 0.7135 (mmp) cc_final: 0.6875 (mmt) REVERT: G 87 LYS cc_start: 0.9029 (ptpt) cc_final: 0.8782 (ptmm) REVERT: G 97 MET cc_start: 0.8548 (ptp) cc_final: 0.8229 (ptp) REVERT: G 111 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8010 (mtmt) REVERT: G 181 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8398 (mtm180) REVERT: G 329 MET cc_start: 0.8244 (mmm) cc_final: 0.7511 (mmt) REVERT: G 514 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7505 (p0) REVERT: H 1 MET cc_start: 0.7842 (mmt) cc_final: 0.7415 (tpp) REVERT: H 85 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8828 (mt) REVERT: H 108 THR cc_start: 0.9484 (m) cc_final: 0.9122 (p) REVERT: H 111 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9179 (tt) REVERT: H 134 ARG cc_start: 0.8471 (mtm180) cc_final: 0.7546 (mtp-110) REVERT: H 193 THR cc_start: 0.8606 (p) cc_final: 0.8305 (p) REVERT: H 271 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9090 (mt) REVERT: H 282 TYR cc_start: 0.8454 (t80) cc_final: 0.7846 (t80) REVERT: H 284 GLN cc_start: 0.8469 (mt0) cc_final: 0.8207 (mt0) REVERT: I 41 LYS cc_start: 0.8191 (tptp) cc_final: 0.7796 (tptp) REVERT: I 94 SER cc_start: 0.9241 (p) cc_final: 0.8752 (p) REVERT: P 91 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9009 (tp) REVERT: P 219 ASN cc_start: 0.8267 (m-40) cc_final: 0.7977 (m-40) REVERT: P 269 ASN cc_start: 0.7849 (p0) cc_final: 0.7546 (p0) REVERT: P 271 TYR cc_start: 0.8108 (m-80) cc_final: 0.7720 (m-80) REVERT: P 283 MET cc_start: 0.8374 (tpp) cc_final: 0.8092 (mmm) REVERT: P 324 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (tt) REVERT: Q 78 ARG cc_start: 0.8398 (ptm-80) cc_final: 0.8151 (ptm-80) REVERT: R 33 HIS cc_start: 0.1761 (OUTLIER) cc_final: 0.1409 (t-90) REVERT: R 94 ASN cc_start: 0.8894 (t0) cc_final: 0.8642 (t0) REVERT: S 57 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7527 (mm-30) REVERT: S 69 TYR cc_start: 0.8454 (m-80) cc_final: 0.8045 (m-80) REVERT: S 83 SER cc_start: 0.8658 (t) cc_final: 0.8229 (p) REVERT: T 80 LYS cc_start: 0.8014 (tmmt) cc_final: 0.7474 (tptm) REVERT: T 84 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7677 (mm) REVERT: T 142 GLN cc_start: 0.8501 (mt0) cc_final: 0.8148 (mp10) REVERT: W 45 GLU cc_start: 0.9164 (tp30) cc_final: 0.8673 (tp30) REVERT: W 123 SER cc_start: 0.8926 (m) cc_final: 0.8595 (p) REVERT: X 32 TYR cc_start: 0.9056 (t80) cc_final: 0.8421 (t80) REVERT: X 47 ARG cc_start: 0.7661 (tpt90) cc_final: 0.6127 (tpt90) REVERT: X 88 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6424 (t) REVERT: Z 10 MET cc_start: 0.8687 (mmm) cc_final: 0.8479 (mmm) REVERT: Z 69 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8387 (mp) REVERT: Z 74 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (tt) REVERT: Z 98 MET cc_start: 0.6539 (ttm) cc_final: 0.5947 (ttm) REVERT: a 3 PHE cc_start: 0.7861 (m-80) cc_final: 0.7620 (m-80) REVERT: a 25 TYR cc_start: 0.8100 (m-80) cc_final: 0.7889 (m-80) REVERT: a 35 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7963 (mm-30) REVERT: a 38 VAL cc_start: 0.9179 (t) cc_final: 0.8868 (p) REVERT: b 10 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7323 (tttt) REVERT: b 47 LYS cc_start: 0.9009 (ttpt) cc_final: 0.8666 (ttpp) REVERT: b 58 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6322 (mmm-85) REVERT: q 58 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7669 (mtt180) REVERT: q 142 THR cc_start: 0.8585 (m) cc_final: 0.8374 (t) REVERT: s 78 TYR cc_start: 0.6527 (m-80) cc_final: 0.6242 (m-80) outliers start: 126 outliers final: 83 residues processed: 866 average time/residue: 0.2204 time to fit residues: 309.7382 Evaluate side-chains 863 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 764 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 220 TYR Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 84 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 88 CYS Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 141 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 393 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS E 47 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN V 50 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.147150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110933 restraints weight = 54175.404| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.43 r_work: 0.3276 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34791 Z= 0.145 Angle : 0.819 74.285 47163 Z= 0.319 Chirality : 0.044 0.336 5138 Planarity : 0.005 0.128 5966 Dihedral : 9.017 162.665 4939 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 3.56 % Allowed : 19.08 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4124 helix: 1.17 (0.12), residues: 1862 sheet: -1.02 (0.26), residues: 384 loop : -1.01 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 92 TYR 0.020 0.001 TYR R 43 PHE 0.025 0.001 PHE P 213 TRP 0.024 0.001 TRP G 100 HIS 0.007 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00343 (34750) covalent geometry : angle 0.63144 (47071) SS BOND : bond 0.00288 ( 4) SS BOND : angle 3.28587 ( 8) hydrogen bonds : bond 0.03850 ( 1414) hydrogen bonds : angle 4.66781 ( 4122) metal coordination : bond 0.01710 ( 37) metal coordination : angle 12.34097 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 793 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8145 (tmm) cc_final: 0.7669 (tmm) REVERT: A 98 LEU cc_start: 0.8701 (mm) cc_final: 0.8418 (mm) REVERT: B 80 ASP cc_start: 0.8391 (m-30) cc_final: 0.8183 (m-30) REVERT: B 219 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8749 (ttmm) REVERT: C 58 SER cc_start: 0.9120 (t) cc_final: 0.8748 (p) REVERT: C 78 SER cc_start: 0.9176 (t) cc_final: 0.8872 (p) REVERT: C 150 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8930 (p) REVERT: C 178 PHE cc_start: 0.8753 (m-80) cc_final: 0.8451 (m-10) REVERT: D 83 ASN cc_start: 0.8101 (p0) cc_final: 0.7705 (p0) REVERT: D 197 MET cc_start: 0.8305 (ptm) cc_final: 0.7936 (ptm) REVERT: E 91 TRP cc_start: 0.7812 (t60) cc_final: 0.7345 (t60) REVERT: E 142 ARG cc_start: 0.7494 (tpp80) cc_final: 0.6885 (mmt180) REVERT: E 158 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7400 (mmtp) REVERT: E 168 PHE cc_start: 0.8042 (m-80) cc_final: 0.7822 (m-10) REVERT: E 184 MET cc_start: 0.6697 (tmm) cc_final: 0.6457 (tmm) REVERT: F 51 TRP cc_start: 0.7548 (p-90) cc_final: 0.7041 (p-90) REVERT: F 74 ASP cc_start: 0.8740 (m-30) cc_final: 0.8090 (p0) REVERT: F 140 GLU cc_start: 0.7001 (pt0) cc_final: 0.6661 (tt0) REVERT: F 182 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6717 (pt) REVERT: F 204 TYR cc_start: 0.8595 (t80) cc_final: 0.7727 (t80) REVERT: F 209 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: F 226 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.6976 (ptpt) REVERT: F 450 MET cc_start: 0.8493 (mmt) cc_final: 0.7968 (mmt) REVERT: G 39 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8066 (tm-30) REVERT: G 54 GLU cc_start: 0.8897 (tt0) cc_final: 0.8304 (tm-30) REVERT: G 58 MET cc_start: 0.7175 (mmp) cc_final: 0.6928 (mmt) REVERT: G 87 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8776 (ptmm) REVERT: G 97 MET cc_start: 0.8400 (ptp) cc_final: 0.8111 (ptp) REVERT: G 111 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8029 (mtmt) REVERT: G 181 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8456 (mtm180) REVERT: G 329 MET cc_start: 0.8214 (mmm) cc_final: 0.7487 (mmt) REVERT: G 388 ASN cc_start: 0.8745 (p0) cc_final: 0.8469 (p0) REVERT: G 514 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7541 (p0) REVERT: H 85 LEU cc_start: 0.9086 (mt) cc_final: 0.8630 (mt) REVERT: H 108 THR cc_start: 0.9494 (m) cc_final: 0.9150 (p) REVERT: H 111 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9179 (tt) REVERT: H 134 ARG cc_start: 0.8450 (mtm180) cc_final: 0.7569 (mtp-110) REVERT: H 193 THR cc_start: 0.8678 (p) cc_final: 0.8353 (p) REVERT: H 260 MET cc_start: 0.9159 (tmm) cc_final: 0.8878 (tmm) REVERT: H 271 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9068 (mt) REVERT: H 282 TYR cc_start: 0.8418 (t80) cc_final: 0.7867 (t80) REVERT: H 284 GLN cc_start: 0.8444 (mt0) cc_final: 0.8195 (mt0) REVERT: I 41 LYS cc_start: 0.8223 (tptp) cc_final: 0.7851 (tptp) REVERT: I 94 SER cc_start: 0.9238 (p) cc_final: 0.8723 (p) REVERT: I 208 ASP cc_start: 0.8744 (t0) cc_final: 0.8189 (t70) REVERT: P 91 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8973 (tp) REVERT: P 269 ASN cc_start: 0.7882 (p0) cc_final: 0.7609 (p0) REVERT: P 271 TYR cc_start: 0.8135 (m-80) cc_final: 0.7782 (m-80) REVERT: P 283 MET cc_start: 0.8366 (tpp) cc_final: 0.8106 (mmm) REVERT: Q 78 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.8092 (ptm-80) REVERT: R 33 HIS cc_start: 0.1533 (OUTLIER) cc_final: 0.1122 (t-90) REVERT: R 94 ASN cc_start: 0.8850 (t0) cc_final: 0.8562 (t0) REVERT: S 57 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7588 (mm-30) REVERT: S 62 GLN cc_start: 0.9187 (mt0) cc_final: 0.8828 (mt0) REVERT: S 69 TYR cc_start: 0.8485 (m-80) cc_final: 0.7413 (m-80) REVERT: S 75 LYS cc_start: 0.8412 (pttt) cc_final: 0.7772 (mttt) REVERT: S 80 ASN cc_start: 0.8200 (t0) cc_final: 0.7833 (t0) REVERT: S 83 SER cc_start: 0.8558 (t) cc_final: 0.8270 (p) REVERT: T 80 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7742 (tmmt) REVERT: V 35 LEU cc_start: 0.9110 (mm) cc_final: 0.8901 (mt) REVERT: W 45 GLU cc_start: 0.9173 (tp30) cc_final: 0.8669 (tp30) REVERT: W 119 LYS cc_start: 0.7923 (mppt) cc_final: 0.7249 (mmmt) REVERT: W 123 SER cc_start: 0.8942 (m) cc_final: 0.8576 (p) REVERT: X 32 TYR cc_start: 0.9045 (t80) cc_final: 0.8426 (t80) REVERT: X 37 ASP cc_start: 0.6782 (p0) cc_final: 0.6400 (t0) REVERT: X 39 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9116 (p) REVERT: X 47 ARG cc_start: 0.7462 (tpt90) cc_final: 0.5954 (tpt90) REVERT: Z 69 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8349 (mp) REVERT: Z 74 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8718 (tt) REVERT: Z 80 ASP cc_start: 0.8698 (m-30) cc_final: 0.8328 (m-30) REVERT: Z 98 MET cc_start: 0.6536 (ttm) cc_final: 0.5944 (ttm) REVERT: a 38 VAL cc_start: 0.9130 (t) cc_final: 0.8913 (p) REVERT: a 55 SER cc_start: 0.7127 (OUTLIER) cc_final: 0.6892 (m) REVERT: b 10 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7280 (tttt) REVERT: b 47 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8647 (ttpp) REVERT: b 58 ARG cc_start: 0.6945 (mmm-85) cc_final: 0.6386 (mmm-85) REVERT: q 34 ARG cc_start: 0.7313 (ttp-110) cc_final: 0.6626 (mtm-85) REVERT: q 77 VAL cc_start: 0.6891 (t) cc_final: 0.6507 (p) REVERT: r 92 LYS cc_start: 0.8447 (ttmm) cc_final: 0.7986 (ttpt) REVERT: s 78 TYR cc_start: 0.6591 (m-80) cc_final: 0.6309 (m-80) outliers start: 129 outliers final: 89 residues processed: 857 average time/residue: 0.2178 time to fit residues: 303.8374 Evaluate side-chains 872 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 769 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 92 GLN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 107 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 291 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 363 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN E 68 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN G 74 ASN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 GLN V 50 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.146989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110699 restraints weight = 53970.107| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.47 r_work: 0.3285 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34791 Z= 0.143 Angle : 0.816 73.819 47163 Z= 0.319 Chirality : 0.043 0.287 5138 Planarity : 0.005 0.128 5966 Dihedral : 8.898 164.055 4939 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 3.45 % Allowed : 19.30 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4124 helix: 1.15 (0.12), residues: 1872 sheet: -1.08 (0.25), residues: 389 loop : -0.99 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 92 TYR 0.021 0.001 TYR R 43 PHE 0.041 0.001 PHE P 213 TRP 0.024 0.001 TRP G 100 HIS 0.008 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00337 (34750) covalent geometry : angle 0.63033 (47071) SS BOND : bond 0.00587 ( 4) SS BOND : angle 3.09804 ( 8) hydrogen bonds : bond 0.03789 ( 1414) hydrogen bonds : angle 4.65147 ( 4122) metal coordination : bond 0.01692 ( 37) metal coordination : angle 12.25913 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 788 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8147 (tmm) cc_final: 0.7674 (tmm) REVERT: B 80 ASP cc_start: 0.8370 (m-30) cc_final: 0.8161 (m-30) REVERT: B 219 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8719 (ttmm) REVERT: C 58 SER cc_start: 0.9120 (t) cc_final: 0.8725 (p) REVERT: C 74 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7619 (tm-30) REVERT: C 78 SER cc_start: 0.9178 (t) cc_final: 0.8859 (p) REVERT: C 150 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8926 (p) REVERT: C 178 PHE cc_start: 0.8730 (m-80) cc_final: 0.8406 (m-10) REVERT: D 83 ASN cc_start: 0.8043 (p0) cc_final: 0.7636 (p0) REVERT: D 197 MET cc_start: 0.8371 (ptm) cc_final: 0.8000 (ptm) REVERT: E 91 TRP cc_start: 0.7766 (t60) cc_final: 0.7315 (t60) REVERT: E 136 THR cc_start: 0.7729 (m) cc_final: 0.7356 (m) REVERT: E 142 ARG cc_start: 0.7552 (tpp80) cc_final: 0.6911 (mmt180) REVERT: E 158 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8113 (mmmt) REVERT: E 168 PHE cc_start: 0.8060 (m-80) cc_final: 0.7854 (m-10) REVERT: E 184 MET cc_start: 0.6694 (tmm) cc_final: 0.6452 (tmm) REVERT: F 51 TRP cc_start: 0.7593 (p-90) cc_final: 0.7011 (p-90) REVERT: F 74 ASP cc_start: 0.8717 (m-30) cc_final: 0.8095 (p0) REVERT: F 140 GLU cc_start: 0.7083 (pt0) cc_final: 0.6696 (tt0) REVERT: F 149 MET cc_start: 0.7645 (mmm) cc_final: 0.6411 (mmm) REVERT: F 159 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6613 (ttp-110) REVERT: F 182 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6577 (pt) REVERT: F 208 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: F 209 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: F 226 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.6932 (ptpt) REVERT: F 450 MET cc_start: 0.8442 (mmt) cc_final: 0.8097 (mmm) REVERT: G 39 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8038 (tm-30) REVERT: G 54 GLU cc_start: 0.8894 (tt0) cc_final: 0.8311 (tm-30) REVERT: G 58 MET cc_start: 0.7161 (mmp) cc_final: 0.6917 (mmp) REVERT: G 87 LYS cc_start: 0.9006 (ptpt) cc_final: 0.8788 (ptmm) REVERT: G 97 MET cc_start: 0.8364 (ptp) cc_final: 0.8137 (ptp) REVERT: G 111 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8041 (mtpt) REVERT: G 181 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8469 (mtm180) REVERT: G 304 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8626 (mt-10) REVERT: G 306 MET cc_start: 0.9031 (mtp) cc_final: 0.8728 (mtp) REVERT: G 329 MET cc_start: 0.8191 (mmm) cc_final: 0.7474 (mmt) REVERT: G 388 ASN cc_start: 0.8765 (p0) cc_final: 0.8455 (p0) REVERT: G 460 HIS cc_start: 0.6614 (t-90) cc_final: 0.6371 (t-90) REVERT: G 514 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7577 (p0) REVERT: G 530 TYR cc_start: 0.8796 (m-80) cc_final: 0.7996 (m-80) REVERT: H 59 GLU cc_start: 0.8730 (tt0) cc_final: 0.8396 (tt0) REVERT: H 85 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8610 (mt) REVERT: H 108 THR cc_start: 0.9494 (m) cc_final: 0.9123 (p) REVERT: H 111 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9181 (tt) REVERT: H 134 ARG cc_start: 0.8456 (mtm180) cc_final: 0.7612 (mtp-110) REVERT: H 193 THR cc_start: 0.8746 (p) cc_final: 0.8431 (p) REVERT: H 214 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7992 (mm-30) REVERT: H 260 MET cc_start: 0.9163 (tmm) cc_final: 0.8854 (tmm) REVERT: H 271 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9047 (mt) REVERT: H 282 TYR cc_start: 0.8406 (t80) cc_final: 0.7879 (t80) REVERT: H 284 GLN cc_start: 0.8440 (mt0) cc_final: 0.8194 (mt0) REVERT: I 41 LYS cc_start: 0.8220 (tptp) cc_final: 0.7810 (tptp) REVERT: I 94 SER cc_start: 0.9256 (p) cc_final: 0.8809 (p) REVERT: I 137 ASP cc_start: 0.8558 (t0) cc_final: 0.8346 (t0) REVERT: I 208 ASP cc_start: 0.8735 (t0) cc_final: 0.8137 (t0) REVERT: P 91 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8974 (tp) REVERT: P 269 ASN cc_start: 0.7893 (p0) cc_final: 0.7600 (p0) REVERT: P 271 TYR cc_start: 0.8127 (m-80) cc_final: 0.7753 (m-80) REVERT: P 283 MET cc_start: 0.8357 (tpp) cc_final: 0.8128 (mmm) REVERT: R 33 HIS cc_start: 0.1540 (OUTLIER) cc_final: 0.1136 (t-90) REVERT: R 94 ASN cc_start: 0.8813 (t0) cc_final: 0.8507 (t0) REVERT: S 43 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8800 (mp0) REVERT: S 57 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7574 (mm-30) REVERT: S 62 GLN cc_start: 0.9229 (mt0) cc_final: 0.8909 (mt0) REVERT: S 69 TYR cc_start: 0.8498 (m-80) cc_final: 0.8124 (m-80) REVERT: S 80 ASN cc_start: 0.8173 (t0) cc_final: 0.7886 (t0) REVERT: V 7 LYS cc_start: 0.8618 (mmtp) cc_final: 0.8366 (tppt) REVERT: V 35 LEU cc_start: 0.9119 (mm) cc_final: 0.8910 (mt) REVERT: V 62 GLU cc_start: 0.8193 (tp30) cc_final: 0.7697 (tp30) REVERT: W 45 GLU cc_start: 0.9142 (tp30) cc_final: 0.8637 (tp30) REVERT: W 119 LYS cc_start: 0.7929 (mppt) cc_final: 0.7265 (mmmt) REVERT: W 123 SER cc_start: 0.8963 (m) cc_final: 0.8583 (p) REVERT: X 32 TYR cc_start: 0.9006 (t80) cc_final: 0.8388 (t80) REVERT: X 37 ASP cc_start: 0.6696 (p0) cc_final: 0.6439 (t0) REVERT: X 39 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9182 (p) REVERT: Z 69 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8437 (mp) REVERT: Z 74 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8718 (tt) REVERT: Z 98 MET cc_start: 0.6555 (ttm) cc_final: 0.5952 (ttm) REVERT: a 38 VAL cc_start: 0.9130 (t) cc_final: 0.8911 (p) REVERT: a 40 ARG cc_start: 0.8646 (ttt-90) cc_final: 0.8266 (ttt90) REVERT: b 10 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7301 (tttt) REVERT: b 47 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8645 (ttpp) REVERT: b 58 ARG cc_start: 0.6950 (mmm-85) cc_final: 0.6389 (mmm-85) REVERT: q 77 VAL cc_start: 0.6770 (t) cc_final: 0.6369 (p) REVERT: r 92 LYS cc_start: 0.8459 (ttmm) cc_final: 0.7980 (ttpt) REVERT: s 78 TYR cc_start: 0.6549 (m-80) cc_final: 0.6231 (m-80) outliers start: 125 outliers final: 91 residues processed: 855 average time/residue: 0.2253 time to fit residues: 312.9294 Evaluate side-chains 877 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 771 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 220 TYR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 107 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 360 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 393 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN E 74 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 705 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN S 92 GLN V 50 GLN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 18 GLN ** 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 = 0.3933 r_free = 0.3933 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111231 restraints weight = 53850.954| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.69 r_work: 0.3278 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34791 Z= 0.138 Angle : 0.818 73.334 47163 Z= 0.320 Chirality : 0.043 0.241 5138 Planarity : 0.005 0.128 5966 Dihedral : 8.803 164.754 4939 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 3.20 % Allowed : 19.80 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4124 helix: 1.16 (0.12), residues: 1881 sheet: -1.11 (0.25), residues: 393 loop : -0.97 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG V 92 TYR 0.023 0.001 TYR F 163 PHE 0.034 0.001 PHE P 213 TRP 0.028 0.001 TRP G 100 HIS 0.007 0.001 HIS P 323 Details of bonding type rmsd covalent geometry : bond 0.00325 (34750) covalent geometry : angle 0.63594 (47071) SS BOND : bond 0.00551 ( 4) SS BOND : angle 3.33923 ( 8) hydrogen bonds : bond 0.03728 ( 1414) hydrogen bonds : angle 4.63055 ( 4122) metal coordination : bond 0.01598 ( 37) metal coordination : angle 12.18200 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 792 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8102 (tmm) cc_final: 0.7642 (tmm) REVERT: B 80 ASP cc_start: 0.8261 (m-30) cc_final: 0.8043 (m-30) REVERT: B 199 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8166 (mt-10) REVERT: B 219 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8636 (ttmm) REVERT: C 58 SER cc_start: 0.9085 (t) cc_final: 0.8699 (p) REVERT: C 74 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7449 (tm-30) REVERT: C 78 SER cc_start: 0.9109 (t) cc_final: 0.8802 (p) REVERT: C 150 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8856 (p) REVERT: C 178 PHE cc_start: 0.8653 (m-80) cc_final: 0.8343 (m-10) REVERT: D 83 ASN cc_start: 0.7997 (p0) cc_final: 0.7607 (p0) REVERT: D 197 MET cc_start: 0.8148 (ptm) cc_final: 0.7780 (ptm) REVERT: E 87 ARG cc_start: 0.7645 (mmt90) cc_final: 0.7425 (mmt90) REVERT: E 91 TRP cc_start: 0.7718 (t60) cc_final: 0.7277 (t60) REVERT: E 136 THR cc_start: 0.7576 (m) cc_final: 0.7213 (m) REVERT: E 142 ARG cc_start: 0.7557 (tpp80) cc_final: 0.6913 (mmt180) REVERT: E 158 LYS cc_start: 0.8394 (mmmt) cc_final: 0.7325 (mmtp) REVERT: E 184 MET cc_start: 0.6632 (tmm) cc_final: 0.6409 (tmm) REVERT: F 51 TRP cc_start: 0.7574 (p-90) cc_final: 0.6945 (p-90) REVERT: F 74 ASP cc_start: 0.8832 (m-30) cc_final: 0.8229 (p0) REVERT: F 140 GLU cc_start: 0.7110 (pt0) cc_final: 0.6728 (tt0) REVERT: F 159 ARG cc_start: 0.6725 (ttp80) cc_final: 0.6482 (ttp-110) REVERT: F 182 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6561 (pt) REVERT: F 208 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: F 209 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7351 (pt0) REVERT: F 226 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.6958 (ptpt) REVERT: F 450 MET cc_start: 0.8368 (mmt) cc_final: 0.8122 (mmm) REVERT: G 39 GLN cc_start: 0.8504 (tm-30) cc_final: 0.7962 (tm-30) REVERT: G 54 GLU cc_start: 0.8716 (tt0) cc_final: 0.8220 (tm-30) REVERT: G 58 MET cc_start: 0.7192 (mmp) cc_final: 0.6917 (mmp) REVERT: G 111 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7931 (mtpt) REVERT: G 181 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8334 (mtm180) REVERT: G 304 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8442 (mt-10) REVERT: G 329 MET cc_start: 0.8043 (mmm) cc_final: 0.7361 (mmt) REVERT: G 388 ASN cc_start: 0.8693 (p0) cc_final: 0.8395 (p0) REVERT: G 514 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7449 (p0) REVERT: G 530 TYR cc_start: 0.8673 (m-80) cc_final: 0.7995 (m-80) REVERT: H 59 GLU cc_start: 0.8512 (tt0) cc_final: 0.8148 (tt0) REVERT: H 85 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8549 (mt) REVERT: H 108 THR cc_start: 0.9450 (m) cc_final: 0.9053 (p) REVERT: H 111 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9176 (tt) REVERT: H 134 ARG cc_start: 0.8378 (mtm180) cc_final: 0.7528 (mtp-110) REVERT: H 193 THR cc_start: 0.8702 (p) cc_final: 0.8375 (p) REVERT: H 214 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7977 (mm-30) REVERT: H 260 MET cc_start: 0.9111 (tmm) cc_final: 0.8767 (tmm) REVERT: H 271 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9004 (mt) REVERT: H 282 TYR cc_start: 0.8250 (t80) cc_final: 0.7771 (t80) REVERT: H 284 GLN cc_start: 0.8305 (mt0) cc_final: 0.8047 (mt0) REVERT: I 41 LYS cc_start: 0.8275 (tptp) cc_final: 0.7802 (tptp) REVERT: I 94 SER cc_start: 0.9163 (p) cc_final: 0.8732 (p) REVERT: I 208 ASP cc_start: 0.8639 (t0) cc_final: 0.8035 (t0) REVERT: P 91 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8913 (tp) REVERT: P 211 ASP cc_start: 0.7901 (p0) cc_final: 0.7698 (p0) REVERT: P 269 ASN cc_start: 0.7895 (p0) cc_final: 0.7597 (p0) REVERT: P 271 TYR cc_start: 0.8102 (m-80) cc_final: 0.7774 (m-80) REVERT: R 33 HIS cc_start: 0.1527 (OUTLIER) cc_final: 0.1088 (t-90) REVERT: R 94 ASN cc_start: 0.8761 (t0) cc_final: 0.8484 (t0) REVERT: S 43 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8805 (mp0) REVERT: S 57 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7279 (mm-30) REVERT: S 62 GLN cc_start: 0.9132 (mt0) cc_final: 0.8824 (mt0) REVERT: S 69 TYR cc_start: 0.8433 (m-80) cc_final: 0.8064 (m-80) REVERT: S 80 ASN cc_start: 0.8015 (t0) cc_final: 0.7775 (t0) REVERT: T 97 LYS cc_start: 0.6958 (tttt) cc_final: 0.6386 (pttt) REVERT: V 7 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8329 (tppt) REVERT: V 62 GLU cc_start: 0.8089 (tp30) cc_final: 0.7626 (tp30) REVERT: W 45 GLU cc_start: 0.9052 (tp30) cc_final: 0.8543 (tp30) REVERT: W 119 LYS cc_start: 0.7903 (mppt) cc_final: 0.7264 (mmmt) REVERT: W 123 SER cc_start: 0.8953 (m) cc_final: 0.8582 (p) REVERT: X 32 TYR cc_start: 0.8938 (t80) cc_final: 0.8297 (t80) REVERT: X 37 ASP cc_start: 0.6591 (p0) cc_final: 0.6390 (t0) REVERT: Z 69 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8362 (mp) REVERT: Z 74 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8661 (tt) REVERT: Z 98 MET cc_start: 0.6452 (ttm) cc_final: 0.5879 (ttm) REVERT: a 38 VAL cc_start: 0.9086 (t) cc_final: 0.8864 (p) REVERT: b 10 LYS cc_start: 0.7625 (mtmt) cc_final: 0.7309 (tttt) REVERT: b 47 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8649 (ttpp) REVERT: b 58 ARG cc_start: 0.7046 (mmm-85) cc_final: 0.6416 (mmm-85) REVERT: q 34 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.6079 (mtm-85) REVERT: q 77 VAL cc_start: 0.7091 (t) cc_final: 0.6696 (p) REVERT: q 132 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7662 (ttpt) REVERT: r 92 LYS cc_start: 0.8297 (ttmm) cc_final: 0.7864 (ttpt) outliers start: 116 outliers final: 87 residues processed: 849 average time/residue: 0.2197 time to fit residues: 302.8970 Evaluate side-chains 866 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 765 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 286 CYS Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 53 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 344 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 HIS ** 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 46 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN G 74 ASN G 140 GLN ** G 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 HIS q 87 HIS q 91 HIS ** r 18 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111062 restraints weight = 54381.479| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.58 r_work: 0.3255 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34791 Z= 0.167 Angle : 0.842 74.548 47163 Z= 0.332 Chirality : 0.044 0.313 5138 Planarity : 0.005 0.128 5966 Dihedral : 8.778 166.955 4939 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 2.98 % Allowed : 20.29 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4124 helix: 1.12 (0.12), residues: 1878 sheet: -1.05 (0.25), residues: 400 loop : -1.01 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 184 TYR 0.021 0.002 TYR R 43 PHE 0.019 0.001 PHE P 263 TRP 0.025 0.001 TRP G 100 HIS 0.007 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00401 (34750) covalent geometry : angle 0.65892 (47071) SS BOND : bond 0.00835 ( 4) SS BOND : angle 3.34278 ( 8) hydrogen bonds : bond 0.03878 ( 1414) hydrogen bonds : angle 4.65207 ( 4122) metal coordination : bond 0.02046 ( 37) metal coordination : angle 12.41060 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8248 Ramachandran restraints generated. 4124 Oldfield, 0 Emsley, 4124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 769 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8205 (tmm) cc_final: 0.7922 (tmm) REVERT: B 80 ASP cc_start: 0.8399 (m-30) cc_final: 0.8172 (m-30) REVERT: B 104 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8884 (tmm) REVERT: B 219 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8699 (ttmm) REVERT: C 58 SER cc_start: 0.9119 (t) cc_final: 0.8711 (p) REVERT: C 74 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 78 SER cc_start: 0.9194 (t) cc_final: 0.8863 (p) REVERT: C 150 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 178 PHE cc_start: 0.8706 (m-80) cc_final: 0.8396 (m-10) REVERT: D 83 ASN cc_start: 0.8055 (p0) cc_final: 0.7658 (p0) REVERT: D 351 MET cc_start: 0.8837 (tpp) cc_final: 0.8460 (tpp) REVERT: E 74 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7362 (mm-40) REVERT: E 91 TRP cc_start: 0.7771 (t60) cc_final: 0.7325 (t60) REVERT: E 136 THR cc_start: 0.7621 (m) cc_final: 0.7271 (m) REVERT: E 142 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7002 (mmt180) REVERT: E 158 LYS cc_start: 0.8402 (mmmt) cc_final: 0.7296 (mmtp) REVERT: F 51 TRP cc_start: 0.7538 (p-90) cc_final: 0.6840 (p-90) REVERT: F 74 ASP cc_start: 0.8826 (m-30) cc_final: 0.8249 (p0) REVERT: F 140 GLU cc_start: 0.7091 (pt0) cc_final: 0.6886 (tt0) REVERT: F 159 ARG cc_start: 0.6745 (ttp80) cc_final: 0.6532 (ttp-110) REVERT: F 182 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6565 (pt) REVERT: F 208 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: F 209 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: F 226 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.6990 (ptpt) REVERT: F 233 VAL cc_start: 0.8527 (t) cc_final: 0.8274 (p) REVERT: F 450 MET cc_start: 0.8386 (mmt) cc_final: 0.8130 (mmm) REVERT: G 54 GLU cc_start: 0.8908 (tt0) cc_final: 0.8211 (tm-30) REVERT: G 58 MET cc_start: 0.7228 (mmp) cc_final: 0.6959 (mmp) REVERT: G 97 MET cc_start: 0.7983 (ptp) cc_final: 0.7603 (ptm) REVERT: G 111 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8066 (mtpt) REVERT: G 181 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8517 (mtm180) REVERT: G 329 MET cc_start: 0.8209 (mmm) cc_final: 0.7512 (mmt) REVERT: G 388 ASN cc_start: 0.8770 (p0) cc_final: 0.8398 (p0) REVERT: G 514 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.7700 (p0) REVERT: H 3 PHE cc_start: 0.7607 (t80) cc_final: 0.7394 (t80) REVERT: H 59 GLU cc_start: 0.8705 (tt0) cc_final: 0.8355 (tt0) REVERT: H 85 LEU cc_start: 0.9104 (mt) cc_final: 0.8643 (mt) REVERT: H 108 THR cc_start: 0.9487 (m) cc_final: 0.9089 (p) REVERT: H 111 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9211 (tt) REVERT: H 134 ARG cc_start: 0.8489 (mtm180) cc_final: 0.7666 (mtp-110) REVERT: H 193 THR cc_start: 0.8926 (p) cc_final: 0.8603 (p) REVERT: H 214 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8027 (mm-30) REVERT: H 260 MET cc_start: 0.9176 (tmm) cc_final: 0.8855 (tmm) REVERT: H 271 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9032 (mt) REVERT: H 282 TYR cc_start: 0.8383 (t80) cc_final: 0.7855 (t80) REVERT: H 284 GLN cc_start: 0.8425 (mt0) cc_final: 0.8204 (mt0) REVERT: I 41 LYS cc_start: 0.8315 (tptp) cc_final: 0.7835 (tptp) REVERT: I 94 SER cc_start: 0.9261 (p) cc_final: 0.8861 (p) REVERT: I 208 ASP cc_start: 0.8759 (t0) cc_final: 0.8130 (t0) REVERT: P 71 ASN cc_start: 0.9083 (t0) cc_final: 0.8805 (t0) REVERT: P 91 ILE cc_start: 0.9247 (tp) cc_final: 0.9004 (tp) REVERT: P 269 ASN cc_start: 0.7977 (p0) cc_final: 0.7642 (p0) REVERT: P 271 TYR cc_start: 0.8198 (m-80) cc_final: 0.7889 (m-80) REVERT: P 283 MET cc_start: 0.8161 (mmm) cc_final: 0.7791 (mmm) REVERT: R 33 HIS cc_start: 0.1577 (OUTLIER) cc_final: 0.1150 (t-90) REVERT: S 43 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8797 (mp0) REVERT: S 57 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7649 (mm-30) REVERT: S 62 GLN cc_start: 0.9220 (mt0) cc_final: 0.8909 (mt0) REVERT: S 75 LYS cc_start: 0.8418 (pttt) cc_final: 0.7783 (mttt) REVERT: S 80 ASN cc_start: 0.8189 (t0) cc_final: 0.7922 (t0) REVERT: T 97 LYS cc_start: 0.7065 (tttt) cc_final: 0.6253 (pttt) REVERT: V 7 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8404 (tppt) REVERT: V 62 GLU cc_start: 0.8284 (tp30) cc_final: 0.7782 (tp30) REVERT: W 45 GLU cc_start: 0.9140 (tp30) cc_final: 0.8650 (tp30) REVERT: W 119 LYS cc_start: 0.7956 (mppt) cc_final: 0.7288 (mmmt) REVERT: W 123 SER cc_start: 0.8967 (m) cc_final: 0.8584 (p) REVERT: X 32 TYR cc_start: 0.9023 (t80) cc_final: 0.8464 (t80) REVERT: X 37 ASP cc_start: 0.6826 (p0) cc_final: 0.6538 (t0) REVERT: X 109 GLN cc_start: 0.8090 (tp40) cc_final: 0.7855 (tp-100) REVERT: Z 45 PHE cc_start: 0.8604 (t80) cc_final: 0.8374 (t80) REVERT: Z 69 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8518 (mp) REVERT: Z 74 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8765 (tt) REVERT: Z 98 MET cc_start: 0.6462 (ttm) cc_final: 0.5851 (ttm) REVERT: a 35 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7995 (mm-30) REVERT: a 38 VAL cc_start: 0.9109 (t) cc_final: 0.8891 (p) REVERT: b 10 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7297 (tttt) REVERT: b 47 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8650 (ttpp) REVERT: b 58 ARG cc_start: 0.7060 (mmm-85) cc_final: 0.6362 (mmm-85) REVERT: q 77 VAL cc_start: 0.6980 (t) cc_final: 0.6591 (p) REVERT: r 92 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8032 (ttpt) outliers start: 108 outliers final: 87 residues processed: 826 average time/residue: 0.2211 time to fit residues: 298.4335 Evaluate side-chains 844 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 744 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 226 LYS Chi-restraints excluded: chain F residue 270 ASN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 181 ARG Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 427 LEU Chi-restraints excluded: chain G residue 466 LEU Chi-restraints excluded: chain G residue 473 MET Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 514 ASN Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 611 THR Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 689 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 256 SER Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 54 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 62 THR Chi-restraints excluded: chain P residue 86 CYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 89 LEU Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 46 CYS Chi-restraints excluded: chain X residue 66 CYS Chi-restraints excluded: chain X residue 68 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 69 ILE Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 110 VAL Chi-restraints excluded: chain a residue 41 VAL Chi-restraints excluded: chain a residue 48 MET Chi-restraints excluded: chain a residue 66 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 83 ASN Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 129 THR Chi-restraints excluded: chain q residue 142 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5612 > 50: distance: 44 - 50: 29.901 distance: 50 - 51: 41.669 distance: 51 - 52: 21.300 distance: 51 - 54: 33.763 distance: 52 - 53: 11.885 distance: 52 - 59: 40.017 distance: 54 - 55: 41.200 distance: 55 - 56: 17.869 distance: 56 - 57: 24.297 distance: 57 - 58: 46.530 distance: 59 - 60: 13.290 distance: 60 - 61: 42.646 distance: 60 - 63: 55.862 distance: 61 - 66: 24.792 distance: 63 - 64: 10.249 distance: 63 - 65: 29.663 distance: 66 - 67: 16.868 distance: 67 - 68: 3.600 distance: 67 - 70: 30.101 distance: 68 - 69: 22.611 distance: 68 - 74: 43.046 distance: 70 - 71: 25.935 distance: 71 - 72: 16.351 distance: 71 - 73: 24.129 distance: 74 - 75: 11.007 distance: 75 - 76: 29.598 distance: 75 - 78: 40.960 distance: 76 - 82: 69.229 distance: 78 - 79: 21.289 distance: 79 - 80: 56.047 distance: 79 - 81: 41.167 distance: 82 - 83: 7.661 distance: 83 - 84: 42.710 distance: 83 - 86: 33.285 distance: 84 - 85: 9.029 distance: 84 - 87: 23.542 distance: 87 - 88: 19.443 distance: 88 - 89: 31.633 distance: 88 - 91: 19.879 distance: 89 - 90: 42.047 distance: 89 - 96: 46.217 distance: 91 - 92: 8.751 distance: 92 - 93: 42.129 distance: 93 - 94: 16.783 distance: 94 - 95: 49.335 distance: 96 - 97: 11.757 distance: 97 - 98: 15.191 distance: 97 - 100: 19.851 distance: 98 - 99: 31.124 distance: 98 - 103: 36.489 distance: 100 - 101: 12.521 distance: 100 - 102: 14.098 distance: 104 - 107: 41.086 distance: 105 - 106: 39.326 distance: 105 - 109: 46.158 distance: 107 - 108: 37.825 distance: 109 - 110: 40.520 distance: 109 - 115: 51.415 distance: 110 - 111: 17.219 distance: 110 - 113: 45.278 distance: 114 - 115: 13.246 distance: 116 - 117: 10.913 distance: 116 - 122: 39.622 distance: 117 - 118: 30.887 distance: 117 - 120: 29.987 distance: 118 - 119: 37.825 distance: 118 - 123: 18.327