Starting phenix.real_space_refine on Wed May 6 00:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnm_38507/05_2026/8xnm_38507.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 12 5.49 5 S 248 5.16 5 C 22177 2.51 5 N 5897 2.21 5 O 6299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.04s 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: 34662 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1258 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3088 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 21, 'TRANS': 363} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2532 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 293} Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "P" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2720 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 19, 'TRANS': 319} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 660 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1192 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "r" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 11, 'TRANS': 83} Chain breaks: 1 Chain: "s" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 189 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'UQ9': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UQ9:plan-2': 1, 'UQ9:plan-3': 1, 'UQ9:plan-4': 1, 'UQ9:plan-7': 1, 'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "q" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 62 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1178 SG CYS B 99 79.416 61.558 106.521 1.00 29.52 S ATOM 1911 SG CYS B 194 82.508 58.651 110.103 1.00 29.28 S ATOM 1184 SG CYS B 100 78.115 57.518 104.993 1.00 30.11 S ATOM 1681 SG CYS B 164 76.892 57.909 111.021 1.00 28.96 S ATOM 7691 SG CYS E 134 138.573 53.970 153.835 1.00 56.01 S ATOM 7725 SG CYS E 139 141.503 55.692 153.049 1.00 56.50 S ATOM 8009 SG CYS E 175 136.250 57.416 156.419 1.00 54.42 S ATOM 8032 SG CYS E 179 139.031 59.202 157.368 1.00 57.95 S ATOM 11562 SG CYS F 425 119.527 62.468 156.382 1.00 45.60 S ATOM 11240 SG CYS F 385 119.789 60.248 150.492 1.00 39.95 S ATOM 11220 SG CYS F 382 115.431 61.121 152.716 1.00 40.29 S ATOM 11201 SG CYS F 379 117.520 57.027 155.445 1.00 43.09 S ATOM 12610 SG CYS G 131 100.199 49.769 138.492 1.00 31.31 S ATOM 12589 SG CYS G 128 102.125 53.860 134.078 1.00 30.26 S ATOM 12650 SG CYS G 137 99.562 55.597 140.113 1.00 33.13 S ATOM 13335 SG CYS G 226 101.546 49.536 147.107 1.00 34.31 S ATOM 13006 SG CYS G 182 104.643 47.801 152.869 1.00 36.31 S ATOM 12982 SG CYS G 179 103.817 53.435 150.511 1.00 35.62 S ATOM 12959 SG CYS G 176 107.508 49.421 147.973 1.00 34.05 S ATOM 12096 SG CYS G 64 104.899 59.456 152.769 1.00 35.53 S ATOM 12182 SG CYS G 75 105.565 61.588 151.193 1.00 36.47 S ATOM 12207 SG CYS G 78 104.423 65.692 153.249 1.00 36.76 S ATOM 12308 SG CYS G 92 103.630 63.514 156.368 1.00 39.04 S ATOM 20363 SG CYS I 123 86.141 53.019 119.507 1.00 27.30 S ATOM 20589 SG CYS I 152 86.024 52.026 114.354 1.00 27.39 S ATOM 20636 SG CYS I 158 91.638 52.325 116.565 1.00 26.60 S ATOM 20615 SG CYS I 155 88.371 56.632 116.344 1.00 27.04 S ATOM 20312 SG CYS I 116 96.010 49.086 126.921 1.00 29.24 S ATOM 20335 SG CYS I 119 91.714 48.713 123.478 1.00 28.85 S ATOM 20293 SG CYS I 113 95.114 44.028 123.458 1.00 28.61 S ATOM 20665 SG CYS I 162 97.863 48.810 121.570 1.00 28.07 S ATOM 25164 SG CYS R 79 111.493 42.657 125.756 1.00 32.60 S ATOM 25340 SG CYS R 104 108.704 42.914 128.275 1.00 32.49 S ATOM 25362 SG CYS R 107 108.632 41.842 124.061 1.00 30.78 S Time building chain proxies: 8.44, per 1000 atoms: 0.24 Number of scatterers: 34662 At special positions: 0 Unit cell: (166.1, 129.8, 204.6, 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 248 16.00 P 12 15.00 O 6299 8.00 N 5897 7.00 C 22177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 78 " - pdb=" SG CYS X 110 " distance=2.02 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 194 " pdb=" SF4 F 502 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 302 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 302 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 303 " pdb="FE3 SF4 I 303 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 303 " - pdb=" SG CYS I 162 " pdb="FE2 SF4 I 303 " - pdb=" SG CYS I 119 " pdb="FE1 SF4 I 303 " - pdb=" SG CYS I 116 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " Number of angles added : 3 8464 Ramachandran restraints generated. 4232 Oldfield, 0 Emsley, 4232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8010 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 31 sheets defined 48.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 55 through 73 removed outlier: 3.970A pdb=" N ALA A 59 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.312A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 removed outlier: 3.639A pdb=" N ASP B 79 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.015A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.710A pdb=" N LYS B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 4.013A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 58 " --> pdb=" O HIS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.320A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.116A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 129 through 138 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.514A pdb=" N ALA D 150 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 219 removed outlier: 4.013A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 4.178A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.922A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 434 Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.709A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.620A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.951A pdb=" N TYR E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.680A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 4.162A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 101 Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.553A 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: 3.923A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.503A 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 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.602A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.533A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.644A 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: 3.778A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.563A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 removed outlier: 3.831A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 333' Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.548A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.661A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.774A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.350A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.518A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.598A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.725A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.715A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.819A pdb=" N ASP G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 318 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.670A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.026A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.638A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 629 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.642A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.302A 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 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.509A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.140A 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: 3.739A 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: 4.551A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 156 removed outlier: 4.361A pdb=" N ARG H 134 " --> pdb=" O PHE H 130 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET H 146 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.736A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 216 through 242 removed outlier: 4.162A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 277 Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.528A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.866A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.144A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.805A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 90 Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.670A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 91 through 96' Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.106A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.626A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.753A 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: 4.081A 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 306 removed outlier: 3.882A 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: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 358 through 363 removed outlier: 4.676A pdb=" N SER P 363 " --> pdb=" O TYR P 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.413A 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 165 Processing helix chain 'R' and resid 44 through 49 removed outlier: 3.727A pdb=" N PHE R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 67 removed outlier: 4.039A pdb=" N ALA R 65 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 5.952A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 Processing helix chain 'T' and resid 111 through 126 Processing helix chain 'T' and resid 131 through 138 removed outlier: 3.678A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.678A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.587A pdb=" N ARG W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Proline residue: W 47 - end of helix Processing helix chain 'W' and resid 58 through 73 removed outlier: 3.617A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 98 Processing helix chain 'W' and resid 102 through 108 Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.510A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.427A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA X 34 " --> pdb=" O HIS X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 52 through 77 removed outlier: 3.575A pdb=" N CYS X 56 " --> pdb=" O ASP X 52 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS X 58 " --> pdb=" O ARG X 54 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU X 59 " --> pdb=" O ARG X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 111 Processing helix chain 'X' and resid 140 through 144 removed outlier: 3.993A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 99 removed outlier: 3.534A pdb=" N GLY Z 39 " --> pdb=" O MET Z 35 " (cutoff:3.500A) Proline residue: Z 73 - end of helix Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 1 through 3 No H-bonds generated for 'chain 'a' and resid 1 through 3' Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.633A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.760A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 17 removed outlier: 3.556A pdb=" N HIS q 17 " --> pdb=" O GLN q 13 " (cutoff:3.500A) Processing helix chain 'q' and resid 19 through 31 Processing helix chain 'q' and resid 55 through 58 Processing helix chain 'q' and resid 78 through 82 Processing helix chain 'q' and resid 83 through 91 removed outlier: 4.126A pdb=" N ARG q 88 " --> pdb=" O PRO q 84 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP q 89 " --> pdb=" O GLU q 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 'r' and resid 53 through 57 Processing helix chain 'r' and resid 58 through 63 removed outlier: 3.954A pdb=" N GLU r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL r 63 " --> pdb=" O GLY r 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 58 through 63' Processing helix chain 's' and resid 43 through 54 removed outlier: 4.201A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 130 through 134 removed outlier: 6.007A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.516A 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 86 through 87 removed outlier: 3.506A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 109 through 117 removed outlier: 5.889A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.147A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.563A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 97 through 102 removed outlier: 6.927A pdb=" N VAL D 98 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N CYS D 109 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU D 100 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS D 442 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 394 through 401 Processing sheet with id=AA8, first strand: chain 'E' and resid 171 through 173 removed outlier: 5.588A pdb=" N MET E 184 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 194 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 286 through 291 removed outlier: 3.514A pdb=" N GLU F 290 " --> pdb=" O LYS F 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB3, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AB4, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.312A pdb=" N ARG G 266 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB7, 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: 6.823A pdb=" N ALA G 339 " --> pdb=" O PHE G 546 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.203A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC1, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC2, 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: 5.421A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.360A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC5, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.119A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC7, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC8, first strand: chain 'R' and resid 70 through 71 removed outlier: 5.820A pdb=" N ASN R 70 " --> pdb=" O LYS R 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 76 through 79 removed outlier: 3.588A pdb=" N VAL R 91 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 53 through 58 removed outlier: 3.576A pdb=" N LYS S 64 " --> pdb=" O HIS S 22 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 130 through 131 Processing sheet with id=AD3, first strand: chain 'q' and resid 37 through 41 removed outlier: 6.595A pdb=" N TYR q 48 " --> pdb=" O VAL q 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'q' and resid 67 through 68 1449 hydrogen bonds defined for protein. 4155 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: 7.08 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.46: 16892 1.46 - 1.76: 18166 1.76 - 2.06: 362 2.06 - 2.36: 80 2.36 - 2.66: 1 Bond restraints: 35501 Sorted by residual: bond pdb=" C VAL H 208 " pdb=" N GLY H 210 " ideal model delta sigma weight residual 1.329 2.662 -1.333 1.40e-02 5.10e+03 9.06e+03 bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.648 0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb=" CB7 CDL q 201 " pdb=" OB8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.12e+02 bond pdb=" CA7 CDL q 201 " pdb=" OA8 CDL q 201 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.10e-02 8.26e+03 1.11e+02 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.400 -0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 35496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 47460 6.89 - 13.79: 509 13.79 - 20.68: 145 20.68 - 27.57: 2 27.57 - 34.47: 4 Bond angle restraints: 48120 Sorted by residual: angle pdb=" O VAL H 208 " pdb=" C VAL H 208 " pdb=" N GLY H 210 " ideal model delta sigma weight residual 122.57 88.10 34.47 1.25e+00 6.40e-01 7.60e+02 angle pdb=" CA VAL H 208 " pdb=" C VAL H 208 " pdb=" N GLY H 210 " ideal model delta sigma weight residual 116.60 149.81 -33.21 1.45e+00 4.76e-01 5.24e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.39 89.01 25.38 1.45e+00 4.76e-01 3.06e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.59 16.74 1.14e+00 7.69e-01 2.16e+02 angle pdb=" S1 FES E 301 " pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 87.46 16.87 1.20e+00 6.94e-01 1.98e+02 ... (remaining 48115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 20796 28.38 - 56.76: 588 56.76 - 85.13: 63 85.13 - 113.51: 5 113.51 - 141.89: 3 Dihedral angle restraints: 21455 sinusoidal: 9028 harmonic: 12427 Sorted by residual: dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.56 -68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" C TYR D 214 " pdb=" N TYR D 214 " pdb=" CA TYR D 214 " pdb=" CB TYR D 214 " ideal model delta harmonic sigma weight residual -122.60 -104.96 -17.64 0 2.50e+00 1.60e-01 4.98e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.67 -16.93 0 2.50e+00 1.60e-01 4.58e+01 ... (remaining 21452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4725 0.183 - 0.365: 461 0.365 - 0.548: 40 0.548 - 0.730: 4 0.730 - 0.913: 24 Chirality restraints: 5254 Sorted by residual: chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 -9.64 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb="FE4 SF4 G 802 " pdb=" S1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb="FE3 SF4 I 303 " pdb=" S1 SF4 I 303 " pdb=" S2 SF4 I 303 " pdb=" S4 SF4 I 303 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 5251 not shown) Planarity restraints: 6117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 D 501 " 0.006 2.00e-02 2.50e+03 2.60e-01 2.03e+03 pdb=" C1M UQ9 D 501 " -0.004 2.00e-02 2.50e+03 pdb=" C2 UQ9 D 501 " -0.075 2.00e-02 2.50e+03 pdb=" C3 UQ9 D 501 " 0.050 2.00e-02 2.50e+03 pdb=" C4 UQ9 D 501 " 0.062 2.00e-02 2.50e+03 pdb=" C5 UQ9 D 501 " -0.182 2.00e-02 2.50e+03 pdb=" C6 UQ9 D 501 " 0.085 2.00e-02 2.50e+03 pdb=" C7 UQ9 D 501 " 0.452 2.00e-02 2.50e+03 pdb=" O2 UQ9 D 501 " -0.257 2.00e-02 2.50e+03 pdb=" O3 UQ9 D 501 " 0.150 2.00e-02 2.50e+03 pdb=" O4 UQ9 D 501 " 0.318 2.00e-02 2.50e+03 pdb=" O5 UQ9 D 501 " -0.606 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ9 D 501 " -0.245 2.00e-02 2.50e+03 2.05e-01 5.27e+02 pdb=" C13 UQ9 D 501 " 0.341 2.00e-02 2.50e+03 pdb=" C14 UQ9 D 501 " 0.074 2.00e-02 2.50e+03 pdb=" C15 UQ9 D 501 " -0.171 2.00e-02 2.50e+03 pdb=" C16 UQ9 D 501 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ9 D 501 " 0.015 2.00e-02 2.50e+03 1.03e-01 1.32e+02 pdb=" C11 UQ9 D 501 " -0.094 2.00e-02 2.50e+03 pdb=" C7 UQ9 D 501 " -0.123 2.00e-02 2.50e+03 pdb=" C8 UQ9 D 501 " 0.166 2.00e-02 2.50e+03 pdb=" C9 UQ9 D 501 " 0.036 2.00e-02 2.50e+03 ... (remaining 6114 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 79 2.38 - 3.01: 23873 3.01 - 3.64: 54767 3.64 - 4.27: 87295 4.27 - 4.90: 140601 Nonbonded interactions: 306615 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.756 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.983 3.040 nonbonded pdb=" O PHE G 63 " pdb=" SG CYS G 64 " model vdw 2.009 3.400 nonbonded pdb=" N THR G 174 " pdb=" N ARG G 175 " model vdw 2.079 2.560 ... (remaining 306610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.020 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 1.333 35541 Z= 1.128 Angle : 2.190 48.492 48210 Z= 1.450 Chirality : 0.124 0.913 5254 Planarity : 0.008 0.260 6117 Dihedral : 12.864 141.891 13436 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 43.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 0.38 % Allowed : 7.49 % Favored : 92.14 % Cbeta Deviations : 1.30 % 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: -2.03 (0.12), residues: 4232 helix: -0.64 (0.12), residues: 1792 sheet: -1.10 (0.28), residues: 337 loop : -2.03 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.033 0.002 TYR D 214 PHE 0.030 0.002 PHE D 200 TRP 0.031 0.002 TRP V 114 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.01585 (35501) covalent geometry : angle 2.06496 (48120) SS BOND : bond 0.00956 ( 3) SS BOND : angle 2.44399 ( 6) hydrogen bonds : bond 0.23649 ( 1449) hydrogen bonds : angle 9.06826 ( 4155) metal coordination : bond 0.50037 ( 37) metal coordination : angle 17.59947 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8464 Ramachandran restraints generated. 4232 Oldfield, 0 Emsley, 4232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8464 Ramachandran restraints generated. 4232 Oldfield, 0 Emsley, 4232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1677 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7157 (mtmt) REVERT: C 219 VAL cc_start: 0.8539 (m) cc_final: 0.8321 (m) REVERT: D 144 MET cc_start: 0.8030 (mpp) cc_final: 0.7806 (mpp) REVERT: D 160 ASN cc_start: 0.8157 (t0) cc_final: 0.7776 (t0) REVERT: D 453 THR cc_start: 0.7874 (p) cc_final: 0.7638 (p) REVERT: E 141 LEU cc_start: 0.8599 (mt) cc_final: 0.8274 (mt) REVERT: E 184 MET cc_start: 0.7622 (tmm) cc_final: 0.7159 (tmm) REVERT: H 93 HIS cc_start: 0.7188 (m-70) cc_final: 0.6891 (m170) REVERT: H 291 LYS cc_start: 0.7307 (tppt) cc_final: 0.6199 (mttp) REVERT: I 63 TRP cc_start: 0.7488 (m-10) cc_final: 0.7267 (m100) REVERT: I 64 THR cc_start: 0.7784 (p) cc_final: 0.7402 (t) REVERT: I 66 LEU cc_start: 0.9164 (mt) cc_final: 0.8898 (mp) REVERT: I 204 ASN cc_start: 0.7580 (m-40) cc_final: 0.7224 (m-40) REVERT: P 84 TYR cc_start: 0.7695 (p90) cc_final: 0.7126 (p90) REVERT: P 242 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7743 (p) REVERT: P 259 VAL cc_start: 0.7558 (p) cc_final: 0.7247 (m) REVERT: R 52 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7553 (tm-30) REVERT: V 14 LEU cc_start: 0.8121 (mp) cc_final: 0.7667 (mt) REVERT: V 44 TYR cc_start: 0.7414 (t80) cc_final: 0.6840 (t80) REVERT: W 122 LEU cc_start: 0.8751 (tp) cc_final: 0.8469 (tp) REVERT: Z 8 GLN cc_start: 0.6986 (tt0) cc_final: 0.6733 (tt0) REVERT: Z 43 LEU cc_start: 0.8389 (mt) cc_final: 0.8111 (mt) REVERT: a 58 ASN cc_start: 0.2488 (m-40) cc_final: 0.0888 (m-40) REVERT: q 51 ASP cc_start: 0.7495 (t0) cc_final: 0.7180 (t0) REVERT: q 134 ILE cc_start: 0.8942 (mm) cc_final: 0.8701 (mt) REVERT: s 44 THR cc_start: 0.7724 (m) cc_final: 0.7298 (m) outliers start: 14 outliers final: 0 residues processed: 1684 average time/residue: 0.2479 time to fit residues: 655.1698 Evaluate side-chains 976 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 975 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS C 73 GLN C 88 HIS C 195 HIS D 112 HIS D 117 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN E 89 ASN E 152 GLN ** F 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 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** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 GLN G 260 ASN G 415 ASN G 444 HIS G 495 ASN G 604 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS H 258 ASN H 304 HIS I 126 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 79 GLN P 138 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS P 238 GLN Q 167 ASN R 33 HIS R 56 ASN R 70 ASN R 113 GLN V 21 HIS V 41 HIS ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN W 54 GLN W 94 GLN W 105 HIS X 69 ASN X 104 GLN X 140 ASN Z 54 ASN Z 76 GLN ** Z 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN a 44 GLN q 31 ASN q 52 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 HIS q 116 ASN q 123 GLN r 21 GLN ** r 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN s 49 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084705 restraints weight = 103522.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087257 restraints weight = 47314.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088947 restraints weight = 27216.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090017 restraints weight = 18210.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090786 restraints weight = 13747.624| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 35541 Z= 0.213 Angle : 1.022 64.521 48210 Z= 0.433 Chirality : 0.049 0.260 5254 Planarity : 0.007 0.165 6117 Dihedral : 9.339 157.374 4996 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 3.85 % Allowed : 17.88 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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 (0.12), residues: 4234 helix: 0.32 (0.12), residues: 1857 sheet: -1.10 (0.26), residues: 360 loop : -1.32 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG s 56 TYR 0.031 0.003 TYR V 44 PHE 0.030 0.003 PHE T 126 TRP 0.019 0.002 TRP E 91 HIS 0.009 0.002 HIS R 33 Details of bonding type rmsd covalent geometry : bond 0.00480 (35501) covalent geometry : angle 0.82872 (48120) SS BOND : bond 0.00421 ( 3) SS BOND : angle 4.87686 ( 6) hydrogen bonds : bond 0.05765 ( 1449) hydrogen bonds : angle 5.90135 ( 4155) metal coordination : bond 0.02519 ( 37) metal coordination : angle 14.27909 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1078 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7492 (mtm) cc_final: 0.7003 (mpp) REVERT: A 38 GLU cc_start: 0.7624 (tt0) cc_final: 0.7401 (tt0) REVERT: A 58 VAL cc_start: 0.8609 (t) cc_final: 0.8305 (t) REVERT: A 62 PHE cc_start: 0.9118 (t80) cc_final: 0.8897 (t80) REVERT: A 90 MET cc_start: 0.8091 (mmm) cc_final: 0.6301 (ptt) REVERT: B 124 SER cc_start: 0.8571 (p) cc_final: 0.6932 (p) REVERT: B 157 TYR cc_start: 0.8802 (m-80) cc_final: 0.8579 (m-80) REVERT: B 161 MET cc_start: 0.8302 (ttt) cc_final: 0.7666 (ttt) REVERT: B 163 SER cc_start: 0.8859 (m) cc_final: 0.8198 (t) REVERT: B 188 ASP cc_start: 0.8193 (m-30) cc_final: 0.7759 (m-30) REVERT: B 199 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8027 (mt-10) REVERT: B 201 LEU cc_start: 0.9250 (tp) cc_final: 0.8944 (tp) REVERT: B 215 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7487 (tp30) REVERT: C 112 ASP cc_start: 0.8046 (t0) cc_final: 0.7720 (t0) REVERT: C 221 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 235 ASN cc_start: 0.8439 (t0) cc_final: 0.8224 (t0) REVERT: C 241 PHE cc_start: 0.7339 (m-10) cc_final: 0.7052 (m-10) REVERT: D 140 ASP cc_start: 0.8456 (t0) cc_final: 0.8100 (t0) REVERT: D 250 ASN cc_start: 0.8871 (m-40) cc_final: 0.8671 (m-40) REVERT: D 375 MET cc_start: 0.8534 (tpt) cc_final: 0.8287 (tpt) REVERT: D 455 ASP cc_start: 0.6430 (m-30) cc_final: 0.6095 (m-30) REVERT: D 460 GLU cc_start: 0.7988 (pt0) cc_final: 0.7664 (pt0) REVERT: E 46 ASN cc_start: 0.8106 (t0) cc_final: 0.7351 (t0) REVERT: E 137 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.7593 (p) REVERT: E 140 MET cc_start: 0.8350 (tmm) cc_final: 0.7897 (ppp) REVERT: E 141 LEU cc_start: 0.9418 (mt) cc_final: 0.8543 (mt) REVERT: E 184 MET cc_start: 0.8395 (tmm) cc_final: 0.8140 (tmm) REVERT: F 80 MET cc_start: 0.8699 (tpp) cc_final: 0.8375 (tpp) REVERT: F 220 GLN cc_start: 0.7343 (tt0) cc_final: 0.6987 (tt0) REVERT: G 140 GLN cc_start: 0.7946 (pt0) cc_final: 0.7487 (pt0) REVERT: G 311 LYS cc_start: 0.8451 (tptp) cc_final: 0.8105 (pttm) REVERT: G 329 MET cc_start: 0.8709 (mmm) cc_final: 0.8355 (mmm) REVERT: G 360 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8691 (mtpp) REVERT: G 636 TYR cc_start: 0.8148 (p90) cc_final: 0.7927 (p90) REVERT: G 684 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8940 (pp) REVERT: H 31 MET cc_start: 0.9133 (mtp) cc_final: 0.8305 (mtp) REVERT: H 34 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8157 (ptt-90) REVERT: H 54 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8671 (tmtt) REVERT: H 59 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7095 (tm-30) REVERT: H 91 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8506 (ptp) REVERT: H 97 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8452 (p0) REVERT: H 127 TYR cc_start: 0.6903 (m-80) cc_final: 0.6609 (m-80) REVERT: H 195 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7546 (mmm-85) REVERT: I 35 THR cc_start: 0.8701 (m) cc_final: 0.8357 (p) REVERT: I 36 TYR cc_start: 0.8741 (p90) cc_final: 0.7710 (p90) REVERT: I 37 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8621 (ttmm) REVERT: I 50 MET cc_start: 0.7280 (ppp) cc_final: 0.5465 (ttt) REVERT: I 73 THR cc_start: 0.8696 (p) cc_final: 0.8364 (p) REVERT: I 149 MET cc_start: 0.8426 (mmm) cc_final: 0.7774 (mmm) REVERT: I 193 ASN cc_start: 0.8775 (m-40) cc_final: 0.8415 (m-40) REVERT: I 208 ASP cc_start: 0.8685 (t0) cc_final: 0.7799 (t70) REVERT: P 259 VAL cc_start: 0.8596 (p) cc_final: 0.7784 (m) REVERT: P 283 MET cc_start: 0.8248 (mmm) cc_final: 0.7852 (tpp) REVERT: P 324 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8731 (mm) REVERT: R 51 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7840 (mmt90) REVERT: R 52 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7532 (pp30) REVERT: R 75 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7669 (mtp180) REVERT: S 53 ILE cc_start: 0.8998 (mp) cc_final: 0.8582 (mp) REVERT: T 126 PHE cc_start: 0.6944 (m-10) cc_final: 0.6647 (m-10) REVERT: V 44 TYR cc_start: 0.9096 (t80) cc_final: 0.8864 (t80) REVERT: W 24 PHE cc_start: 0.8303 (m-10) cc_final: 0.8097 (m-10) REVERT: W 93 LEU cc_start: 0.8951 (tt) cc_final: 0.8700 (tp) REVERT: X 44 MET cc_start: 0.9085 (tpp) cc_final: 0.8351 (mmm) REVERT: X 101 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7619 (mmt180) REVERT: X 141 PRO cc_start: 0.7890 (Cg_endo) cc_final: 0.7641 (Cg_exo) REVERT: Z 71 LEU cc_start: 0.8251 (mt) cc_final: 0.7941 (mt) REVERT: Z 74 LEU cc_start: 0.8727 (tp) cc_final: 0.8423 (tp) REVERT: Z 131 GLU cc_start: 0.7803 (mm-30) cc_final: 0.6566 (pt0) REVERT: a 2 TRP cc_start: 0.8461 (p-90) cc_final: 0.7960 (p-90) REVERT: a 12 MET cc_start: 0.8858 (ttp) cc_final: 0.8609 (ttm) REVERT: a 40 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7399 (ttp80) REVERT: q 13 GLN cc_start: 0.7708 (mm-40) cc_final: 0.6983 (mm-40) REVERT: q 49 TYR cc_start: 0.8417 (m-80) cc_final: 0.8019 (m-80) REVERT: q 51 ASP cc_start: 0.8548 (t0) cc_final: 0.7903 (t0) REVERT: q 133 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8577 (mmtp) REVERT: r 11 LEU cc_start: 0.8026 (tt) cc_final: 0.7771 (tt) REVERT: r 18 GLN cc_start: 0.8536 (mp10) cc_final: 0.7622 (mp10) REVERT: r 57 ARG cc_start: 0.7190 (ttp-110) cc_final: 0.6632 (ptt90) REVERT: r 110 GLN cc_start: 0.8943 (tt0) cc_final: 0.8529 (tt0) REVERT: r 112 TYR cc_start: 0.7622 (m-80) cc_final: 0.7306 (m-80) REVERT: s 44 THR cc_start: 0.8327 (m) cc_final: 0.7839 (p) outliers start: 143 outliers final: 61 residues processed: 1154 average time/residue: 0.2227 time to fit residues: 419.9836 Evaluate side-chains 922 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 855 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 206 CYS Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 240 ILE Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain Q residue 165 SER Chi-restraints excluded: chain Q residue 167 ASN Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain T residue 85 TYR Chi-restraints excluded: chain V residue 34 ILE Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 84 LEU Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 40 ARG Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 5 GLU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 62 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 410 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 0.4980 chunk 171 optimal weight: 0.8980 chunk 389 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 112 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN F 441 HIS G 123 ASN G 140 GLN G 415 ASN G 652 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 284 GLN I 159 GLN ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN P 166 HIS P 171 ASN Q 92 ASN Q 167 ASN S 92 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN Z 54 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.081620 restraints weight = 103550.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084065 restraints weight = 47407.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085604 restraints weight = 27449.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086726 restraints weight = 18701.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087505 restraints weight = 14111.579| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35541 Z= 0.187 Angle : 0.935 72.813 48210 Z= 0.375 Chirality : 0.046 0.225 5254 Planarity : 0.006 0.162 6117 Dihedral : 8.984 160.501 4995 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 4.36 % Allowed : 18.82 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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: -0.54 (0.13), residues: 4234 helix: 0.62 (0.12), residues: 1882 sheet: -0.98 (0.26), residues: 376 loop : -1.16 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 405 TYR 0.030 0.002 TYR T 90 PHE 0.027 0.002 PHE s 45 TRP 0.020 0.002 TRP D 202 HIS 0.011 0.001 HIS P 323 Details of bonding type rmsd covalent geometry : bond 0.00431 (35501) covalent geometry : angle 0.73063 (48120) SS BOND : bond 0.00446 ( 3) SS BOND : angle 1.61051 ( 6) hydrogen bonds : bond 0.04814 ( 1449) hydrogen bonds : angle 5.52271 ( 4155) metal coordination : bond 0.02405 ( 37) metal coordination : angle 13.98562 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 913 time to evaluate : 1.333 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: A 27 MET cc_start: 0.7574 (mtm) cc_final: 0.7265 (mpp) REVERT: A 87 MET cc_start: 0.8802 (tmm) cc_final: 0.8460 (tmm) REVERT: A 90 MET cc_start: 0.8155 (mmm) cc_final: 0.6551 (ptt) REVERT: B 103 GLU cc_start: 0.8759 (tp30) cc_final: 0.7679 (tt0) REVERT: B 122 ARG cc_start: 0.8510 (mmm160) cc_final: 0.7902 (mmm160) REVERT: B 124 SER cc_start: 0.8852 (p) cc_final: 0.8570 (t) REVERT: B 141 MET cc_start: 0.9120 (mmm) cc_final: 0.8246 (tpp) REVERT: B 161 MET cc_start: 0.8432 (ttt) cc_final: 0.7721 (ttp) REVERT: B 188 ASP cc_start: 0.8280 (m-30) cc_final: 0.7443 (m-30) REVERT: B 201 LEU cc_start: 0.9137 (tp) cc_final: 0.8694 (tp) REVERT: B 215 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7568 (tp30) REVERT: C 112 ASP cc_start: 0.7930 (t0) cc_final: 0.7697 (t0) REVERT: C 114 THR cc_start: 0.8435 (m) cc_final: 0.8068 (m) REVERT: C 186 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6799 (mp) REVERT: C 216 LYS cc_start: 0.9294 (mmtt) cc_final: 0.9094 (mmtm) REVERT: C 221 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8296 (mm-30) REVERT: C 235 ASN cc_start: 0.8200 (t0) cc_final: 0.8000 (t0) REVERT: D 140 ASP cc_start: 0.8434 (t0) cc_final: 0.7908 (t0) REVERT: D 250 ASN cc_start: 0.8821 (m-40) cc_final: 0.8579 (m-40) REVERT: D 375 MET cc_start: 0.8603 (tpt) cc_final: 0.8312 (tpt) REVERT: D 460 GLU cc_start: 0.8337 (pt0) cc_final: 0.7936 (pt0) REVERT: E 184 MET cc_start: 0.8480 (tmm) cc_final: 0.8196 (tmm) REVERT: E 192 TYR cc_start: 0.8833 (m-80) cc_final: 0.8486 (m-80) REVERT: E 199 ASP cc_start: 0.7836 (t0) cc_final: 0.7463 (t0) REVERT: F 178 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: F 450 MET cc_start: 0.8834 (mtp) cc_final: 0.8237 (mtp) REVERT: G 126 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8500 (pp) REVERT: G 154 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8977 (pt) REVERT: G 306 MET cc_start: 0.7469 (mtp) cc_final: 0.7203 (mmm) REVERT: G 360 LYS cc_start: 0.9007 (mtpp) cc_final: 0.8578 (mtmt) REVERT: G 401 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8929 (tp) REVERT: G 590 THR cc_start: 0.9294 (p) cc_final: 0.8888 (t) REVERT: G 618 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7656 (tt0) REVERT: G 632 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.7949 (pt) REVERT: H 31 MET cc_start: 0.9265 (mtp) cc_final: 0.8950 (mtp) REVERT: H 33 LEU cc_start: 0.8330 (mp) cc_final: 0.7482 (mp) REVERT: H 34 ARG cc_start: 0.8663 (ptt-90) cc_final: 0.8236 (ptt-90) REVERT: H 47 GLN cc_start: 0.9030 (tm-30) cc_final: 0.8686 (tm-30) REVERT: H 68 MET cc_start: 0.6831 (mmm) cc_final: 0.4575 (ptp) REVERT: H 91 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8412 (ptp) REVERT: H 93 HIS cc_start: 0.7459 (m170) cc_final: 0.6927 (m170) REVERT: H 97 ASN cc_start: 0.8613 (p0) cc_final: 0.8089 (p0) REVERT: H 127 TYR cc_start: 0.6812 (m-80) cc_final: 0.6478 (m-80) REVERT: H 138 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6840 (tm-30) REVERT: H 174 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8586 (mm) REVERT: H 206 GLU cc_start: 0.7250 (mp0) cc_final: 0.6996 (mp0) REVERT: H 228 TYR cc_start: 0.9147 (m-10) cc_final: 0.8887 (m-10) REVERT: I 50 MET cc_start: 0.7197 (ppp) cc_final: 0.5673 (ttt) REVERT: I 76 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.8239 (t80) REVERT: I 181 GLU cc_start: 0.8552 (mp0) cc_final: 0.8328 (mp0) REVERT: I 188 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: I 208 ASP cc_start: 0.8789 (t0) cc_final: 0.7962 (t70) REVERT: P 238 GLN cc_start: 0.9057 (tt0) cc_final: 0.8608 (tt0) REVERT: P 291 TYR cc_start: 0.8794 (p90) cc_final: 0.8427 (p90) REVERT: P 316 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7702 (tptm) REVERT: P 324 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9042 (mm) REVERT: P 341 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8584 (mm-40) REVERT: R 34 THR cc_start: 0.7761 (p) cc_final: 0.7557 (p) REVERT: R 42 ASP cc_start: 0.8362 (m-30) cc_final: 0.8136 (t70) REVERT: R 52 GLN cc_start: 0.7979 (tm-30) cc_final: 0.6495 (pp30) REVERT: T 142 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8381 (tp-100) REVERT: T 143 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7707 (mt-10) REVERT: V 44 TYR cc_start: 0.9133 (t80) cc_final: 0.8825 (t80) REVERT: W 24 PHE cc_start: 0.8481 (m-10) cc_final: 0.8226 (m-10) REVERT: W 93 LEU cc_start: 0.9079 (tt) cc_final: 0.8839 (tt) REVERT: X 44 MET cc_start: 0.9130 (tpp) cc_final: 0.8606 (mmm) REVERT: X 101 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7798 (mmt180) REVERT: Z 9 ASP cc_start: 0.6091 (t0) cc_final: 0.5575 (m-30) REVERT: Z 125 TYR cc_start: 0.5700 (m-80) cc_final: 0.4809 (m-80) REVERT: Z 132 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7179 (pt0) REVERT: Z 133 MET cc_start: 0.6713 (tmm) cc_final: 0.6349 (tmm) REVERT: a 2 TRP cc_start: 0.8426 (p-90) cc_final: 0.7922 (p-90) REVERT: b 41 TYR cc_start: 0.8179 (m-80) cc_final: 0.7964 (m-80) REVERT: q 12 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8666 (mt0) REVERT: q 13 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7088 (mm-40) REVERT: q 49 TYR cc_start: 0.8452 (m-80) cc_final: 0.8096 (m-80) REVERT: q 51 ASP cc_start: 0.8376 (t0) cc_final: 0.7991 (t0) REVERT: q 122 GLU cc_start: 0.7680 (mp0) cc_final: 0.7474 (mt-10) REVERT: q 133 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8660 (mmtp) REVERT: r 11 LEU cc_start: 0.8259 (tt) cc_final: 0.8025 (tt) REVERT: r 18 GLN cc_start: 0.8739 (mp10) cc_final: 0.8330 (mp10) REVERT: r 30 GLU cc_start: 0.7060 (pt0) cc_final: 0.6688 (pm20) REVERT: r 57 ARG cc_start: 0.7151 (ttp-110) cc_final: 0.6610 (ptt90) REVERT: r 102 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8603 (ttpt) REVERT: r 109 ASP cc_start: 0.8073 (p0) cc_final: 0.7657 (p0) REVERT: r 112 TYR cc_start: 0.7768 (m-80) cc_final: 0.7456 (m-80) REVERT: s 44 THR cc_start: 0.8562 (m) cc_final: 0.8193 (p) outliers start: 162 outliers final: 86 residues processed: 1006 average time/residue: 0.2081 time to fit residues: 349.6816 Evaluate side-chains 895 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 797 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 455 GLN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 516 LEU 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 H residue 23 VAL Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 257 ASP Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 120 ASP Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 387 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 308 optimal weight: 0.0070 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN C 54 HIS ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 83 ASN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS G 569 GLN G 652 ASN H 97 ASN I 159 GLN P 121 GLN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 116 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081361 restraints weight = 103024.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.083840 restraints weight = 46997.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085455 restraints weight = 27061.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086519 restraints weight = 18240.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087287 restraints weight = 13768.273| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35541 Z= 0.160 Angle : 0.905 74.186 48210 Z= 0.352 Chirality : 0.044 0.229 5254 Planarity : 0.005 0.160 6117 Dihedral : 8.749 162.212 4995 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.62 % Rotamer: Outliers : 4.04 % Allowed : 20.27 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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: 4234 helix: 0.80 (0.12), residues: 1875 sheet: -1.11 (0.26), residues: 394 loop : -1.00 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 40 TYR 0.024 0.002 TYR a 61 PHE 0.024 0.002 PHE H 19 TRP 0.024 0.001 TRP b 26 HIS 0.007 0.001 HIS Q 71 Details of bonding type rmsd covalent geometry : bond 0.00367 (35501) covalent geometry : angle 0.69057 (48120) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.84017 ( 6) hydrogen bonds : bond 0.04364 ( 1449) hydrogen bonds : angle 5.28102 ( 4155) metal coordination : bond 0.01670 ( 37) metal coordination : angle 14.03045 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 875 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7474 (mtm) cc_final: 0.7172 (mpp) REVERT: A 90 MET cc_start: 0.8158 (mmm) cc_final: 0.6674 (ptt) REVERT: B 103 GLU cc_start: 0.8773 (tp30) cc_final: 0.7930 (tt0) REVERT: B 122 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8022 (mmm160) REVERT: B 137 LEU cc_start: 0.9051 (tp) cc_final: 0.8539 (mp) REVERT: B 141 MET cc_start: 0.9179 (mmm) cc_final: 0.8279 (tpp) REVERT: B 151 GLN cc_start: 0.8476 (mt0) cc_final: 0.7640 (mp10) REVERT: B 161 MET cc_start: 0.8318 (ttt) cc_final: 0.7782 (ttp) REVERT: B 188 ASP cc_start: 0.8238 (m-30) cc_final: 0.7462 (m-30) REVERT: B 199 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7937 (mt-10) REVERT: B 201 LEU cc_start: 0.9069 (tp) cc_final: 0.8702 (tp) REVERT: C 112 ASP cc_start: 0.8045 (t0) cc_final: 0.7804 (t0) REVERT: C 114 THR cc_start: 0.8591 (m) cc_final: 0.8272 (m) REVERT: C 221 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8509 (mm-30) REVERT: D 110 ASP cc_start: 0.8855 (t70) cc_final: 0.8426 (t70) REVERT: D 270 ASN cc_start: 0.9105 (m-40) cc_final: 0.8779 (m110) REVERT: D 333 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7656 (mtt180) REVERT: D 375 MET cc_start: 0.8564 (tpt) cc_final: 0.8359 (tpt) REVERT: D 406 GLU cc_start: 0.8185 (tt0) cc_final: 0.7970 (tt0) REVERT: E 143 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.9035 (t70) REVERT: E 192 TYR cc_start: 0.8776 (m-80) cc_final: 0.8308 (m-80) REVERT: E 199 ASP cc_start: 0.7945 (t0) cc_final: 0.7561 (t0) REVERT: F 450 MET cc_start: 0.8855 (mtp) cc_final: 0.8245 (mtp) REVERT: G 42 MET cc_start: 0.8721 (tpp) cc_final: 0.8514 (mmm) REVERT: G 329 MET cc_start: 0.8865 (tpp) cc_final: 0.8432 (mmm) REVERT: G 360 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8681 (mtpp) REVERT: G 401 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9020 (tp) REVERT: G 590 THR cc_start: 0.9321 (p) cc_final: 0.8956 (t) REVERT: G 618 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7604 (mt-10) REVERT: G 632 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8240 (pt) REVERT: G 684 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8886 (pp) REVERT: H 33 LEU cc_start: 0.8484 (mp) cc_final: 0.8060 (mt) REVERT: H 34 ARG cc_start: 0.8672 (ptt-90) cc_final: 0.8282 (ptt-90) REVERT: H 47 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8521 (tm-30) REVERT: H 68 MET cc_start: 0.6929 (mmm) cc_final: 0.4641 (ttp) REVERT: H 92 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7560 (Cg_endo) REVERT: H 93 HIS cc_start: 0.7247 (m170) cc_final: 0.7006 (m170) REVERT: H 97 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7890 (p0) REVERT: H 110 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8385 (m) REVERT: H 127 TYR cc_start: 0.6714 (m-80) cc_final: 0.6353 (m-80) REVERT: H 138 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6838 (tm-30) REVERT: I 36 TYR cc_start: 0.8805 (p90) cc_final: 0.7710 (p90) REVERT: I 50 MET cc_start: 0.7200 (ppp) cc_final: 0.6732 (pmm) REVERT: I 76 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8155 (t80) REVERT: I 188 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: I 193 ASN cc_start: 0.8709 (m-40) cc_final: 0.8318 (m-40) REVERT: I 208 ASP cc_start: 0.8736 (t0) cc_final: 0.7711 (t70) REVERT: P 121 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: P 128 ASN cc_start: 0.8869 (t0) cc_final: 0.8657 (t0) REVERT: P 291 TYR cc_start: 0.8853 (p90) cc_final: 0.8497 (p90) REVERT: P 316 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7709 (tptm) REVERT: P 324 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8991 (mm) REVERT: P 341 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8623 (mm-40) REVERT: Q 60 ASP cc_start: 0.8480 (t0) cc_final: 0.8226 (m-30) REVERT: Q 93 ASN cc_start: 0.8807 (m-40) cc_final: 0.8477 (m110) REVERT: R 52 GLN cc_start: 0.7864 (tm-30) cc_final: 0.6465 (pp30) REVERT: R 54 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7675 (mt-10) REVERT: R 75 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.7711 (mtp180) REVERT: T 105 MET cc_start: 0.7971 (mmm) cc_final: 0.7692 (pmm) REVERT: W 19 SER cc_start: 0.8430 (m) cc_final: 0.8013 (p) REVERT: W 24 PHE cc_start: 0.8550 (m-10) cc_final: 0.8254 (m-10) REVERT: W 45 GLU cc_start: 0.8597 (tp30) cc_final: 0.8241 (tp30) REVERT: W 93 LEU cc_start: 0.9058 (tt) cc_final: 0.8801 (tt) REVERT: X 44 MET cc_start: 0.9089 (tpp) cc_final: 0.8781 (tpp) REVERT: X 71 PHE cc_start: 0.7127 (m-80) cc_final: 0.6892 (m-80) REVERT: X 101 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7620 (mmt180) REVERT: Z 10 MET cc_start: 0.8149 (mmm) cc_final: 0.7921 (mmt) REVERT: Z 51 MET cc_start: 0.8599 (tmm) cc_final: 0.8376 (tmm) REVERT: Z 125 TYR cc_start: 0.6062 (m-80) cc_final: 0.5064 (m-80) REVERT: Z 132 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6989 (pt0) REVERT: Z 133 MET cc_start: 0.7020 (tmm) cc_final: 0.6760 (tmm) REVERT: a 2 TRP cc_start: 0.8392 (p-90) cc_final: 0.7747 (p-90) REVERT: a 48 MET cc_start: 0.8095 (ttm) cc_final: 0.7651 (ttp) REVERT: a 61 TYR cc_start: 0.6554 (m-80) cc_final: 0.6311 (m-80) REVERT: b 18 VAL cc_start: 0.9108 (t) cc_final: 0.8882 (p) REVERT: b 35 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (mt) REVERT: b 41 TYR cc_start: 0.8245 (m-80) cc_final: 0.7934 (m-80) REVERT: q 12 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8658 (mt0) REVERT: q 13 GLN cc_start: 0.7782 (mm-40) cc_final: 0.6837 (mm-40) REVERT: q 49 TYR cc_start: 0.8577 (m-80) cc_final: 0.8209 (m-80) REVERT: q 51 ASP cc_start: 0.8281 (t0) cc_final: 0.7908 (t0) REVERT: q 133 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8665 (mmtp) REVERT: r 11 LEU cc_start: 0.8374 (tt) cc_final: 0.8101 (tt) REVERT: r 18 GLN cc_start: 0.8875 (mp10) cc_final: 0.8459 (mp10) REVERT: r 57 ARG cc_start: 0.7130 (ttp-110) cc_final: 0.6694 (ptt90) REVERT: r 109 ASP cc_start: 0.8086 (p0) cc_final: 0.7623 (p0) REVERT: r 110 GLN cc_start: 0.9099 (tt0) cc_final: 0.8870 (tt0) REVERT: r 112 TYR cc_start: 0.7893 (m-80) cc_final: 0.7460 (m-80) REVERT: s 44 THR cc_start: 0.8648 (m) cc_final: 0.8231 (p) outliers start: 150 outliers final: 94 residues processed: 953 average time/residue: 0.2006 time to fit residues: 320.3283 Evaluate side-chains 892 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 786 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 401 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 632 ILE Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 121 GLN Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 324 ILE Chi-restraints excluded: chain P residue 350 ILE Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 42 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 120 ASP Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 274 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 104 optimal weight: 0.0570 chunk 287 optimal weight: 5.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN I 159 GLN ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 109 ASN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078484 restraints weight = 104959.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080885 restraints weight = 48124.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082405 restraints weight = 27959.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083522 restraints weight = 19178.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084326 restraints weight = 14380.061| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 35541 Z= 0.188 Angle : 0.935 76.472 48210 Z= 0.357 Chirality : 0.045 0.300 5254 Planarity : 0.005 0.134 6117 Dihedral : 8.576 164.041 4995 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 4.50 % Allowed : 21.38 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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: 4234 helix: 0.90 (0.12), residues: 1862 sheet: -1.08 (0.26), residues: 398 loop : -0.90 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 126 TYR 0.036 0.002 TYR Z 143 PHE 0.023 0.002 PHE E 242 TRP 0.026 0.002 TRP b 26 HIS 0.006 0.001 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.00436 (35501) covalent geometry : angle 0.70660 (48120) SS BOND : bond 0.00334 ( 3) SS BOND : angle 2.14059 ( 6) hydrogen bonds : bond 0.04207 ( 1449) hydrogen bonds : angle 5.22893 ( 4155) metal coordination : bond 0.02208 ( 37) metal coordination : angle 14.66615 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 827 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8712 (pt) REVERT: A 22 PHE cc_start: 0.9150 (m-80) cc_final: 0.8923 (m-80) REVERT: A 27 MET cc_start: 0.7361 (mtm) cc_final: 0.7112 (mpp) REVERT: A 55 PHE cc_start: 0.7286 (m-80) cc_final: 0.7057 (m-80) REVERT: A 72 LEU cc_start: 0.8832 (tp) cc_final: 0.8579 (pp) REVERT: A 87 MET cc_start: 0.8764 (tmm) cc_final: 0.8334 (tmm) REVERT: A 90 MET cc_start: 0.8214 (mmm) cc_final: 0.6802 (ptt) REVERT: B 103 GLU cc_start: 0.8812 (tp30) cc_final: 0.7907 (tt0) REVERT: B 141 MET cc_start: 0.9215 (mmm) cc_final: 0.8376 (tpp) REVERT: B 151 GLN cc_start: 0.8572 (mt0) cc_final: 0.7512 (mp10) REVERT: B 161 MET cc_start: 0.8378 (ttt) cc_final: 0.7920 (ttp) REVERT: B 188 ASP cc_start: 0.8284 (m-30) cc_final: 0.7595 (m-30) REVERT: B 199 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8123 (mt-10) REVERT: B 201 LEU cc_start: 0.9195 (tp) cc_final: 0.8600 (tp) REVERT: C 112 ASP cc_start: 0.8083 (t0) cc_final: 0.7840 (t0) REVERT: C 114 THR cc_start: 0.8711 (m) cc_final: 0.8417 (m) REVERT: C 199 LYS cc_start: 0.9380 (tppt) cc_final: 0.9132 (tppt) REVERT: D 206 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8943 (mm-30) REVERT: D 270 ASN cc_start: 0.9157 (m-40) cc_final: 0.8876 (m110) REVERT: D 333 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7803 (mtt180) REVERT: D 406 GLU cc_start: 0.8189 (tt0) cc_final: 0.7816 (tt0) REVERT: E 91 TRP cc_start: 0.6892 (t-100) cc_final: 0.6454 (t-100) REVERT: E 143 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.9001 (t70) REVERT: E 192 TYR cc_start: 0.8755 (m-80) cc_final: 0.8163 (m-80) REVERT: E 199 ASP cc_start: 0.7924 (t0) cc_final: 0.7510 (t0) REVERT: F 135 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8676 (Cg_exo) REVERT: F 246 GLU cc_start: 0.8326 (tt0) cc_final: 0.7877 (tm-30) REVERT: F 315 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8579 (mt) REVERT: F 450 MET cc_start: 0.8850 (mtp) cc_final: 0.8318 (mtp) REVERT: G 42 MET cc_start: 0.8807 (tpp) cc_final: 0.8582 (tpp) REVERT: G 215 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7506 (mmt) REVERT: G 315 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8724 (p) REVERT: G 329 MET cc_start: 0.8870 (tpp) cc_final: 0.8058 (mmm) REVERT: G 360 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8732 (mtpp) REVERT: G 590 THR cc_start: 0.9385 (p) cc_final: 0.9006 (t) REVERT: G 618 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7627 (mt-10) REVERT: G 684 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8882 (pp) REVERT: G 696 MET cc_start: 0.8395 (mtm) cc_final: 0.7850 (mtt) REVERT: H 33 LEU cc_start: 0.8676 (mp) cc_final: 0.8118 (mt) REVERT: H 34 ARG cc_start: 0.8726 (ptt-90) cc_final: 0.8310 (ptt-90) REVERT: H 47 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8408 (tm-30) REVERT: H 68 MET cc_start: 0.6944 (mmm) cc_final: 0.4944 (ttp) REVERT: H 91 MET cc_start: 0.8800 (ptp) cc_final: 0.8538 (ptp) REVERT: H 93 HIS cc_start: 0.7271 (m170) cc_final: 0.6810 (m-70) REVERT: H 110 SER cc_start: 0.9127 (OUTLIER) cc_final: 0.8763 (m) REVERT: H 127 TYR cc_start: 0.6629 (m-80) cc_final: 0.6307 (m-80) REVERT: H 138 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7251 (tm-30) REVERT: H 192 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8216 (mm-30) REVERT: H 195 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: H 204 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6839 (mm-30) REVERT: H 215 TYR cc_start: 0.8611 (m-10) cc_final: 0.8350 (m-10) REVERT: H 269 THR cc_start: 0.9436 (m) cc_final: 0.9202 (p) REVERT: I 36 TYR cc_start: 0.8840 (p90) cc_final: 0.7683 (p90) REVERT: I 50 MET cc_start: 0.7173 (ppp) cc_final: 0.6818 (pmm) REVERT: I 62 MET cc_start: 0.6887 (tmm) cc_final: 0.6674 (tmm) REVERT: I 76 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.7983 (t80) REVERT: I 181 GLU cc_start: 0.8634 (mp0) cc_final: 0.8118 (pm20) REVERT: I 188 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7469 (tp30) REVERT: I 193 ASN cc_start: 0.8748 (m-40) cc_final: 0.8347 (m-40) REVERT: I 208 ASP cc_start: 0.8759 (t0) cc_final: 0.7865 (t70) REVERT: P 291 TYR cc_start: 0.8920 (p90) cc_final: 0.8560 (p90) REVERT: P 316 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7803 (tptm) REVERT: P 341 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8624 (mm-40) REVERT: Q 60 ASP cc_start: 0.8569 (t0) cc_final: 0.8117 (m-30) REVERT: Q 93 ASN cc_start: 0.8836 (m-40) cc_final: 0.8505 (m110) REVERT: Q 139 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7417 (mt-10) REVERT: R 52 GLN cc_start: 0.8044 (tm-30) cc_final: 0.6662 (pp30) REVERT: R 54 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7777 (mt-10) REVERT: R 75 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7900 (mtp180) REVERT: S 82 LEU cc_start: 0.8277 (mp) cc_final: 0.7460 (pt) REVERT: T 142 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8767 (tp-100) REVERT: W 19 SER cc_start: 0.8556 (m) cc_final: 0.8101 (p) REVERT: W 56 ASP cc_start: 0.8082 (m-30) cc_final: 0.7846 (m-30) REVERT: W 93 LEU cc_start: 0.9101 (tt) cc_final: 0.8818 (tt) REVERT: W 126 TYR cc_start: 0.9055 (m-10) cc_final: 0.8817 (m-10) REVERT: X 44 MET cc_start: 0.9100 (tpp) cc_final: 0.8743 (mmm) REVERT: X 101 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7639 (mmt180) REVERT: Z 9 ASP cc_start: 0.6012 (t0) cc_final: 0.5379 (m-30) REVERT: Z 10 MET cc_start: 0.8249 (mmm) cc_final: 0.7955 (mmt) REVERT: Z 51 MET cc_start: 0.8709 (tmm) cc_final: 0.8322 (tmm) REVERT: Z 132 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7367 (pt0) REVERT: Z 133 MET cc_start: 0.7171 (tmm) cc_final: 0.6868 (tmm) REVERT: a 2 TRP cc_start: 0.8428 (p-90) cc_final: 0.7741 (p-90) REVERT: a 35 GLU cc_start: 0.6934 (tt0) cc_final: 0.6630 (tt0) REVERT: a 48 MET cc_start: 0.8287 (ttm) cc_final: 0.7987 (ttp) REVERT: a 61 TYR cc_start: 0.6692 (m-80) cc_final: 0.6342 (m-80) REVERT: b 18 VAL cc_start: 0.9264 (t) cc_final: 0.8995 (p) REVERT: b 32 MET cc_start: 0.8987 (mmm) cc_final: 0.8707 (mmm) REVERT: q 12 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8736 (mp10) REVERT: q 13 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6614 (mm-40) REVERT: q 49 TYR cc_start: 0.8576 (m-80) cc_final: 0.8170 (m-80) REVERT: q 51 ASP cc_start: 0.8283 (t0) cc_final: 0.7933 (t0) REVERT: q 96 ASP cc_start: 0.8639 (t0) cc_final: 0.7946 (t0) REVERT: q 133 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8592 (mmtp) REVERT: r 18 GLN cc_start: 0.9063 (mp10) cc_final: 0.8781 (mp10) REVERT: r 29 GLN cc_start: 0.8057 (mp10) cc_final: 0.7819 (mp10) REVERT: r 30 GLU cc_start: 0.7063 (pt0) cc_final: 0.6641 (pm20) REVERT: r 57 ARG cc_start: 0.7006 (ttp-110) cc_final: 0.6593 (ptt90) REVERT: r 109 ASP cc_start: 0.8099 (p0) cc_final: 0.7634 (p0) REVERT: r 110 GLN cc_start: 0.9118 (tt0) cc_final: 0.8840 (tt0) REVERT: r 112 TYR cc_start: 0.8096 (m-80) cc_final: 0.7728 (m-80) REVERT: s 44 THR cc_start: 0.8780 (m) cc_final: 0.8221 (p) outliers start: 167 outliers final: 104 residues processed: 921 average time/residue: 0.2107 time to fit residues: 323.4451 Evaluate side-chains 882 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 768 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 79 ILE Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 117 GLU Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 120 ASP Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 55 optimal weight: 5.9990 chunk 378 optimal weight: 0.8980 chunk 325 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN G 415 ASN G 569 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.080007 restraints weight = 103418.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.082456 restraints weight = 47409.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083962 restraints weight = 27402.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085071 restraints weight = 18757.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085842 restraints weight = 14172.134| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35541 Z= 0.142 Angle : 0.905 76.129 48210 Z= 0.343 Chirality : 0.045 0.362 5254 Planarity : 0.005 0.163 6117 Dihedral : 8.368 165.948 4995 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.82 % Allowed : 22.35 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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: -0.16 (0.13), residues: 4234 helix: 0.92 (0.12), residues: 1866 sheet: -1.14 (0.26), residues: 390 loop : -0.83 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 126 TYR 0.019 0.002 TYR V 44 PHE 0.020 0.002 PHE E 242 TRP 0.028 0.001 TRP D 202 HIS 0.004 0.001 HIS P 285 Details of bonding type rmsd covalent geometry : bond 0.00326 (35501) covalent geometry : angle 0.68237 (48120) SS BOND : bond 0.00447 ( 3) SS BOND : angle 2.01665 ( 6) hydrogen bonds : bond 0.04013 ( 1449) hydrogen bonds : angle 5.12169 ( 4155) metal coordination : bond 0.01493 ( 37) metal coordination : angle 14.23271 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 848 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8688 (pt) REVERT: A 22 PHE cc_start: 0.9141 (m-80) cc_final: 0.8891 (m-80) REVERT: A 27 MET cc_start: 0.7315 (mtm) cc_final: 0.7108 (mpp) REVERT: A 55 PHE cc_start: 0.7456 (m-80) cc_final: 0.7240 (m-80) REVERT: A 90 MET cc_start: 0.8073 (mmm) cc_final: 0.7803 (mmt) REVERT: B 103 GLU cc_start: 0.8687 (tp30) cc_final: 0.7832 (tt0) REVERT: B 127 GLN cc_start: 0.8083 (mp10) cc_final: 0.7688 (pm20) REVERT: B 141 MET cc_start: 0.9268 (mmm) cc_final: 0.8437 (tpp) REVERT: B 151 GLN cc_start: 0.8420 (mt0) cc_final: 0.7579 (mp10) REVERT: B 161 MET cc_start: 0.8268 (ttt) cc_final: 0.7708 (ttt) REVERT: B 188 ASP cc_start: 0.8271 (m-30) cc_final: 0.7738 (m-30) REVERT: B 199 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: B 201 LEU cc_start: 0.9154 (tp) cc_final: 0.8678 (tp) REVERT: C 112 ASP cc_start: 0.8105 (t0) cc_final: 0.7851 (t0) REVERT: D 140 ASP cc_start: 0.8585 (t0) cc_final: 0.8062 (t0) REVERT: D 147 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8617 (m110) REVERT: D 270 ASN cc_start: 0.9116 (m-40) cc_final: 0.8829 (m110) REVERT: D 326 CYS cc_start: 0.8669 (m) cc_final: 0.8364 (m) REVERT: D 333 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7710 (mtt90) REVERT: D 406 GLU cc_start: 0.8180 (tt0) cc_final: 0.7979 (tt0) REVERT: D 455 ASP cc_start: 0.6737 (m-30) cc_final: 0.6334 (m-30) REVERT: E 143 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8973 (t70) REVERT: E 192 TYR cc_start: 0.8732 (m-80) cc_final: 0.8128 (m-80) REVERT: E 199 ASP cc_start: 0.7896 (t0) cc_final: 0.7480 (t0) REVERT: F 135 PRO cc_start: 0.8942 (Cg_endo) cc_final: 0.8631 (Cg_exo) REVERT: F 246 GLU cc_start: 0.8148 (tt0) cc_final: 0.7925 (tm-30) REVERT: F 450 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: G 215 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7244 (mmt) REVERT: G 329 MET cc_start: 0.8874 (tpp) cc_final: 0.8053 (mmm) REVERT: G 360 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8725 (mtpp) REVERT: G 530 TYR cc_start: 0.8761 (m-80) cc_final: 0.8440 (m-80) REVERT: G 590 THR cc_start: 0.9309 (p) cc_final: 0.9024 (t) REVERT: G 618 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7442 (mt-10) REVERT: G 684 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8869 (pp) REVERT: H 33 LEU cc_start: 0.8533 (mp) cc_final: 0.7873 (mt) REVERT: H 34 ARG cc_start: 0.8635 (ptt-90) cc_final: 0.8260 (ptt-90) REVERT: H 47 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8230 (tm-30) REVERT: H 61 MET cc_start: 0.6301 (tpp) cc_final: 0.6060 (tpp) REVERT: H 68 MET cc_start: 0.6929 (mmm) cc_final: 0.5200 (ttp) REVERT: H 93 HIS cc_start: 0.7026 (m170) cc_final: 0.6259 (m-70) REVERT: H 110 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8775 (m) REVERT: H 127 TYR cc_start: 0.6517 (m-80) cc_final: 0.6229 (m-80) REVERT: H 183 MET cc_start: 0.8710 (mtm) cc_final: 0.8414 (mtp) REVERT: H 215 TYR cc_start: 0.8588 (m-10) cc_final: 0.8152 (m-10) REVERT: I 36 TYR cc_start: 0.8774 (p90) cc_final: 0.7583 (p90) REVERT: I 50 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6915 (pmm) REVERT: I 62 MET cc_start: 0.6921 (tmm) cc_final: 0.6385 (tmm) REVERT: I 76 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8081 (t80) REVERT: I 181 GLU cc_start: 0.8625 (mp0) cc_final: 0.8062 (pm20) REVERT: I 188 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: I 193 ASN cc_start: 0.8732 (m-40) cc_final: 0.8337 (m-40) REVERT: I 208 ASP cc_start: 0.8769 (t0) cc_final: 0.7968 (t70) REVERT: P 291 TYR cc_start: 0.8885 (p90) cc_final: 0.8573 (p90) REVERT: P 316 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7784 (tptm) REVERT: P 341 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8640 (mm-40) REVERT: Q 60 ASP cc_start: 0.8525 (t0) cc_final: 0.8005 (m-30) REVERT: Q 93 ASN cc_start: 0.8801 (m-40) cc_final: 0.8485 (m110) REVERT: Q 139 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7362 (mt-10) REVERT: R 52 GLN cc_start: 0.8097 (tm-30) cc_final: 0.6729 (pp30) REVERT: R 54 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7679 (mt-10) REVERT: R 75 ARG cc_start: 0.8271 (mtp-110) cc_final: 0.7678 (mtp180) REVERT: R 96 ASP cc_start: 0.8006 (t0) cc_final: 0.7341 (t0) REVERT: T 84 LEU cc_start: 0.8841 (pp) cc_final: 0.8286 (mp) REVERT: T 125 GLU cc_start: 0.8672 (tp30) cc_final: 0.8244 (tm-30) REVERT: V 44 TYR cc_start: 0.8645 (t80) cc_final: 0.8425 (t80) REVERT: V 59 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8765 (p) REVERT: W 19 SER cc_start: 0.8546 (m) cc_final: 0.8182 (p) REVERT: W 30 GLU cc_start: 0.8465 (mp0) cc_final: 0.8243 (mp0) REVERT: W 93 LEU cc_start: 0.9044 (tt) cc_final: 0.8766 (tt) REVERT: X 44 MET cc_start: 0.9072 (tpp) cc_final: 0.8837 (mmm) REVERT: X 101 ARG cc_start: 0.8045 (mmt90) cc_final: 0.7596 (mmt180) REVERT: Z 51 MET cc_start: 0.8679 (tmm) cc_final: 0.8284 (tmm) REVERT: Z 132 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7274 (pt0) REVERT: a 2 TRP cc_start: 0.8336 (p-90) cc_final: 0.7866 (p-90) REVERT: a 35 GLU cc_start: 0.6877 (tt0) cc_final: 0.6600 (tt0) REVERT: a 48 MET cc_start: 0.8319 (ttm) cc_final: 0.8068 (ttp) REVERT: a 61 TYR cc_start: 0.6697 (m-80) cc_final: 0.6288 (m-80) REVERT: b 32 MET cc_start: 0.9021 (mmm) cc_final: 0.8685 (mmm) REVERT: q 12 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8715 (mp10) REVERT: q 13 GLN cc_start: 0.7576 (mm-40) cc_final: 0.6754 (mm-40) REVERT: q 41 GLU cc_start: 0.8445 (tt0) cc_final: 0.8072 (tp30) REVERT: q 49 TYR cc_start: 0.8521 (m-80) cc_final: 0.8305 (m-80) REVERT: q 51 ASP cc_start: 0.8289 (t0) cc_final: 0.7968 (t0) REVERT: q 96 ASP cc_start: 0.8697 (t0) cc_final: 0.8003 (t0) REVERT: q 133 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8598 (mmtp) REVERT: r 11 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8237 (tt) REVERT: r 18 GLN cc_start: 0.9134 (mp10) cc_final: 0.8718 (mp10) REVERT: r 30 GLU cc_start: 0.7208 (pt0) cc_final: 0.6725 (pm20) REVERT: r 57 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6797 (ptt90) REVERT: r 105 GLU cc_start: 0.7515 (mp0) cc_final: 0.7091 (mp0) REVERT: r 109 ASP cc_start: 0.8112 (p0) cc_final: 0.7628 (p0) REVERT: r 110 GLN cc_start: 0.9158 (tt0) cc_final: 0.8863 (tt0) REVERT: r 112 TYR cc_start: 0.8095 (m-80) cc_final: 0.7727 (m-80) REVERT: s 40 TYR cc_start: 0.6894 (m-80) cc_final: 0.6556 (m-80) REVERT: s 44 THR cc_start: 0.8688 (m) cc_final: 0.8293 (p) outliers start: 142 outliers final: 90 residues processed: 924 average time/residue: 0.2074 time to fit residues: 319.5879 Evaluate side-chains 888 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 784 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 455 GLN Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 654 VAL Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 345 LEU Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 117 GLU Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 113 THR Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 129 THR Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 277 optimal weight: 0.7980 chunk 361 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN G 569 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 HIS P 238 GLN Q 51 GLN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 135 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077898 restraints weight = 105083.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080264 restraints weight = 48160.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081825 restraints weight = 28486.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.082795 restraints weight = 19140.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083547 restraints weight = 14658.032| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35541 Z= 0.175 Angle : 0.932 78.179 48210 Z= 0.357 Chirality : 0.045 0.307 5254 Planarity : 0.005 0.166 6117 Dihedral : 8.306 168.695 4995 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.69 % Allowed : 22.86 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % 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: -0.17 (0.13), residues: 4234 helix: 0.87 (0.12), residues: 1885 sheet: -1.09 (0.26), residues: 392 loop : -0.82 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 61 TYR 0.035 0.002 TYR V 44 PHE 0.026 0.002 PHE E 242 TRP 0.032 0.001 TRP I 197 HIS 0.007 0.001 HIS S 48 Details of bonding type rmsd covalent geometry : bond 0.00411 (35501) covalent geometry : angle 0.71022 (48120) SS BOND : bond 0.00542 ( 3) SS BOND : angle 1.94993 ( 6) hydrogen bonds : bond 0.04078 ( 1449) hydrogen bonds : angle 5.12747 ( 4155) metal coordination : bond 0.01945 ( 37) metal coordination : angle 14.47329 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 806 time to evaluate : 1.364 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: A 22 PHE cc_start: 0.9138 (m-80) cc_final: 0.8911 (m-80) REVERT: A 27 MET cc_start: 0.7249 (mtm) cc_final: 0.6976 (mpp) REVERT: A 90 MET cc_start: 0.7954 (mmm) cc_final: 0.7737 (mmt) REVERT: B 113 ASP cc_start: 0.8465 (t0) cc_final: 0.7950 (t70) REVERT: B 141 MET cc_start: 0.9279 (mmm) cc_final: 0.8476 (tpp) REVERT: B 151 GLN cc_start: 0.8437 (mt0) cc_final: 0.7615 (mp10) REVERT: B 161 MET cc_start: 0.8429 (ttt) cc_final: 0.7878 (ttt) REVERT: B 188 ASP cc_start: 0.8396 (m-30) cc_final: 0.7868 (m-30) REVERT: B 199 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: B 201 LEU cc_start: 0.9238 (tp) cc_final: 0.8917 (tp) REVERT: C 112 ASP cc_start: 0.8106 (t0) cc_final: 0.7750 (t0) REVERT: C 199 LYS cc_start: 0.9237 (tppt) cc_final: 0.8991 (mmtp) REVERT: D 270 ASN cc_start: 0.9141 (m-40) cc_final: 0.8886 (m110) REVERT: D 333 ARG cc_start: 0.8030 (mtt90) cc_final: 0.7745 (mtt90) REVERT: D 406 GLU cc_start: 0.8230 (tt0) cc_final: 0.8008 (tt0) REVERT: D 455 ASP cc_start: 0.6969 (m-30) cc_final: 0.6512 (m-30) REVERT: E 47 ASN cc_start: 0.7981 (p0) cc_final: 0.7721 (p0) REVERT: E 140 MET cc_start: 0.8206 (ppp) cc_final: 0.7921 (ppp) REVERT: E 192 TYR cc_start: 0.8608 (m-80) cc_final: 0.7967 (m-80) REVERT: F 135 PRO cc_start: 0.8957 (Cg_endo) cc_final: 0.8667 (Cg_exo) REVERT: F 161 GLU cc_start: 0.8893 (mp0) cc_final: 0.8683 (mp0) REVERT: F 246 GLU cc_start: 0.8156 (tt0) cc_final: 0.7952 (tm-30) REVERT: F 433 TRP cc_start: 0.8606 (m-10) cc_final: 0.8261 (m-10) REVERT: F 450 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8416 (mtp) REVERT: G 42 MET cc_start: 0.8940 (tpp) cc_final: 0.8703 (mmm) REVERT: G 117 MET cc_start: 0.8231 (mmm) cc_final: 0.7363 (mmm) REVERT: G 215 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7331 (mmt) REVERT: G 329 MET cc_start: 0.8922 (tpp) cc_final: 0.8074 (mmm) REVERT: G 530 TYR cc_start: 0.8834 (m-80) cc_final: 0.8485 (m-80) REVERT: G 590 THR cc_start: 0.9371 (p) cc_final: 0.9096 (t) REVERT: G 618 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7517 (mt-10) REVERT: H 33 LEU cc_start: 0.8725 (mp) cc_final: 0.7978 (mt) REVERT: H 34 ARG cc_start: 0.8688 (ptt-90) cc_final: 0.8294 (ptt-90) REVERT: H 35 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8459 (mmtt) REVERT: H 47 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8326 (tm-30) REVERT: H 68 MET cc_start: 0.6938 (mmm) cc_final: 0.5365 (ttp) REVERT: H 93 HIS cc_start: 0.7042 (m170) cc_final: 0.6236 (m-70) REVERT: H 110 SER cc_start: 0.9203 (OUTLIER) cc_final: 0.8839 (m) REVERT: H 127 TYR cc_start: 0.6638 (m-80) cc_final: 0.6331 (m-80) REVERT: H 138 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7728 (tm-30) REVERT: H 155 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9027 (tt) REVERT: H 174 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8230 (mm) REVERT: H 195 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7602 (mmm-85) REVERT: H 215 TYR cc_start: 0.8664 (m-10) cc_final: 0.8018 (m-10) REVERT: H 260 MET cc_start: 0.8153 (tmm) cc_final: 0.7943 (tmm) REVERT: I 36 TYR cc_start: 0.8780 (p90) cc_final: 0.7577 (p90) REVERT: I 50 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6715 (pmm) REVERT: I 62 MET cc_start: 0.7051 (tmm) cc_final: 0.6362 (tmm) REVERT: I 76 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8126 (t80) REVERT: I 88 PHE cc_start: 0.8556 (m-80) cc_final: 0.8186 (m-80) REVERT: I 188 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: I 208 ASP cc_start: 0.8791 (t0) cc_final: 0.8029 (t70) REVERT: P 291 TYR cc_start: 0.8926 (p90) cc_final: 0.8627 (p90) REVERT: P 316 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7877 (tptm) REVERT: P 341 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8683 (mm-40) REVERT: Q 60 ASP cc_start: 0.8492 (t0) cc_final: 0.8070 (m-30) REVERT: Q 78 ARG cc_start: 0.8537 (mtm180) cc_final: 0.8266 (mtp180) REVERT: Q 93 ASN cc_start: 0.8852 (m-40) cc_final: 0.8533 (m110) REVERT: Q 139 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7404 (mt-10) REVERT: R 52 GLN cc_start: 0.8085 (tm-30) cc_final: 0.6879 (pp30) REVERT: R 75 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.7641 (mtp180) REVERT: R 96 ASP cc_start: 0.8046 (t0) cc_final: 0.7440 (t0) REVERT: T 84 LEU cc_start: 0.8853 (pp) cc_final: 0.8297 (mp) REVERT: T 125 GLU cc_start: 0.8800 (tp30) cc_final: 0.8308 (tm-30) REVERT: T 137 LYS cc_start: 0.8794 (pttm) cc_final: 0.8328 (pttm) REVERT: T 138 LEU cc_start: 0.8594 (pp) cc_final: 0.8281 (pp) REVERT: T 139 MET cc_start: 0.7899 (mmp) cc_final: 0.7149 (mmm) REVERT: T 143 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7227 (pt0) REVERT: W 19 SER cc_start: 0.8558 (m) cc_final: 0.8143 (p) REVERT: W 30 GLU cc_start: 0.8527 (mp0) cc_final: 0.8287 (mp0) REVERT: W 45 GLU cc_start: 0.8586 (tp30) cc_final: 0.7788 (tp30) REVERT: W 93 LEU cc_start: 0.9029 (tt) cc_final: 0.8770 (tt) REVERT: X 44 MET cc_start: 0.9011 (tpp) cc_final: 0.8748 (mmm) REVERT: X 101 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7613 (mmt180) REVERT: Z 9 ASP cc_start: 0.6116 (t0) cc_final: 0.5540 (m-30) REVERT: Z 35 MET cc_start: 0.8162 (tpt) cc_final: 0.7861 (ttp) REVERT: Z 51 MET cc_start: 0.8682 (tmm) cc_final: 0.8259 (tmm) REVERT: Z 132 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7516 (mt-10) REVERT: Z 133 MET cc_start: 0.7432 (tmm) cc_final: 0.7097 (tmm) REVERT: a 2 TRP cc_start: 0.8399 (p-90) cc_final: 0.7956 (p-90) REVERT: a 35 GLU cc_start: 0.7052 (tt0) cc_final: 0.6704 (tt0) REVERT: a 61 TYR cc_start: 0.6840 (m-80) cc_final: 0.6416 (m-80) REVERT: b 30 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (mt) REVERT: b 32 MET cc_start: 0.9161 (mmm) cc_final: 0.8520 (mmm) REVERT: q 8 LYS cc_start: 0.9226 (tmmt) cc_final: 0.8948 (tmmt) REVERT: q 13 GLN cc_start: 0.7604 (mm-40) cc_final: 0.6727 (mm-40) REVERT: q 49 TYR cc_start: 0.8588 (m-80) cc_final: 0.8339 (m-80) REVERT: q 51 ASP cc_start: 0.8305 (t0) cc_final: 0.8021 (t0) REVERT: q 96 ASP cc_start: 0.8755 (t0) cc_final: 0.8149 (t0) REVERT: q 133 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8570 (mmtp) REVERT: r 18 GLN cc_start: 0.9043 (mp10) cc_final: 0.8478 (mp10) REVERT: r 30 GLU cc_start: 0.7189 (pt0) cc_final: 0.6871 (pm20) REVERT: r 57 ARG cc_start: 0.7256 (ttp-110) cc_final: 0.6917 (ptt90) REVERT: r 109 ASP cc_start: 0.8136 (p0) cc_final: 0.7695 (p0) REVERT: r 110 GLN cc_start: 0.9161 (tt0) cc_final: 0.8894 (tt0) REVERT: r 112 TYR cc_start: 0.8232 (m-80) cc_final: 0.7855 (m-80) REVERT: s 44 THR cc_start: 0.8702 (m) cc_final: 0.8092 (p) outliers start: 137 outliers final: 97 residues processed: 881 average time/residue: 0.2021 time to fit residues: 297.4527 Evaluate side-chains 873 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 765 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 357 MET Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 455 GLN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain G residue 659 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 122 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 33 HIS Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain q residue 95 ASP Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 245 optimal weight: 0.0030 chunk 299 optimal weight: 0.3980 chunk 252 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 342 optimal weight: 0.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN P 71 ASN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.079704 restraints weight = 104029.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082139 restraints weight = 47361.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083637 restraints weight = 27322.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084774 restraints weight = 18598.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085536 restraints weight = 13839.173| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 35541 Z= 0.138 Angle : 0.909 76.704 48210 Z= 0.344 Chirality : 0.044 0.315 5254 Planarity : 0.005 0.166 6117 Dihedral : 8.152 169.934 4995 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.02 % Allowed : 23.64 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4234 helix: 0.89 (0.12), residues: 1871 sheet: -1.08 (0.27), residues: 390 loop : -0.80 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 61 TYR 0.021 0.002 TYR H 282 PHE 0.043 0.002 PHE A 62 TRP 0.026 0.001 TRP D 202 HIS 0.006 0.001 HIS P 323 Details of bonding type rmsd covalent geometry : bond 0.00321 (35501) covalent geometry : angle 0.69054 (48120) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.81976 ( 6) hydrogen bonds : bond 0.03912 ( 1449) hydrogen bonds : angle 5.09401 ( 4155) metal coordination : bond 0.01255 ( 37) metal coordination : angle 14.15713 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 832 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.9037 (m) cc_final: 0.8748 (t) REVERT: A 22 PHE cc_start: 0.9136 (m-80) cc_final: 0.8906 (m-80) REVERT: B 141 MET cc_start: 0.9244 (mmm) cc_final: 0.8549 (tpp) REVERT: B 151 GLN cc_start: 0.8461 (mt0) cc_final: 0.7578 (mp10) REVERT: B 161 MET cc_start: 0.8335 (ttt) cc_final: 0.7777 (ttt) REVERT: B 188 ASP cc_start: 0.8322 (m-30) cc_final: 0.7822 (m-30) REVERT: B 199 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: B 201 LEU cc_start: 0.9169 (tp) cc_final: 0.8857 (tp) REVERT: C 112 ASP cc_start: 0.8100 (t0) cc_final: 0.7835 (t0) REVERT: C 114 THR cc_start: 0.8487 (m) cc_final: 0.8211 (m) REVERT: C 199 LYS cc_start: 0.9252 (tppt) cc_final: 0.9017 (mmtp) REVERT: C 221 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8432 (mm-30) REVERT: D 105 MET cc_start: 0.7222 (mmp) cc_final: 0.6992 (mmp) REVERT: D 197 MET cc_start: 0.8085 (mtp) cc_final: 0.7879 (mtp) REVERT: D 270 ASN cc_start: 0.9105 (m-40) cc_final: 0.8831 (m110) REVERT: D 326 CYS cc_start: 0.8725 (m) cc_final: 0.8399 (m) REVERT: D 333 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7674 (mtt180) REVERT: D 406 GLU cc_start: 0.8264 (tt0) cc_final: 0.8047 (tt0) REVERT: E 47 ASN cc_start: 0.7948 (p0) cc_final: 0.7688 (p0) REVERT: E 140 MET cc_start: 0.8126 (ppp) cc_final: 0.7815 (ppp) REVERT: E 143 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8864 (t70) REVERT: E 184 MET cc_start: 0.8488 (tmm) cc_final: 0.8083 (tmm) REVERT: E 192 TYR cc_start: 0.8528 (m-80) cc_final: 0.7922 (m-80) REVERT: F 135 PRO cc_start: 0.8943 (Cg_endo) cc_final: 0.8667 (Cg_exo) REVERT: F 433 TRP cc_start: 0.8576 (m-10) cc_final: 0.8375 (m-10) REVERT: F 450 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: G 329 MET cc_start: 0.8885 (tpp) cc_final: 0.8034 (mmm) REVERT: G 530 TYR cc_start: 0.8790 (m-80) cc_final: 0.8445 (m-80) REVERT: G 590 THR cc_start: 0.9335 (p) cc_final: 0.9092 (t) REVERT: G 618 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7480 (mt-10) REVERT: H 31 MET cc_start: 0.9199 (mtt) cc_final: 0.8909 (mtp) REVERT: H 33 LEU cc_start: 0.8652 (mp) cc_final: 0.7688 (mt) REVERT: H 34 ARG cc_start: 0.8636 (ptt-90) cc_final: 0.8168 (ptt-90) REVERT: H 35 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8353 (mmtt) REVERT: H 47 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8160 (tm-30) REVERT: H 61 MET cc_start: 0.6080 (tpp) cc_final: 0.5805 (tpp) REVERT: H 68 MET cc_start: 0.6721 (mmm) cc_final: 0.5408 (ttp) REVERT: H 110 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8802 (m) REVERT: H 127 TYR cc_start: 0.6583 (m-80) cc_final: 0.6073 (m-80) REVERT: H 138 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7642 (tm-30) REVERT: H 159 SER cc_start: 0.8514 (t) cc_final: 0.8024 (p) REVERT: H 215 TYR cc_start: 0.8436 (m-10) cc_final: 0.7956 (m-10) REVERT: H 260 MET cc_start: 0.8017 (tmm) cc_final: 0.7760 (tmm) REVERT: I 36 TYR cc_start: 0.8724 (p90) cc_final: 0.7552 (p90) REVERT: I 50 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6747 (pmm) REVERT: I 62 MET cc_start: 0.7075 (tmm) cc_final: 0.6621 (tmm) REVERT: I 76 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.8161 (t80) REVERT: I 78 PHE cc_start: 0.9241 (m-80) cc_final: 0.8944 (m-80) REVERT: I 88 PHE cc_start: 0.8508 (m-80) cc_final: 0.8131 (m-80) REVERT: I 188 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: I 193 ASN cc_start: 0.8771 (m-40) cc_final: 0.8484 (m-40) REVERT: I 208 ASP cc_start: 0.8744 (t0) cc_final: 0.7952 (t70) REVERT: P 291 TYR cc_start: 0.8890 (p90) cc_final: 0.8647 (p90) REVERT: P 316 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7812 (tptm) REVERT: P 341 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8724 (mm-40) REVERT: Q 57 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7116 (pp20) REVERT: Q 60 ASP cc_start: 0.8422 (t0) cc_final: 0.7835 (m-30) REVERT: Q 93 ASN cc_start: 0.8767 (m-40) cc_final: 0.8455 (m110) REVERT: Q 139 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7419 (mt-10) REVERT: R 52 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7247 (pp30) REVERT: R 75 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.7565 (mtp180) REVERT: R 96 ASP cc_start: 0.8014 (t0) cc_final: 0.7443 (t0) REVERT: S 75 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8637 (mttp) REVERT: T 84 LEU cc_start: 0.8863 (pp) cc_final: 0.8286 (mp) REVERT: T 110 LEU cc_start: 0.8056 (mt) cc_final: 0.7713 (mt) REVERT: T 122 MET cc_start: 0.8916 (mtp) cc_final: 0.7986 (mmm) REVERT: T 125 GLU cc_start: 0.8764 (tp30) cc_final: 0.8289 (tm-30) REVERT: T 139 MET cc_start: 0.7895 (mmp) cc_final: 0.7234 (mmm) REVERT: W 19 SER cc_start: 0.8567 (m) cc_final: 0.8149 (p) REVERT: W 30 GLU cc_start: 0.8529 (mp0) cc_final: 0.8267 (mp0) REVERT: W 45 GLU cc_start: 0.8563 (tp30) cc_final: 0.7656 (tp30) REVERT: W 48 ASN cc_start: 0.8853 (t0) cc_final: 0.8628 (t0) REVERT: W 93 LEU cc_start: 0.9007 (tt) cc_final: 0.8767 (tt) REVERT: X 42 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8020 (mt-10) REVERT: X 44 MET cc_start: 0.8964 (tpp) cc_final: 0.8728 (mmm) REVERT: X 86 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.7166 (t60) REVERT: X 101 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7655 (mmt180) REVERT: Z 9 ASP cc_start: 0.5795 (t0) cc_final: 0.5389 (m-30) REVERT: Z 35 MET cc_start: 0.8251 (tpt) cc_final: 0.7882 (ttp) REVERT: Z 51 MET cc_start: 0.8621 (tmm) cc_final: 0.8231 (tmm) REVERT: Z 132 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7633 (mt-10) REVERT: Z 133 MET cc_start: 0.7461 (tmm) cc_final: 0.7012 (tmm) REVERT: a 35 GLU cc_start: 0.7072 (tt0) cc_final: 0.6780 (tt0) REVERT: a 48 MET cc_start: 0.8202 (ttp) cc_final: 0.7957 (ttp) REVERT: a 61 TYR cc_start: 0.6745 (m-80) cc_final: 0.6528 (m-80) REVERT: b 30 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7604 (mt) REVERT: b 32 MET cc_start: 0.9125 (mmm) cc_final: 0.8496 (mmm) REVERT: b 81 LEU cc_start: 0.8017 (tt) cc_final: 0.7780 (tp) REVERT: q 8 LYS cc_start: 0.9236 (tmmt) cc_final: 0.8976 (tmmt) REVERT: q 13 GLN cc_start: 0.7577 (mm-40) cc_final: 0.6736 (mm-40) REVERT: q 41 GLU cc_start: 0.8460 (tt0) cc_final: 0.8152 (tp30) REVERT: q 51 ASP cc_start: 0.8349 (t0) cc_final: 0.8073 (t0) REVERT: q 96 ASP cc_start: 0.8650 (t0) cc_final: 0.8130 (t0) REVERT: q 133 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8589 (mmtp) REVERT: r 18 GLN cc_start: 0.8910 (mp10) cc_final: 0.8548 (mp10) REVERT: r 57 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.7102 (ptt90) REVERT: r 62 GLU cc_start: 0.5724 (mm-30) cc_final: 0.5499 (mm-30) REVERT: r 109 ASP cc_start: 0.8107 (p0) cc_final: 0.7655 (p0) REVERT: r 110 GLN cc_start: 0.9187 (tt0) cc_final: 0.8918 (tt0) REVERT: r 112 TYR cc_start: 0.8234 (m-80) cc_final: 0.7855 (m-80) REVERT: s 44 THR cc_start: 0.8774 (m) cc_final: 0.8207 (p) outliers start: 112 outliers final: 83 residues processed: 896 average time/residue: 0.2076 time to fit residues: 309.2959 Evaluate side-chains 867 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 773 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 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 431 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain G residue 619 ASP Chi-restraints excluded: chain G residue 627 SER Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 86 TRP Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 47 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 374 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 371 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN Q 51 GLN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN q 87 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.091844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079550 restraints weight = 104149.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082002 restraints weight = 47936.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083521 restraints weight = 27871.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084619 restraints weight = 19023.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085374 restraints weight = 14308.462| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 35541 Z= 0.146 Angle : 0.929 77.077 48210 Z= 0.356 Chirality : 0.045 0.299 5254 Planarity : 0.005 0.150 6117 Dihedral : 8.096 171.443 4995 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 23.86 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 4234 helix: 0.88 (0.12), residues: 1880 sheet: -1.07 (0.27), residues: 373 loop : -0.79 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 61 TYR 0.027 0.002 TYR B 112 PHE 0.043 0.002 PHE A 62 TRP 0.029 0.001 TRP D 202 HIS 0.006 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00347 (35501) covalent geometry : angle 0.71683 (48120) SS BOND : bond 0.00193 ( 3) SS BOND : angle 2.48939 ( 6) hydrogen bonds : bond 0.03890 ( 1449) hydrogen bonds : angle 5.07879 ( 4155) metal coordination : bond 0.01358 ( 37) metal coordination : angle 14.15519 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 818 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.9040 (m) cc_final: 0.8752 (t) REVERT: A 22 PHE cc_start: 0.9127 (m-80) cc_final: 0.8911 (m-80) REVERT: A 27 MET cc_start: 0.6957 (mpp) cc_final: 0.6712 (mpp) REVERT: B 113 ASP cc_start: 0.8448 (t0) cc_final: 0.8077 (t0) REVERT: B 141 MET cc_start: 0.9247 (mmm) cc_final: 0.8529 (tpp) REVERT: B 151 GLN cc_start: 0.8449 (mt0) cc_final: 0.7577 (mp10) REVERT: B 152 MET cc_start: 0.9019 (tpp) cc_final: 0.8715 (tpp) REVERT: B 161 MET cc_start: 0.8363 (ttt) cc_final: 0.7802 (ttt) REVERT: B 188 ASP cc_start: 0.8332 (m-30) cc_final: 0.7802 (m-30) REVERT: B 199 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: B 201 LEU cc_start: 0.9149 (tp) cc_final: 0.8839 (tp) REVERT: C 76 GLN cc_start: 0.8389 (pt0) cc_final: 0.8050 (pt0) REVERT: C 112 ASP cc_start: 0.8093 (t0) cc_final: 0.7854 (t0) REVERT: C 114 THR cc_start: 0.8487 (m) cc_final: 0.8235 (m) REVERT: C 199 LYS cc_start: 0.9236 (tppt) cc_final: 0.8999 (mmtp) REVERT: C 239 GLU cc_start: 0.7729 (tp30) cc_final: 0.7483 (tt0) REVERT: D 105 MET cc_start: 0.7143 (mmp) cc_final: 0.6921 (mmp) REVERT: D 197 MET cc_start: 0.8063 (mtp) cc_final: 0.7849 (mtp) REVERT: D 214 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: D 270 ASN cc_start: 0.9137 (m-40) cc_final: 0.8891 (m110) REVERT: D 326 CYS cc_start: 0.8733 (m) cc_final: 0.8414 (m) REVERT: D 371 MET cc_start: 0.8915 (ttp) cc_final: 0.8664 (ttp) REVERT: D 455 ASP cc_start: 0.7041 (m-30) cc_final: 0.6568 (m-30) REVERT: E 47 ASN cc_start: 0.7917 (p0) cc_final: 0.7606 (p0) REVERT: E 140 MET cc_start: 0.8097 (ppp) cc_final: 0.7763 (ppp) REVERT: E 143 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8878 (t70) REVERT: E 192 TYR cc_start: 0.8505 (m-80) cc_final: 0.7841 (m-80) REVERT: F 135 PRO cc_start: 0.8911 (Cg_endo) cc_final: 0.8652 (Cg_exo) REVERT: F 429 ASP cc_start: 0.8496 (t0) cc_final: 0.7777 (t0) REVERT: F 433 TRP cc_start: 0.8581 (m-10) cc_final: 0.8318 (m-10) REVERT: F 450 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8357 (mtp) REVERT: G 117 MET cc_start: 0.8139 (mmm) cc_final: 0.7119 (mmm) REVERT: G 213 MET cc_start: 0.7862 (ptm) cc_final: 0.7658 (ppp) REVERT: G 269 GLU cc_start: 0.8438 (pm20) cc_final: 0.7593 (pm20) REVERT: G 329 MET cc_start: 0.8884 (tpp) cc_final: 0.8027 (mmm) REVERT: G 390 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8050 (p) REVERT: G 530 TYR cc_start: 0.8811 (m-80) cc_final: 0.8411 (m-80) REVERT: G 590 THR cc_start: 0.9412 (p) cc_final: 0.9097 (t) REVERT: G 618 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7480 (mt-10) REVERT: G 680 LEU cc_start: 0.7719 (tt) cc_final: 0.7079 (mp) REVERT: H 31 MET cc_start: 0.9165 (mtt) cc_final: 0.8912 (mtp) REVERT: H 33 LEU cc_start: 0.8750 (mp) cc_final: 0.7666 (mt) REVERT: H 34 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8220 (ptt-90) REVERT: H 35 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8312 (mmtt) REVERT: H 47 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8225 (tm-30) REVERT: H 61 MET cc_start: 0.6048 (tpp) cc_final: 0.5758 (tpp) REVERT: H 68 MET cc_start: 0.6735 (mmm) cc_final: 0.5556 (ttp) REVERT: H 110 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8811 (m) REVERT: H 127 TYR cc_start: 0.6552 (m-80) cc_final: 0.6343 (m-80) REVERT: H 138 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 195 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7661 (mmm-85) REVERT: H 215 TYR cc_start: 0.8459 (m-10) cc_final: 0.7907 (m-10) REVERT: H 225 MET cc_start: 0.8313 (mtt) cc_final: 0.7897 (mtt) REVERT: H 260 MET cc_start: 0.8006 (tmm) cc_final: 0.7718 (tmm) REVERT: H 287 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7979 (m-70) REVERT: I 36 TYR cc_start: 0.8724 (p90) cc_final: 0.7561 (p90) REVERT: I 50 MET cc_start: 0.7238 (ppp) cc_final: 0.6853 (pmm) REVERT: I 62 MET cc_start: 0.6975 (tmm) cc_final: 0.6148 (tmm) REVERT: I 76 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8164 (t80) REVERT: I 88 PHE cc_start: 0.8505 (m-80) cc_final: 0.8118 (m-80) REVERT: I 98 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7256 (mtt-85) REVERT: I 145 TYR cc_start: 0.8548 (t80) cc_final: 0.8118 (t80) REVERT: I 181 GLU cc_start: 0.8502 (mp0) cc_final: 0.8031 (pm20) REVERT: I 188 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7722 (tp30) REVERT: I 193 ASN cc_start: 0.8761 (m-40) cc_final: 0.8465 (m-40) REVERT: I 208 ASP cc_start: 0.8747 (t0) cc_final: 0.7971 (t70) REVERT: P 216 HIS cc_start: 0.7956 (t-90) cc_final: 0.7596 (t70) REVERT: P 316 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7754 (tptm) REVERT: P 336 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7781 (tm-30) REVERT: Q 57 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7135 (pp20) REVERT: Q 60 ASP cc_start: 0.8407 (t0) cc_final: 0.7790 (m-30) REVERT: Q 93 ASN cc_start: 0.8783 (m-40) cc_final: 0.8472 (m110) REVERT: Q 139 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7460 (mt-10) REVERT: R 52 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7295 (pp30) REVERT: R 75 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7562 (mtp180) REVERT: R 96 ASP cc_start: 0.8044 (t0) cc_final: 0.7475 (t0) REVERT: S 75 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8644 (mttp) REVERT: T 77 ASP cc_start: 0.8258 (t0) cc_final: 0.7880 (p0) REVERT: T 110 LEU cc_start: 0.7968 (mt) cc_final: 0.7650 (mt) REVERT: T 122 MET cc_start: 0.8892 (mtp) cc_final: 0.8219 (mmm) REVERT: T 125 GLU cc_start: 0.8754 (tp30) cc_final: 0.8406 (tm-30) REVERT: T 139 MET cc_start: 0.7889 (mmp) cc_final: 0.6717 (mmm) REVERT: T 143 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7267 (pt0) REVERT: W 19 SER cc_start: 0.8585 (m) cc_final: 0.8178 (p) REVERT: W 30 GLU cc_start: 0.8543 (mp0) cc_final: 0.8246 (mp0) REVERT: W 93 LEU cc_start: 0.8991 (tt) cc_final: 0.8755 (tt) REVERT: X 42 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8059 (mt-10) REVERT: X 44 MET cc_start: 0.8966 (tpp) cc_final: 0.8717 (mmm) REVERT: X 101 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7737 (mmt180) REVERT: Z 9 ASP cc_start: 0.5626 (t0) cc_final: 0.5205 (m-30) REVERT: Z 35 MET cc_start: 0.8287 (tpt) cc_final: 0.7830 (ttp) REVERT: Z 51 MET cc_start: 0.8614 (tmm) cc_final: 0.8218 (tmm) REVERT: Z 123 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: Z 132 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7658 (mt-10) REVERT: Z 133 MET cc_start: 0.7504 (tmm) cc_final: 0.7019 (tmm) REVERT: a 2 TRP cc_start: 0.8378 (p-90) cc_final: 0.7797 (p-90) REVERT: a 48 MET cc_start: 0.8244 (ttp) cc_final: 0.7986 (ttp) REVERT: a 61 TYR cc_start: 0.6862 (m-80) cc_final: 0.6429 (m-80) REVERT: a 62 VAL cc_start: 0.7405 (t) cc_final: 0.7205 (p) REVERT: b 30 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7690 (mt) REVERT: b 32 MET cc_start: 0.9132 (mmm) cc_final: 0.8909 (mmt) REVERT: q 8 LYS cc_start: 0.9248 (tmmt) cc_final: 0.8985 (tmmt) REVERT: q 13 GLN cc_start: 0.7589 (mm-40) cc_final: 0.6745 (mm-40) REVERT: q 41 GLU cc_start: 0.8412 (tt0) cc_final: 0.8156 (tp30) REVERT: q 51 ASP cc_start: 0.8377 (t0) cc_final: 0.8112 (t0) REVERT: q 67 GLU cc_start: 0.7297 (tp30) cc_final: 0.6824 (tp30) REVERT: q 96 ASP cc_start: 0.8680 (t0) cc_final: 0.8219 (t0) REVERT: q 133 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8585 (mmtp) REVERT: r 18 GLN cc_start: 0.9037 (mp10) cc_final: 0.8664 (mp10) REVERT: r 57 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7188 (ptt90) REVERT: r 62 GLU cc_start: 0.5692 (mm-30) cc_final: 0.5424 (mm-30) REVERT: r 105 GLU cc_start: 0.7486 (mp0) cc_final: 0.7029 (mp0) REVERT: r 109 ASP cc_start: 0.8111 (p0) cc_final: 0.7647 (p0) REVERT: r 110 GLN cc_start: 0.9217 (tt0) cc_final: 0.8995 (tt0) REVERT: r 112 TYR cc_start: 0.8238 (m-80) cc_final: 0.7878 (m-80) REVERT: s 44 THR cc_start: 0.8792 (m) cc_final: 0.8384 (p) REVERT: s 49 ASN cc_start: 0.9144 (t0) cc_final: 0.8746 (t0) outliers start: 116 outliers final: 81 residues processed: 891 average time/residue: 0.2017 time to fit residues: 301.6182 Evaluate side-chains 875 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 780 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 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 431 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 172 ASN Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain Z residue 31 SER Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 123 GLU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 360 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 311 optimal weight: 6.9990 chunk 268 optimal weight: 0.6980 chunk 341 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079861 restraints weight = 104513.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082260 restraints weight = 47553.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083783 restraints weight = 27565.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084874 restraints weight = 18720.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085664 restraints weight = 13985.451| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35541 Z= 0.145 Angle : 0.926 76.694 48210 Z= 0.358 Chirality : 0.044 0.273 5254 Planarity : 0.005 0.146 6117 Dihedral : 8.085 172.929 4995 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.91 % Allowed : 24.10 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 4234 helix: 0.89 (0.12), residues: 1871 sheet: -1.08 (0.27), residues: 372 loop : -0.77 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 57 TYR 0.045 0.002 TYR V 44 PHE 0.050 0.002 PHE A 62 TRP 0.037 0.001 TRP I 197 HIS 0.006 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00344 (35501) covalent geometry : angle 0.71935 (48120) SS BOND : bond 0.00199 ( 3) SS BOND : angle 2.61706 ( 6) hydrogen bonds : bond 0.03846 ( 1449) hydrogen bonds : angle 5.12181 ( 4155) metal coordination : bond 0.01325 ( 37) metal coordination : angle 13.98447 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 814 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.9050 (m) cc_final: 0.8761 (t) REVERT: A 22 PHE cc_start: 0.9107 (m-80) cc_final: 0.8894 (m-80) REVERT: A 27 MET cc_start: 0.6959 (mpp) cc_final: 0.6723 (mpp) REVERT: A 55 PHE cc_start: 0.7268 (m-80) cc_final: 0.7007 (m-80) REVERT: B 129 ASP cc_start: 0.8831 (m-30) cc_final: 0.8520 (m-30) REVERT: B 141 MET cc_start: 0.9262 (mmm) cc_final: 0.8526 (tpp) REVERT: B 151 GLN cc_start: 0.8466 (mt0) cc_final: 0.7569 (mp10) REVERT: B 152 MET cc_start: 0.8990 (tpp) cc_final: 0.8689 (tpp) REVERT: B 161 MET cc_start: 0.8363 (ttt) cc_final: 0.7749 (ttt) REVERT: B 188 ASP cc_start: 0.8362 (m-30) cc_final: 0.7861 (m-30) REVERT: B 199 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: B 201 LEU cc_start: 0.9123 (tp) cc_final: 0.8769 (tp) REVERT: C 76 GLN cc_start: 0.8379 (pt0) cc_final: 0.8037 (pt0) REVERT: C 112 ASP cc_start: 0.8157 (t0) cc_final: 0.7922 (t0) REVERT: C 114 THR cc_start: 0.8462 (m) cc_final: 0.8250 (m) REVERT: C 199 LYS cc_start: 0.9222 (tppt) cc_final: 0.8808 (mmtp) REVERT: D 105 MET cc_start: 0.7173 (mmp) cc_final: 0.6973 (mmp) REVERT: D 197 MET cc_start: 0.8062 (mtp) cc_final: 0.7844 (mtp) REVERT: D 214 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: D 270 ASN cc_start: 0.9122 (m-40) cc_final: 0.8889 (m110) REVERT: D 292 MET cc_start: 0.8915 (mmm) cc_final: 0.8640 (tpp) REVERT: D 326 CYS cc_start: 0.8742 (m) cc_final: 0.8467 (m) REVERT: D 371 MET cc_start: 0.8933 (ttp) cc_final: 0.8688 (ttp) REVERT: E 47 ASN cc_start: 0.7916 (p0) cc_final: 0.7715 (p0) REVERT: E 59 TYR cc_start: 0.8700 (m-80) cc_final: 0.8395 (m-80) REVERT: E 83 ASP cc_start: 0.8555 (t0) cc_final: 0.8245 (t0) REVERT: E 140 MET cc_start: 0.8069 (ppp) cc_final: 0.7738 (ppp) REVERT: E 143 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8905 (t70) REVERT: E 192 TYR cc_start: 0.8461 (m-80) cc_final: 0.7809 (m-80) REVERT: F 126 LYS cc_start: 0.8383 (pttp) cc_final: 0.7651 (ptmt) REVERT: F 135 PRO cc_start: 0.8882 (Cg_endo) cc_final: 0.8615 (Cg_exo) REVERT: F 429 ASP cc_start: 0.8454 (t0) cc_final: 0.7745 (t0) REVERT: F 433 TRP cc_start: 0.8577 (m-10) cc_final: 0.8309 (m-10) REVERT: F 450 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8335 (mtp) REVERT: G 117 MET cc_start: 0.8191 (mmm) cc_final: 0.7243 (mmm) REVERT: G 161 GLU cc_start: 0.7821 (tp30) cc_final: 0.7282 (tp30) REVERT: G 213 MET cc_start: 0.7881 (ptm) cc_final: 0.7204 (ppp) REVERT: G 215 MET cc_start: 0.7891 (mmt) cc_final: 0.7160 (mmt) REVERT: G 269 GLU cc_start: 0.8420 (pm20) cc_final: 0.7613 (pm20) REVERT: G 329 MET cc_start: 0.8898 (tpp) cc_final: 0.8051 (mmm) REVERT: G 390 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8099 (p) REVERT: G 530 TYR cc_start: 0.8798 (m-80) cc_final: 0.8396 (m-80) REVERT: G 590 THR cc_start: 0.9317 (p) cc_final: 0.9033 (t) REVERT: G 618 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7473 (mt-10) REVERT: G 680 LEU cc_start: 0.7712 (tt) cc_final: 0.7085 (mp) REVERT: H 31 MET cc_start: 0.9166 (mtt) cc_final: 0.8931 (mtp) REVERT: H 34 ARG cc_start: 0.8736 (ptt-90) cc_final: 0.8242 (ptt-90) REVERT: H 47 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8245 (tm-30) REVERT: H 54 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8419 (tttm) REVERT: H 61 MET cc_start: 0.5960 (tpp) cc_final: 0.5664 (tpp) REVERT: H 68 MET cc_start: 0.6676 (mmm) cc_final: 0.5653 (ttp) REVERT: H 110 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8858 (m) REVERT: H 127 TYR cc_start: 0.6482 (m-80) cc_final: 0.6228 (m-80) REVERT: H 138 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7859 (tm-30) REVERT: H 195 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7380 (mmm-85) REVERT: H 215 TYR cc_start: 0.8451 (m-10) cc_final: 0.7857 (m-10) REVERT: H 225 MET cc_start: 0.8268 (mtt) cc_final: 0.7943 (mtt) REVERT: H 260 MET cc_start: 0.7984 (tmm) cc_final: 0.7674 (tmm) REVERT: H 277 TYR cc_start: 0.6715 (m-10) cc_final: 0.6178 (m-80) REVERT: I 36 TYR cc_start: 0.8693 (p90) cc_final: 0.7555 (p90) REVERT: I 50 MET cc_start: 0.7238 (ppp) cc_final: 0.6877 (pmm) REVERT: I 88 PHE cc_start: 0.8511 (m-80) cc_final: 0.8079 (m-80) REVERT: I 98 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7288 (mtt-85) REVERT: I 181 GLU cc_start: 0.8480 (mp0) cc_final: 0.8010 (pm20) REVERT: I 188 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: I 193 ASN cc_start: 0.8766 (m-40) cc_final: 0.8490 (m-40) REVERT: I 208 ASP cc_start: 0.8764 (t0) cc_final: 0.7992 (t70) REVERT: P 216 HIS cc_start: 0.7929 (t-90) cc_final: 0.7584 (t70) REVERT: P 238 GLN cc_start: 0.9028 (tt0) cc_final: 0.8471 (tm-30) REVERT: P 316 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7721 (tptm) REVERT: Q 57 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: Q 93 ASN cc_start: 0.8791 (m-40) cc_final: 0.8505 (m110) REVERT: Q 139 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7516 (mt-10) REVERT: R 52 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7436 (pp30) REVERT: R 75 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7606 (mtp180) REVERT: R 96 ASP cc_start: 0.8123 (t0) cc_final: 0.7525 (t0) REVERT: S 75 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8611 (mttp) REVERT: T 77 ASP cc_start: 0.8368 (t0) cc_final: 0.7915 (p0) REVERT: T 84 LEU cc_start: 0.8899 (pp) cc_final: 0.8353 (mp) REVERT: T 110 LEU cc_start: 0.7939 (mt) cc_final: 0.7644 (mt) REVERT: T 122 MET cc_start: 0.8812 (mtp) cc_final: 0.8285 (mmm) REVERT: T 125 GLU cc_start: 0.8841 (tp30) cc_final: 0.8291 (tm-30) REVERT: T 137 LYS cc_start: 0.8962 (pttm) cc_final: 0.8457 (pttm) REVERT: T 139 MET cc_start: 0.7785 (mmp) cc_final: 0.7032 (mmm) REVERT: T 143 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7246 (pt0) REVERT: W 19 SER cc_start: 0.8564 (m) cc_final: 0.8182 (p) REVERT: W 30 GLU cc_start: 0.8495 (mp0) cc_final: 0.8198 (mp0) REVERT: X 42 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8092 (mt-10) REVERT: X 44 MET cc_start: 0.8928 (tpp) cc_final: 0.8680 (mmm) REVERT: X 101 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7739 (mmt180) REVERT: Z 9 ASP cc_start: 0.5661 (t0) cc_final: 0.5240 (m-30) REVERT: Z 51 MET cc_start: 0.8595 (tmm) cc_final: 0.8200 (tmm) REVERT: Z 132 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7663 (mt-10) REVERT: Z 133 MET cc_start: 0.7515 (tmm) cc_final: 0.7023 (tmm) REVERT: a 48 MET cc_start: 0.8239 (ttp) cc_final: 0.8003 (ttp) REVERT: a 61 TYR cc_start: 0.6852 (m-80) cc_final: 0.6413 (m-80) REVERT: a 62 VAL cc_start: 0.7407 (t) cc_final: 0.7196 (p) REVERT: b 30 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7764 (mt) REVERT: q 8 LYS cc_start: 0.9219 (tmmt) cc_final: 0.8970 (tmmt) REVERT: q 13 GLN cc_start: 0.7683 (mm-40) cc_final: 0.6934 (mm-40) REVERT: q 41 GLU cc_start: 0.8398 (tt0) cc_final: 0.8148 (tp30) REVERT: q 51 ASP cc_start: 0.8362 (t0) cc_final: 0.8096 (t0) REVERT: q 67 GLU cc_start: 0.7324 (tp30) cc_final: 0.6833 (tp30) REVERT: q 96 ASP cc_start: 0.8719 (t0) cc_final: 0.8278 (t0) REVERT: q 133 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8601 (mmtp) REVERT: r 18 GLN cc_start: 0.9078 (mp10) cc_final: 0.8692 (mp10) REVERT: r 57 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.7204 (ptt90) REVERT: r 62 GLU cc_start: 0.5662 (mm-30) cc_final: 0.5384 (mm-30) REVERT: r 109 ASP cc_start: 0.8107 (p0) cc_final: 0.7645 (p0) REVERT: r 110 GLN cc_start: 0.9204 (tt0) cc_final: 0.8997 (tt0) REVERT: r 112 TYR cc_start: 0.8264 (m-80) cc_final: 0.7902 (m-80) REVERT: s 44 THR cc_start: 0.8729 (m) cc_final: 0.8312 (p) outliers start: 108 outliers final: 79 residues processed: 882 average time/residue: 0.2089 time to fit residues: 306.5437 Evaluate side-chains 870 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 780 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 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 431 LEU Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 567 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 127 ILE Chi-restraints excluded: chain P residue 178 SER Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 LEU Chi-restraints excluded: chain P residue 316 LYS Chi-restraints excluded: chain P residue 366 ILE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 99 MET Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 105 MET Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 66 VAL Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 51 optimal weight: 0.9980 chunk 367 optimal weight: 20.0000 chunk 382 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 333 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** P 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 92 ASN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078619 restraints weight = 104670.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081019 restraints weight = 48040.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082515 restraints weight = 27965.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083606 restraints weight = 19147.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084311 restraints weight = 14442.319| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35541 Z= 0.164 Angle : 0.945 77.518 48210 Z= 0.365 Chirality : 0.045 0.272 5254 Planarity : 0.005 0.166 6117 Dihedral : 8.048 176.343 4995 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 2.80 % Allowed : 24.56 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4234 helix: 0.86 (0.12), residues: 1880 sheet: -1.01 (0.27), residues: 365 loop : -0.76 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 333 TYR 0.032 0.002 TYR V 44 PHE 0.047 0.002 PHE A 62 TRP 0.032 0.002 TRP D 202 HIS 0.006 0.001 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00389 (35501) covalent geometry : angle 0.73537 (48120) SS BOND : bond 0.00176 ( 3) SS BOND : angle 2.47846 ( 6) hydrogen bonds : bond 0.03901 ( 1449) hydrogen bonds : angle 5.14853 ( 4155) metal coordination : bond 0.01609 ( 37) metal coordination : angle 14.20952 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7514.59 seconds wall clock time: 130 minutes 31.71 seconds (7831.71 seconds total)