Starting phenix.real_space_refine on Mon Jul 6 08:55:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnm_38507/07_2026/8xnm_38507_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnm_38507/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnm_38507/07_2026/8xnm_38507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnm_38507/07_2026/8xnm_38507.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnm_38507/07_2026/8xnm_38507_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnm_38507/07_2026/8xnm_38507_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 7.00, per 1000 atoms: 0.20 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: 3.33 Conformation dependent library (CDL) restraints added in 1.2 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: 0.71 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: 7.01 Time building geometry restraints manager: 4.22 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=" 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 bond pdb=" CA GLY F 234 " pdb=" C GLY F 234 " ideal model delta sigma weight residual 1.521 1.404 0.117 1.13e-02 7.83e+03 1.08e+02 bond pdb=" N PRO F 227 " pdb=" CD PRO F 227 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 ... (remaining 35496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 47459 6.89 - 13.79: 510 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: 20826 28.38 - 56.76: 580 56.76 - 85.13: 57 85.13 - 113.51: 5 113.51 - 141.89: 3 Dihedral angle restraints: 21471 sinusoidal: 9044 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 21468 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: 3.960 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: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.870 Find NCS groups from input model: 0.230 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 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= 1.125 Angle : 2.191 48.492 48210 Z= 1.449 Chirality : 0.124 0.913 5254 Planarity : 0.008 0.260 6117 Dihedral : 12.734 141.891 13452 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/Z covalent geometry : bond 0.01585 / 1.04 (35501) covalent geometry : angle 2.06575 / 1.45 (48120) SS BOND : bond 0.00956 / 0.48 ( 3) SS BOND : angle 2.44399 / 1.22 ( 6) hydrogen bonds : bond 0.23649 / 15.57 ( 1449) hydrogen bonds : angle 9.06826 / 6.49 ( 4155) metal coordination : bond 0.50037 / 32.79 ( 37) metal coordination : angle 17.59947 / 12.59 ( 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 : 1.353 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: 0.2223 time to fit residues: 590.9903 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 : 1.635 ------------------------------------------------------------------------------- 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... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 393 ASN ** 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 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: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084859 restraints weight = 103411.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087361 restraints weight = 46884.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088940 restraints weight = 27028.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090077 restraints weight = 18400.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090858 restraints weight = 13813.799| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 35541 Z= 0.214 Angle : 1.018 64.001 48210 Z= 0.433 Chirality : 0.049 0.217 5254 Planarity : 0.007 0.167 6117 Dihedral : 8.908 157.315 5012 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 3.82 % Allowed : 17.99 % Favored : 78.19 % 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: -0.87 (0.12), residues: 4234 helix: 0.33 (0.12), residues: 1857 sheet: -1.07 (0.27), residues: 353 loop : -1.32 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 37 TYR 0.029 0.003 TYR V 44 PHE 0.031 0.003 PHE T 126 TRP 0.018 0.002 TRP E 91 HIS 0.009 0.002 HIS R 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.21 (35501) covalent geometry : angle 0.82791 / 0.43 (48120) SS BOND : bond 0.00590 / 0.30 ( 3) SS BOND : angle 5.06758 / 2.26 ( 6) hydrogen bonds : bond 0.05825 / 3.87 ( 1449) hydrogen bonds : angle 5.92209 / 4.19 ( 4155) metal coordination : bond 0.02606 / 1.60 ( 37) metal coordination : angle 14.16793 / 10.01 ( 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 1208 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1066 time to evaluate : 1.389 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: A 27 MET cc_start: 0.7486 (mtm) cc_final: 0.6989 (mpp) REVERT: A 58 VAL cc_start: 0.8616 (t) cc_final: 0.8258 (t) REVERT: A 90 MET cc_start: 0.8094 (mmm) cc_final: 0.6300 (ptt) REVERT: B 124 SER cc_start: 0.8544 (p) cc_final: 0.6880 (p) REVERT: B 157 TYR cc_start: 0.8801 (m-80) cc_final: 0.8583 (m-80) REVERT: B 161 MET cc_start: 0.8288 (ttt) cc_final: 0.7661 (ttt) REVERT: B 163 SER cc_start: 0.8858 (m) cc_final: 0.8173 (t) REVERT: B 188 ASP cc_start: 0.8203 (m-30) cc_final: 0.7765 (m-30) REVERT: B 199 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8023 (mt-10) REVERT: B 201 LEU cc_start: 0.9239 (tp) cc_final: 0.8942 (tp) REVERT: C 112 ASP cc_start: 0.8028 (t0) cc_final: 0.7705 (t0) REVERT: C 221 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8027 (mm-30) REVERT: C 235 ASN cc_start: 0.8439 (t0) cc_final: 0.8226 (t0) REVERT: C 241 PHE cc_start: 0.7325 (m-10) cc_final: 0.7034 (m-10) REVERT: D 140 ASP cc_start: 0.8448 (t0) cc_final: 0.8102 (t0) REVERT: D 250 ASN cc_start: 0.8884 (m-40) cc_final: 0.8671 (m-40) REVERT: D 375 MET cc_start: 0.8536 (tpt) cc_final: 0.8308 (tpt) REVERT: D 455 ASP cc_start: 0.6415 (m-30) cc_final: 0.6095 (m-30) REVERT: D 460 GLU cc_start: 0.7963 (pt0) cc_final: 0.7643 (pt0) REVERT: E 46 ASN cc_start: 0.8113 (t0) cc_final: 0.7358 (t0) REVERT: E 137 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.7603 (p) REVERT: E 140 MET cc_start: 0.8305 (tmm) cc_final: 0.7870 (ppp) REVERT: E 141 LEU cc_start: 0.9406 (mt) cc_final: 0.8518 (mt) REVERT: E 184 MET cc_start: 0.8403 (tmm) cc_final: 0.8156 (tmm) REVERT: F 80 MET cc_start: 0.8703 (tpp) cc_final: 0.8376 (tpp) REVERT: F 220 GLN cc_start: 0.7387 (tt0) cc_final: 0.6978 (tt0) REVERT: G 140 GLN cc_start: 0.7951 (pt0) cc_final: 0.7510 (pt0) REVERT: G 311 LYS cc_start: 0.8438 (tptp) cc_final: 0.8089 (pttm) REVERT: G 329 MET cc_start: 0.8708 (mmm) cc_final: 0.8168 (mmm) REVERT: G 360 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8647 (mtpp) REVERT: G 579 MET cc_start: 0.8593 (ptp) cc_final: 0.8385 (ptp) REVERT: G 636 TYR cc_start: 0.8168 (p90) cc_final: 0.7940 (p90) REVERT: G 684 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8939 (pp) REVERT: H 31 MET cc_start: 0.9138 (mtp) cc_final: 0.8313 (mtp) REVERT: H 34 ARG cc_start: 0.8680 (ptt-90) cc_final: 0.8172 (ptt-90) REVERT: H 59 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7024 (tm-30) REVERT: H 91 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8495 (ptp) REVERT: H 97 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8472 (p0) REVERT: H 127 TYR cc_start: 0.6926 (m-80) cc_final: 0.6613 (m-80) REVERT: H 146 MET cc_start: 0.8327 (ttm) cc_final: 0.8062 (tpp) REVERT: H 195 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: I 36 TYR cc_start: 0.8711 (p90) cc_final: 0.7719 (p90) REVERT: I 37 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8618 (ttmm) REVERT: I 50 MET cc_start: 0.7332 (ppp) cc_final: 0.5501 (ttt) REVERT: I 73 THR cc_start: 0.8709 (p) cc_final: 0.8381 (p) REVERT: I 149 MET cc_start: 0.8423 (mmm) cc_final: 0.7772 (mmm) REVERT: I 193 ASN cc_start: 0.8775 (m-40) cc_final: 0.8412 (m-40) REVERT: I 208 ASP cc_start: 0.8670 (t0) cc_final: 0.7781 (t70) REVERT: P 259 VAL cc_start: 0.8567 (p) cc_final: 0.7761 (m) REVERT: P 283 MET cc_start: 0.8231 (mmm) cc_final: 0.7841 (tpp) REVERT: P 324 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9024 (mm) REVERT: Q 146 ASP cc_start: 0.7921 (p0) cc_final: 0.7259 (p0) REVERT: Q 148 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8107 (mp0) REVERT: R 51 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7841 (mmt90) REVERT: R 52 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7525 (pp30) REVERT: R 75 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7668 (mtp180) REVERT: S 44 LEU cc_start: 0.9067 (mp) cc_final: 0.8852 (mp) REVERT: S 53 ILE cc_start: 0.8999 (mp) cc_final: 0.8582 (mp) REVERT: T 90 TYR cc_start: 0.7799 (t80) cc_final: 0.7583 (t80) REVERT: T 126 PHE cc_start: 0.6928 (m-10) cc_final: 0.6618 (m-10) REVERT: W 24 PHE cc_start: 0.8239 (m-10) cc_final: 0.8023 (m-10) REVERT: W 92 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8219 (mm-30) REVERT: W 93 LEU cc_start: 0.8992 (tt) cc_final: 0.8728 (tp) REVERT: X 44 MET cc_start: 0.9089 (tpp) cc_final: 0.8366 (mmm) REVERT: X 101 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7613 (mmt180) REVERT: X 141 PRO cc_start: 0.7825 (Cg_endo) cc_final: 0.7577 (Cg_exo) REVERT: Z 71 LEU cc_start: 0.8242 (mt) cc_final: 0.7931 (mt) REVERT: Z 74 LEU cc_start: 0.8732 (tp) cc_final: 0.8413 (tp) REVERT: a 2 TRP cc_start: 0.8460 (p-90) cc_final: 0.7971 (p-90) REVERT: a 12 MET cc_start: 0.8913 (ttp) cc_final: 0.8654 (ttm) REVERT: q 12 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8582 (mt0) REVERT: q 13 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7012 (mm-40) REVERT: q 49 TYR cc_start: 0.8446 (m-80) cc_final: 0.8067 (m-80) REVERT: q 51 ASP cc_start: 0.8531 (t0) cc_final: 0.7858 (t0) REVERT: q 133 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8559 (mmtp) REVERT: r 11 LEU cc_start: 0.8028 (tt) cc_final: 0.7778 (tt) REVERT: r 18 GLN cc_start: 0.8522 (mp10) cc_final: 0.7585 (mp10) REVERT: r 57 ARG cc_start: 0.7197 (ttp-110) cc_final: 0.6641 (ptt90) REVERT: r 110 GLN cc_start: 0.8972 (tt0) cc_final: 0.8553 (tt0) REVERT: r 112 TYR cc_start: 0.7612 (m-80) cc_final: 0.7317 (m-80) REVERT: s 44 THR cc_start: 0.8317 (m) cc_final: 0.7830 (p) outliers start: 142 outliers final: 61 residues processed: 1141 average time/residue: 0.2040 time to fit residues: 379.3661 Evaluate side-chains 912 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 846 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 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 H residue 302 MET 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 44 GLN 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: 6.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 0.4980 chunk 171 optimal weight: 0.6980 chunk 389 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 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 441 HIS G 123 ASN G 140 GLN G 415 ASN G 652 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 284 GLN ** I 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 166 HIS P 171 ASN Q 92 ASN Q 167 ASN S 92 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN Z 54 ASN Z 76 GLN a 44 GLN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 123 GLN ** r 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083953 restraints weight = 102581.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086477 restraints weight = 46446.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088162 restraints weight = 26642.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089209 restraints weight = 17733.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.090000 restraints weight = 13321.094| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35541 Z= 0.163 Angle : 0.916 71.315 48210 Z= 0.369 Chirality : 0.045 0.231 5254 Planarity : 0.006 0.160 6117 Dihedral : 8.633 158.379 5011 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.28 % Favored : 96.69 % Rotamer: Outliers : 4.04 % Allowed : 18.93 % Favored : 77.03 % 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: -0.53 (0.13), residues: 4234 helix: 0.65 (0.12), residues: 1865 sheet: -1.01 (0.26), residues: 377 loop : -1.15 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 405 TYR 0.030 0.002 TYR V 44 PHE 0.028 0.002 PHE A 62 TRP 0.022 0.002 TRP D 202 HIS 0.007 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (35501) covalent geometry : angle 0.72116 / 0.37 (48120) SS BOND : bond 0.00416 / 0.21 ( 3) SS BOND : angle 1.66884 / 0.80 ( 6) hydrogen bonds : bond 0.04732 / 3.15 ( 1449) hydrogen bonds : angle 5.47672 / 3.89 ( 4155) metal coordination : bond 0.01904 / 1.17 ( 37) metal coordination : angle 13.54109 / 9.45 ( 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 1115 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 965 time to evaluate : 1.299 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: 0.7564 (mtm) cc_final: 0.7272 (mpp) REVERT: A 38 GLU cc_start: 0.8058 (tt0) cc_final: 0.7670 (tt0) REVERT: A 87 MET cc_start: 0.8696 (tmm) cc_final: 0.8251 (tmm) REVERT: A 90 MET cc_start: 0.8096 (mmm) cc_final: 0.6351 (ptt) REVERT: A 112 GLU cc_start: 0.8459 (mm-30) cc_final: 0.6778 (mt-10) REVERT: B 122 ARG cc_start: 0.8459 (mmm160) cc_final: 0.7737 (mmm160) REVERT: B 127 GLN cc_start: 0.7388 (mp10) cc_final: 0.6884 (mp10) REVERT: B 141 MET cc_start: 0.9088 (mmm) cc_final: 0.8255 (tpp) REVERT: B 161 MET cc_start: 0.8302 (ttt) cc_final: 0.7577 (ttp) REVERT: B 188 ASP cc_start: 0.8132 (m-30) cc_final: 0.7691 (m-30) REVERT: B 201 LEU cc_start: 0.9093 (tp) cc_final: 0.8653 (tp) REVERT: C 112 ASP cc_start: 0.7926 (t0) cc_final: 0.7694 (t0) REVERT: C 114 THR cc_start: 0.8358 (m) cc_final: 0.7996 (m) REVERT: C 221 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8273 (mm-30) REVERT: C 241 PHE cc_start: 0.7242 (m-10) cc_final: 0.6990 (m-10) REVERT: D 140 ASP cc_start: 0.8401 (t0) cc_final: 0.7879 (t0) REVERT: D 214 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: D 375 MET cc_start: 0.8577 (tpt) cc_final: 0.8375 (tpt) REVERT: D 406 GLU cc_start: 0.8119 (tt0) cc_final: 0.7789 (tt0) REVERT: D 460 GLU cc_start: 0.8256 (pt0) cc_final: 0.7840 (pt0) REVERT: D 463 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6506 (ptt90) REVERT: E 192 TYR cc_start: 0.8786 (m-80) cc_final: 0.8221 (m-80) REVERT: E 199 ASP cc_start: 0.7918 (t0) cc_final: 0.7610 (t0) REVERT: F 450 MET cc_start: 0.8880 (mtp) cc_final: 0.8348 (mtp) REVERT: G 126 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8584 (pp) REVERT: G 154 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8966 (pt) REVERT: G 329 MET cc_start: 0.8774 (mmm) cc_final: 0.8149 (mmm) REVERT: G 360 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8538 (mtmt) REVERT: G 618 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7626 (tt0) REVERT: G 688 GLN cc_start: 0.8260 (mp10) cc_final: 0.8033 (mp10) REVERT: H 31 MET cc_start: 0.9245 (mtp) cc_final: 0.8952 (mtp) REVERT: H 33 LEU cc_start: 0.8078 (mp) cc_final: 0.7348 (mp) REVERT: H 34 ARG cc_start: 0.8590 (ptt-90) cc_final: 0.8162 (ptt-90) REVERT: H 47 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8659 (tm-30) REVERT: H 59 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7908 (tm-30) REVERT: H 68 MET cc_start: 0.6642 (mmm) cc_final: 0.4208 (ptp) REVERT: H 93 HIS cc_start: 0.7612 (m-70) cc_final: 0.7259 (m170) REVERT: H 97 ASN cc_start: 0.8615 (p0) cc_final: 0.8146 (p0) REVERT: H 127 TYR cc_start: 0.6679 (m-80) cc_final: 0.6377 (m-80) REVERT: H 138 GLN cc_start: 0.6652 (tm-30) cc_final: 0.6398 (tm-30) REVERT: H 228 TYR cc_start: 0.9101 (m-10) cc_final: 0.8859 (m-10) REVERT: I 36 TYR cc_start: 0.8736 (p90) cc_final: 0.7573 (p90) REVERT: I 50 MET cc_start: 0.7275 (ppp) cc_final: 0.5620 (ttt) REVERT: I 76 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8118 (t80) REVERT: I 188 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7293 (tp30) REVERT: I 208 ASP cc_start: 0.8716 (t0) cc_final: 0.7770 (t70) REVERT: P 128 ASN cc_start: 0.8736 (t0) cc_final: 0.8505 (t0) REVERT: P 291 TYR cc_start: 0.8756 (p90) cc_final: 0.8406 (p90) REVERT: P 324 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8986 (mm) REVERT: Q 102 ASP cc_start: 0.8380 (p0) cc_final: 0.8140 (p0) REVERT: R 42 ASP cc_start: 0.8201 (m-30) cc_final: 0.7873 (t70) REVERT: R 52 GLN cc_start: 0.7968 (tm-30) cc_final: 0.6400 (pp30) REVERT: T 143 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7675 (mt-10) REVERT: W 37 GLU cc_start: 0.8668 (mp0) cc_final: 0.8431 (mp0) REVERT: W 92 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8170 (mm-30) REVERT: X 5 VAL cc_start: 0.8292 (t) cc_final: 0.8089 (m) REVERT: X 44 MET cc_start: 0.9101 (tpp) cc_final: 0.8568 (mmm) REVERT: X 101 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7747 (mmt180) REVERT: Z 9 ASP cc_start: 0.5953 (t0) cc_final: 0.5396 (m-30) REVERT: Z 51 MET cc_start: 0.8606 (tmm) cc_final: 0.8374 (tmm) REVERT: Z 132 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7085 (pt0) REVERT: Z 133 MET cc_start: 0.6843 (tmm) cc_final: 0.6370 (tmm) REVERT: a 2 TRP cc_start: 0.8347 (p-90) cc_final: 0.7878 (p-90) REVERT: a 35 GLU cc_start: 0.5940 (mt-10) cc_final: 0.5706 (tt0) REVERT: b 35 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8593 (mt) REVERT: b 41 TYR cc_start: 0.8111 (m-80) cc_final: 0.7859 (m-80) REVERT: q 13 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7077 (mm-40) REVERT: q 49 TYR cc_start: 0.8440 (m-80) cc_final: 0.8118 (m-80) REVERT: q 51 ASP cc_start: 0.8343 (t0) cc_final: 0.7960 (t0) REVERT: q 133 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8652 (mmtp) REVERT: r 11 LEU cc_start: 0.8154 (tt) cc_final: 0.7918 (tt) REVERT: r 18 GLN cc_start: 0.8683 (mp10) cc_final: 0.8296 (mp10) REVERT: r 57 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6598 (ptt90) REVERT: r 102 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8609 (ttpt) REVERT: r 112 TYR cc_start: 0.7702 (m-80) cc_final: 0.7388 (m-80) REVERT: s 44 THR cc_start: 0.8497 (m) cc_final: 0.8159 (p) outliers start: 150 outliers final: 70 residues processed: 1046 average time/residue: 0.1893 time to fit residues: 331.1206 Evaluate side-chains 893 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 815 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 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 79 ASN 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 214 TYR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 162 PHE 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 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 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 567 VAL Chi-restraints excluded: chain G residue 652 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain P residue 40 VAL 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 207 PHE 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 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 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 137 LEU Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 127 LEU Chi-restraints excluded: chain a residue 18 ILE 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 62 GLU 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: 0.9990 chunk 230 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 387 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 HIS ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 83 ASN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 381 HIS ** F 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 170 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN F 436 GLN G 66 HIS G 569 GLN G 652 ASN H 97 ASN P 121 GLN ** P 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 92 ASN Q 141 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** W 111 HIS ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 116 ASN r 36 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.088904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.076441 restraints weight = 105014.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078805 restraints weight = 48482.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.080287 restraints weight = 28309.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081453 restraints weight = 19480.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.082170 restraints weight = 14558.139| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 35541 Z= 0.279 Angle : 1.013 77.867 48210 Z= 0.398 Chirality : 0.048 0.238 5254 Planarity : 0.006 0.160 6117 Dihedral : 8.626 163.112 5011 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 5.20 % Allowed : 19.92 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.02 % 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: -0.47 (0.13), residues: 4234 helix: 0.60 (0.12), residues: 1898 sheet: -1.11 (0.26), residues: 388 loop : -1.01 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 78 TYR 0.026 0.002 TYR T 85 PHE 0.031 0.002 PHE A 62 TRP 0.026 0.002 TRP b 26 HIS 0.008 0.001 HIS D 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (35501) covalent geometry : angle 0.77466 / 0.39 (48120) SS BOND : bond 0.03262 / 1.63 ( 3) SS BOND : angle 1.96727 / 0.81 ( 6) hydrogen bonds : bond 0.04681 / 3.13 ( 1449) hydrogen bonds : angle 5.46265 / 3.88 ( 4155) metal coordination : bond 0.02979 / 1.67 ( 37) metal coordination : angle 15.63777 / 10.82 ( 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 1022 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 829 time to evaluate : 1.425 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: 0.7381 (mtm) cc_final: 0.6970 (mpp) REVERT: A 38 GLU cc_start: 0.8168 (tt0) cc_final: 0.7883 (tt0) REVERT: A 90 MET cc_start: 0.8315 (mmm) cc_final: 0.6796 (ptt) REVERT: B 103 GLU cc_start: 0.8770 (tp30) cc_final: 0.7838 (tt0) REVERT: B 141 MET cc_start: 0.9230 (mmm) cc_final: 0.8333 (tpp) REVERT: B 151 GLN cc_start: 0.8623 (mt0) cc_final: 0.7772 (mp10) REVERT: B 161 MET cc_start: 0.8581 (ttt) cc_final: 0.8072 (ttp) REVERT: B 188 ASP cc_start: 0.8344 (m-30) cc_final: 0.7531 (m-30) REVERT: B 199 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 201 LEU cc_start: 0.9144 (tp) cc_final: 0.8809 (tp) REVERT: C 112 ASP cc_start: 0.8065 (t0) cc_final: 0.7817 (t0) REVERT: C 221 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8460 (mm-30) REVERT: C 241 PHE cc_start: 0.7307 (m-10) cc_final: 0.6938 (m-10) REVERT: D 214 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: D 259 GLU cc_start: 0.8752 (tp30) cc_final: 0.8546 (tt0) REVERT: D 333 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7745 (mtt180) REVERT: D 375 MET cc_start: 0.8545 (tpt) cc_final: 0.8315 (tpt) REVERT: E 91 TRP cc_start: 0.6780 (t-100) cc_final: 0.6291 (t-100) REVERT: E 140 MET cc_start: 0.8351 (tmm) cc_final: 0.8108 (ppp) REVERT: E 199 ASP cc_start: 0.8021 (t0) cc_final: 0.7592 (t0) REVERT: F 204 TYR cc_start: 0.8612 (t80) cc_final: 0.8405 (t80) REVERT: F 450 MET cc_start: 0.8835 (mtp) cc_final: 0.8297 (mtp) REVERT: G 39 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: G 97 MET cc_start: 0.8158 (mtm) cc_final: 0.7777 (ptp) REVERT: G 100 TRP cc_start: 0.8825 (m-10) cc_final: 0.8604 (m-10) REVERT: G 315 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8708 (p) REVERT: G 329 MET cc_start: 0.8938 (mmm) cc_final: 0.8261 (mmm) REVERT: G 360 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8586 (mtmt) REVERT: G 590 THR cc_start: 0.9404 (p) cc_final: 0.9055 (t) REVERT: G 618 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7641 (mt-10) REVERT: G 632 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8239 (pt) REVERT: G 684 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8884 (pp) REVERT: G 696 MET cc_start: 0.8570 (mtm) cc_final: 0.8031 (mtt) REVERT: H 33 LEU cc_start: 0.8758 (mp) cc_final: 0.8425 (mt) REVERT: H 34 ARG cc_start: 0.8802 (ptt-90) cc_final: 0.8477 (ptt-90) REVERT: H 47 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8674 (tm-30) REVERT: H 68 MET cc_start: 0.7089 (mmm) cc_final: 0.4920 (ttp) REVERT: H 97 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8000 (p0) REVERT: H 110 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8530 (m) REVERT: H 118 TRP cc_start: 0.8382 (m-10) cc_final: 0.7983 (m-10) REVERT: H 127 TYR cc_start: 0.6919 (m-80) cc_final: 0.6467 (m-80) REVERT: H 195 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.8020 (mmm-85) REVERT: I 35 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8500 (p) REVERT: I 36 TYR cc_start: 0.8900 (p90) cc_final: 0.7618 (p90) REVERT: I 50 MET cc_start: 0.7299 (ppp) cc_final: 0.6846 (pmm) REVERT: I 62 MET cc_start: 0.6997 (tmm) cc_final: 0.6792 (tmm) REVERT: I 76 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8100 (t80) REVERT: I 181 GLU cc_start: 0.8437 (mp0) cc_final: 0.8005 (pm20) REVERT: I 188 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: I 193 ASN cc_start: 0.8785 (m-40) cc_final: 0.8345 (m-40) REVERT: I 208 ASP cc_start: 0.8847 (t0) cc_final: 0.7877 (t70) REVERT: P 291 TYR cc_start: 0.8941 (p90) cc_final: 0.8537 (p90) REVERT: Q 93 ASN cc_start: 0.8907 (m-40) cc_final: 0.8576 (m110) REVERT: Q 102 ASP cc_start: 0.8571 (p0) cc_final: 0.8354 (p0) REVERT: R 34 THR cc_start: 0.7787 (p) cc_final: 0.7545 (p) REVERT: R 42 ASP cc_start: 0.8296 (m-30) cc_final: 0.8040 (t70) REVERT: R 52 GLN cc_start: 0.7870 (tm-30) cc_final: 0.6550 (pp30) REVERT: R 54 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: R 75 ARG cc_start: 0.8386 (mtp-110) cc_final: 0.7574 (mtp180) REVERT: T 90 TYR cc_start: 0.8278 (t80) cc_final: 0.7922 (t80) REVERT: T 98 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7823 (tt) REVERT: T 136 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8617 (mm-30) REVERT: W 19 SER cc_start: 0.8555 (m) cc_final: 0.8070 (p) REVERT: W 37 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: W 45 GLU cc_start: 0.8576 (tp30) cc_final: 0.7878 (tp30) REVERT: X 5 VAL cc_start: 0.8001 (t) cc_final: 0.7798 (m) REVERT: X 44 MET cc_start: 0.9085 (tpp) cc_final: 0.8870 (tpp) REVERT: X 101 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7818 (mmt180) REVERT: Z 51 MET cc_start: 0.8652 (tmm) cc_final: 0.8187 (tmm) REVERT: Z 132 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7305 (pt0) REVERT: Z 133 MET cc_start: 0.7192 (tmm) cc_final: 0.6865 (tmm) REVERT: a 2 TRP cc_start: 0.8455 (p-90) cc_final: 0.7994 (p-90) REVERT: q 12 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8509 (mt0) REVERT: q 13 GLN cc_start: 0.7796 (mm-40) cc_final: 0.6587 (mm-40) REVERT: q 49 TYR cc_start: 0.8623 (m-80) cc_final: 0.8128 (m-80) REVERT: q 51 ASP cc_start: 0.8352 (t0) cc_final: 0.7964 (t0) REVERT: q 133 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8616 (mmtp) REVERT: r 18 GLN cc_start: 0.8834 (mp10) cc_final: 0.8494 (mp10) REVERT: r 30 GLU cc_start: 0.7111 (pt0) cc_final: 0.6729 (pm20) REVERT: r 57 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6694 (ptt90) REVERT: r 109 ASP cc_start: 0.8133 (p0) cc_final: 0.7747 (p0) REVERT: r 112 TYR cc_start: 0.8048 (m-80) cc_final: 0.7738 (m-80) REVERT: s 44 THR cc_start: 0.8690 (m) cc_final: 0.8238 (p) outliers start: 193 outliers final: 123 residues processed: 937 average time/residue: 0.2078 time to fit residues: 325.8030 Evaluate side-chains 896 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 760 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 138 THR 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 157 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR 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 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 116 ASN Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 254 ILE 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 354 VAL Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain G residue 39 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 162 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 315 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 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 659 ILE Chi-restraints excluded: chain G residue 684 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 97 ASN 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 266 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 35 THR 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 167 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain I residue 190 LEU 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 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 253 THR Chi-restraints excluded: chain P residue 257 ASP 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 108 GLU Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain Q residue 159 SER Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 103 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 98 LEU Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 48 THR Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 37 GLU 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 a residue 17 VAL Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain a residue 60 TYR 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 b residue 60 ASP Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 50 GLU 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: 0.7980 chunk 14 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 280 optimal weight: 0.0670 chunk 104 optimal weight: 0.0170 chunk 287 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS D 83 ASN ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 HIS ** 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** F 381 GLN F 436 GLN G 569 GLN H 93 HIS P 71 ASN ** P 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 GLN ** 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** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 44 GLN b 71 GLN q 54 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.091925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.079247 restraints weight = 104388.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081721 restraints weight = 48039.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083350 restraints weight = 27909.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084427 restraints weight = 18963.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085180 restraints weight = 14335.743| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35541 Z= 0.145 Angle : 0.940 76.626 48210 Z= 0.353 Chirality : 0.044 0.225 5254 Planarity : 0.005 0.165 6117 Dihedral : 8.461 165.114 5011 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 3.80 % Allowed : 22.00 % Favored : 74.21 % 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: -0.25 (0.13), residues: 4234 helix: 0.89 (0.12), residues: 1864 sheet: -1.20 (0.26), residues: 396 loop : -0.92 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 167 TYR 0.035 0.002 TYR Z 143 PHE 0.026 0.002 PHE H 223 TRP 0.023 0.001 TRP b 26 HIS 0.006 0.001 HIS H 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (35501) covalent geometry : angle 0.70793 / 0.35 (48120) SS BOND : bond 0.00148 / 0.07 ( 3) SS BOND : angle 1.02366 / 0.51 ( 6) hydrogen bonds : bond 0.04213 / 2.84 ( 1449) hydrogen bonds : angle 5.21081 / 3.70 ( 4155) metal coordination : bond 0.01484 / 0.99 ( 37) metal coordination : angle 14.81436 / 10.45 ( 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 1002 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 861 time to evaluate : 1.473 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: A 11 ILE cc_start: 0.9125 (mm) cc_final: 0.8595 (pt) REVERT: A 27 MET cc_start: 0.7380 (mtm) cc_final: 0.7103 (mpp) REVERT: A 73 LEU cc_start: 0.8954 (mt) cc_final: 0.8723 (mt) REVERT: A 87 MET cc_start: 0.8848 (tmm) cc_final: 0.8446 (tmm) REVERT: A 90 MET cc_start: 0.8195 (mmm) cc_final: 0.6790 (ptt) REVERT: B 103 GLU cc_start: 0.8750 (tp30) cc_final: 0.7823 (tt0) REVERT: B 122 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8091 (mmm160) REVERT: B 141 MET cc_start: 0.9200 (mmm) cc_final: 0.8334 (tpp) REVERT: B 151 GLN cc_start: 0.8568 (mt0) cc_final: 0.7716 (mp10) REVERT: B 161 MET cc_start: 0.8261 (ttt) cc_final: 0.7578 (ttp) REVERT: B 188 ASP cc_start: 0.8270 (m-30) cc_final: 0.7535 (m-30) REVERT: B 199 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: C 112 ASP cc_start: 0.8006 (t0) cc_final: 0.7699 (t0) REVERT: C 167 ARG cc_start: 0.8495 (ttp-170) cc_final: 0.7979 (ttt180) REVERT: D 110 ASP cc_start: 0.8944 (t70) cc_final: 0.8538 (t70) REVERT: D 214 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (m-80) REVERT: D 270 ASN cc_start: 0.9105 (m-40) cc_final: 0.8870 (m110) REVERT: D 326 CYS cc_start: 0.8645 (m) cc_final: 0.8328 (m) REVERT: D 333 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7774 (mtt180) REVERT: D 375 MET cc_start: 0.8591 (tpt) cc_final: 0.8319 (tpt) REVERT: D 406 GLU cc_start: 0.8169 (tt0) cc_final: 0.7786 (tt0) REVERT: E 143 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.9036 (t70) REVERT: E 157 ILE cc_start: 0.8857 (pt) cc_final: 0.8522 (pt) REVERT: E 184 MET cc_start: 0.8475 (tmm) cc_final: 0.8136 (tmm) REVERT: E 199 ASP cc_start: 0.8007 (t0) cc_final: 0.7628 (t0) REVERT: F 135 PRO cc_start: 0.8979 (Cg_endo) cc_final: 0.8668 (Cg_exo) REVERT: F 244 ASN cc_start: 0.8395 (t0) cc_final: 0.8163 (t0) REVERT: F 433 TRP cc_start: 0.8615 (m-10) cc_final: 0.8180 (m-90) REVERT: F 450 MET cc_start: 0.8867 (mtp) cc_final: 0.8367 (mtp) REVERT: G 97 MET cc_start: 0.8156 (mtm) cc_final: 0.7756 (ptp) REVERT: G 100 TRP cc_start: 0.8796 (m-10) cc_final: 0.8366 (m-10) REVERT: G 144 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7586 (tmm) REVERT: G 154 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8955 (pt) REVERT: G 329 MET cc_start: 0.8925 (mmm) cc_final: 0.8274 (mmm) REVERT: G 351 LEU cc_start: 0.9368 (mt) cc_final: 0.9164 (mt) REVERT: G 360 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8700 (mtpp) REVERT: G 530 TYR cc_start: 0.8814 (m-80) cc_final: 0.8552 (m-80) REVERT: G 590 THR cc_start: 0.9341 (p) cc_final: 0.8988 (t) REVERT: G 618 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7601 (mt-10) REVERT: G 684 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8906 (pp) REVERT: G 696 MET cc_start: 0.8544 (mtm) cc_final: 0.8058 (mtt) REVERT: H 33 LEU cc_start: 0.8636 (mp) cc_final: 0.8037 (mt) REVERT: H 34 ARG cc_start: 0.8650 (ptt-90) cc_final: 0.8287 (ptt-90) REVERT: H 47 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8389 (tm-30) REVERT: H 68 MET cc_start: 0.7012 (mmm) cc_final: 0.4933 (ttp) REVERT: H 110 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8812 (m) REVERT: H 111 LEU cc_start: 0.9086 (tt) cc_final: 0.8812 (tt) REVERT: H 127 TYR cc_start: 0.6902 (m-80) cc_final: 0.6353 (m-80) REVERT: H 195 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7706 (mmm-85) REVERT: H 225 MET cc_start: 0.8424 (mtt) cc_final: 0.8095 (mtt) REVERT: I 36 TYR cc_start: 0.8794 (p90) cc_final: 0.7559 (p90) REVERT: I 50 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6793 (pmm) REVERT: I 76 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7930 (t80) REVERT: I 159 GLN cc_start: 0.8808 (tt0) cc_final: 0.8566 (tt0) REVERT: I 181 GLU cc_start: 0.8369 (mp0) cc_final: 0.7994 (pm20) REVERT: I 188 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7391 (tp30) REVERT: I 193 ASN cc_start: 0.8734 (m-40) cc_final: 0.8314 (m-40) REVERT: I 208 ASP cc_start: 0.8763 (t0) cc_final: 0.7884 (t70) REVERT: P 40 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (t) REVERT: P 121 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8467 (tp40) REVERT: P 291 TYR cc_start: 0.8921 (p90) cc_final: 0.8562 (p90) REVERT: Q 93 ASN cc_start: 0.8798 (m-40) cc_final: 0.8491 (m110) REVERT: Q 102 ASP cc_start: 0.8497 (p0) cc_final: 0.8267 (p0) REVERT: Q 139 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7448 (mt-10) REVERT: R 34 THR cc_start: 0.7765 (p) cc_final: 0.7544 (p) REVERT: R 42 ASP cc_start: 0.8283 (m-30) cc_final: 0.8072 (t70) REVERT: R 52 GLN cc_start: 0.7915 (tm-30) cc_final: 0.6562 (pp30) REVERT: R 75 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7863 (mtp180) REVERT: T 90 TYR cc_start: 0.8136 (t80) cc_final: 0.7821 (t80) REVERT: W 19 SER cc_start: 0.8554 (m) cc_final: 0.8110 (p) REVERT: W 24 PHE cc_start: 0.8618 (m-10) cc_final: 0.8331 (m-10) REVERT: W 37 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: W 45 GLU cc_start: 0.8511 (tp30) cc_final: 0.8164 (tp30) REVERT: X 5 VAL cc_start: 0.8272 (t) cc_final: 0.8040 (m) REVERT: X 44 MET cc_start: 0.9095 (tpp) cc_final: 0.8849 (mmm) REVERT: X 129 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.7959 (p) REVERT: Z 51 MET cc_start: 0.8633 (tmm) cc_final: 0.8142 (tmm) REVERT: Z 132 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7307 (pt0) REVERT: Z 133 MET cc_start: 0.7255 (tmm) cc_final: 0.7036 (tmm) REVERT: a 2 TRP cc_start: 0.8344 (p-90) cc_final: 0.7845 (p-90) REVERT: q 8 LYS cc_start: 0.9109 (tmmt) cc_final: 0.8884 (tmmt) REVERT: q 13 GLN cc_start: 0.7690 (mm-40) cc_final: 0.6691 (mm-40) REVERT: q 49 TYR cc_start: 0.8575 (m-80) cc_final: 0.8161 (m-80) REVERT: q 51 ASP cc_start: 0.8269 (t0) cc_final: 0.7929 (t0) REVERT: q 96 ASP cc_start: 0.8621 (t0) cc_final: 0.7886 (t0) REVERT: q 133 LYS cc_start: 0.8955 (mmtp) cc_final: 0.8563 (mmtp) REVERT: r 18 GLN cc_start: 0.8961 (mp10) cc_final: 0.8507 (mp10) REVERT: r 57 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6611 (ptt90) REVERT: r 109 ASP cc_start: 0.8045 (p0) cc_final: 0.7601 (p0) REVERT: r 112 TYR cc_start: 0.8008 (m-80) cc_final: 0.7717 (m-80) REVERT: s 44 THR cc_start: 0.8746 (m) cc_final: 0.8122 (p) outliers start: 141 outliers final: 80 residues processed: 936 average time/residue: 0.2098 time to fit residues: 327.4531 Evaluate side-chains 884 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 791 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 58 VAL 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 199 GLU 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 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 116 ASN 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 G residue 144 MET 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 390 THR Chi-restraints excluded: chain G residue 426 ASP 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 7 LEU Chi-restraints excluded: chain H residue 39 ILE 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 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 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 I residue 190 LEU 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 194 VAL Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain P residue 224 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 R residue 39 ASP Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 118 ILE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 37 GLU 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 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 39 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 55 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 325 optimal weight: 0.2980 chunk 189 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 224 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN ** E 88 GLN ** 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 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 415 ASN G 569 GLN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 ASN ** 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** ** X 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079623 restraints weight = 103967.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082072 restraints weight = 47703.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083627 restraints weight = 27721.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084754 restraints weight = 18843.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085454 restraints weight = 13974.169| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35541 Z= 0.144 Angle : 0.936 76.707 48210 Z= 0.351 Chirality : 0.045 0.343 5254 Planarity : 0.005 0.165 6117 Dihedral : 8.331 166.952 5011 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 3.90 % Allowed : 23.02 % Favored : 73.07 % 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: 1.00 (0.12), residues: 1862 sheet: -1.16 (0.26), residues: 388 loop : -0.88 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 40 TYR 0.035 0.002 TYR V 44 PHE 0.024 0.002 PHE G 214 TRP 0.020 0.001 TRP I 197 HIS 0.006 0.001 HIS P 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (35501) covalent geometry : angle 0.70789 / 0.35 (48120) SS BOND : bond 0.00129 / 0.07 ( 3) SS BOND : angle 0.81392 / 0.43 ( 6) hydrogen bonds : bond 0.04051 / 2.74 ( 1449) hydrogen bonds : angle 5.09822 / 3.63 ( 4155) metal coordination : bond 0.01479 / 0.93 ( 37) metal coordination : angle 14.68167 / 10.33 ( 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 988 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 843 time to evaluate : 1.441 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 11 ILE cc_start: 0.9073 (mm) cc_final: 0.8601 (pt) REVERT: A 27 MET cc_start: 0.7346 (mtm) cc_final: 0.7107 (mpp) REVERT: A 62 PHE cc_start: 0.9044 (t80) cc_final: 0.8827 (t80) REVERT: A 90 MET cc_start: 0.8083 (mmm) cc_final: 0.7806 (mmt) REVERT: B 103 GLU cc_start: 0.8731 (tp30) cc_final: 0.7896 (tt0) REVERT: B 122 ARG cc_start: 0.8726 (mmm160) cc_final: 0.8015 (mmm160) REVERT: B 141 MET cc_start: 0.9214 (mmm) cc_final: 0.8398 (tpp) REVERT: B 151 GLN cc_start: 0.8384 (mt0) cc_final: 0.7492 (mp10) REVERT: B 161 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7515 (ttt) REVERT: B 188 ASP cc_start: 0.8302 (m-30) cc_final: 0.7970 (m-30) REVERT: B 199 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 201 LEU cc_start: 0.9046 (tt) cc_final: 0.8825 (tt) REVERT: B 217 LYS cc_start: 0.8790 (mttp) cc_final: 0.8562 (mttp) REVERT: C 112 ASP cc_start: 0.8123 (t0) cc_final: 0.7846 (t0) REVERT: C 114 THR cc_start: 0.8501 (m) cc_final: 0.8157 (m) REVERT: C 140 ILE cc_start: 0.8554 (tt) cc_final: 0.8349 (tt) REVERT: C 167 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7609 (ttp-170) REVERT: C 199 LYS cc_start: 0.9230 (tppt) cc_final: 0.8996 (mmtp) REVERT: D 116 LEU cc_start: 0.9083 (tt) cc_final: 0.8859 (tt) REVERT: D 140 ASP cc_start: 0.8599 (t0) cc_final: 0.8051 (t0) REVERT: D 144 MET cc_start: 0.8004 (mpp) cc_final: 0.7549 (mpp) REVERT: D 147 ASN cc_start: 0.9250 (OUTLIER) cc_final: 0.8777 (m110) REVERT: D 214 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: D 270 ASN cc_start: 0.9087 (m-40) cc_final: 0.8880 (m110) REVERT: D 333 ARG cc_start: 0.8058 (mtt90) cc_final: 0.7697 (mtt180) REVERT: D 375 MET cc_start: 0.8523 (tpt) cc_final: 0.8250 (tpt) REVERT: D 406 GLU cc_start: 0.8180 (tt0) cc_final: 0.7966 (tt0) REVERT: E 140 MET cc_start: 0.8146 (ppp) cc_final: 0.7918 (ppp) REVERT: E 143 ASP cc_start: 0.9242 (OUTLIER) cc_final: 0.9035 (t70) REVERT: E 184 MET cc_start: 0.8440 (tmm) cc_final: 0.8126 (tmm) REVERT: E 199 ASP cc_start: 0.8023 (t0) cc_final: 0.7630 (t0) REVERT: F 135 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8633 (Cg_exo) REVERT: F 429 ASP cc_start: 0.8478 (t0) cc_final: 0.8239 (t0) REVERT: F 433 TRP cc_start: 0.8609 (m-10) cc_final: 0.8235 (m-10) REVERT: F 450 MET cc_start: 0.8865 (mtp) cc_final: 0.8510 (mtp) REVERT: G 97 MET cc_start: 0.8127 (mtm) cc_final: 0.7789 (ptp) REVERT: G 100 TRP cc_start: 0.8757 (m-10) cc_final: 0.8448 (m-10) REVERT: G 144 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7517 (tmm) REVERT: G 154 LEU cc_start: 0.9254 (mp) cc_final: 0.8959 (pt) REVERT: G 329 MET cc_start: 0.8896 (mmm) cc_final: 0.7973 (mmm) REVERT: G 360 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8729 (mtpp) REVERT: G 530 TYR cc_start: 0.8818 (m-80) cc_final: 0.8474 (m-80) REVERT: G 590 THR cc_start: 0.9343 (p) cc_final: 0.8997 (t) REVERT: G 618 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7481 (mt-10) REVERT: G 684 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8912 (pp) REVERT: G 696 MET cc_start: 0.8576 (mtm) cc_final: 0.8060 (mtt) REVERT: H 33 LEU cc_start: 0.8614 (mp) cc_final: 0.7996 (mt) REVERT: H 34 ARG cc_start: 0.8627 (ptt-90) cc_final: 0.8252 (ptt-90) REVERT: H 47 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8251 (tm-30) REVERT: H 68 MET cc_start: 0.7103 (mmm) cc_final: 0.5258 (ttp) REVERT: H 110 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8819 (m) REVERT: H 127 TYR cc_start: 0.7014 (m-80) cc_final: 0.6263 (m-80) REVERT: H 138 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7501 (tm-30) REVERT: I 36 TYR cc_start: 0.8751 (p90) cc_final: 0.7505 (p90) REVERT: I 50 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6901 (pmm) REVERT: I 76 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8129 (t80) REVERT: I 181 GLU cc_start: 0.8348 (mp0) cc_final: 0.7960 (pm20) REVERT: I 188 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: I 193 ASN cc_start: 0.8714 (m-40) cc_final: 0.8344 (m-40) REVERT: I 208 ASP cc_start: 0.8766 (t0) cc_final: 0.7897 (t70) REVERT: P 238 GLN cc_start: 0.9031 (tt0) cc_final: 0.8716 (tt0) REVERT: P 291 TYR cc_start: 0.8914 (p90) cc_final: 0.8601 (p90) REVERT: Q 70 GLU cc_start: 0.9124 (pm20) cc_final: 0.8763 (pm20) REVERT: Q 78 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8321 (mtp180) REVERT: Q 93 ASN cc_start: 0.8800 (m-40) cc_final: 0.8485 (m110) REVERT: Q 139 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7374 (mt-10) REVERT: R 52 GLN cc_start: 0.7900 (tm-30) cc_final: 0.6933 (pp30) REVERT: R 75 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7887 (mtp180) REVERT: S 71 PHE cc_start: 0.8941 (m-80) cc_final: 0.8733 (m-10) REVERT: T 90 TYR cc_start: 0.8244 (t80) cc_final: 0.7929 (t80) REVERT: V 44 TYR cc_start: 0.8709 (t80) cc_final: 0.8392 (t80) REVERT: W 19 SER cc_start: 0.8569 (m) cc_final: 0.8188 (p) REVERT: W 37 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: W 78 ASP cc_start: 0.8265 (t0) cc_final: 0.8029 (t0) REVERT: X 44 MET cc_start: 0.9062 (tpp) cc_final: 0.8803 (mmm) REVERT: X 127 LYS cc_start: 0.8442 (ptpt) cc_final: 0.8162 (ptmt) REVERT: Z 51 MET cc_start: 0.8634 (tmm) cc_final: 0.8136 (tmm) REVERT: Z 132 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7282 (pt0) REVERT: Z 133 MET cc_start: 0.7288 (tmm) cc_final: 0.7085 (tmm) REVERT: a 2 TRP cc_start: 0.8289 (p-90) cc_final: 0.7884 (p-90) REVERT: q 8 LYS cc_start: 0.9125 (tmmt) cc_final: 0.8872 (tmmt) REVERT: q 13 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6727 (mm-40) REVERT: q 49 TYR cc_start: 0.8532 (m-80) cc_final: 0.8302 (m-80) REVERT: q 51 ASP cc_start: 0.8262 (t0) cc_final: 0.7945 (t0) REVERT: q 96 ASP cc_start: 0.8720 (t0) cc_final: 0.8022 (t0) REVERT: q 133 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8571 (mmtp) REVERT: r 18 GLN cc_start: 0.8985 (mp10) cc_final: 0.8050 (mp10) REVERT: r 30 GLU cc_start: 0.6944 (pt0) cc_final: 0.6550 (pm20) REVERT: r 57 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6762 (ptt90) REVERT: r 109 ASP cc_start: 0.8071 (p0) cc_final: 0.7622 (p0) REVERT: r 112 TYR cc_start: 0.8049 (m-80) cc_final: 0.7728 (m-80) REVERT: s 40 TYR cc_start: 0.6761 (m-80) cc_final: 0.6556 (m-80) REVERT: s 44 THR cc_start: 0.8658 (m) cc_final: 0.8289 (p) outliers start: 145 outliers final: 90 residues processed: 923 average time/residue: 0.2091 time to fit residues: 322.6262 Evaluate side-chains 882 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 781 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 72 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 170 TYR 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 D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 241 THR Chi-restraints excluded: chain F residue 251 SER 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 144 MET Chi-restraints excluded: chain G residue 149 ASP 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 390 THR Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 426 ASP 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 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 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 H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 188 GLU Chi-restraints excluded: chain I residue 190 LEU 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 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 V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 37 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain W residue 113 THR 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 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 20 VAL 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 14 VAL Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 0.0050 chunk 277 optimal weight: 0.0170 chunk 361 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 498 GLN G 569 GLN H 157 ASN ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS I 126 GLN ** 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** ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078158 restraints weight = 104808.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.080547 restraints weight = 48115.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082157 restraints weight = 28194.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.083184 restraints weight = 19049.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083960 restraints weight = 14378.919| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.6464 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= 0.169 Angle : 0.938 78.138 48210 Z= 0.352 Chirality : 0.045 0.309 5254 Planarity : 0.005 0.173 6117 Dihedral : 8.245 169.020 5011 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.77 % Allowed : 23.29 % Favored : 72.94 % 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: -0.09 (0.13), residues: 4234 helix: 0.98 (0.12), residues: 1871 sheet: -1.11 (0.27), residues: 382 loop : -0.81 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 40 TYR 0.033 0.002 TYR V 44 PHE 0.025 0.002 PHE E 242 TRP 0.028 0.002 TRP I 197 HIS 0.008 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (35501) covalent geometry : angle 0.70992 / 0.35 (48120) SS BOND : bond 0.00171 / 0.09 ( 3) SS BOND : angle 0.80710 / 0.44 ( 6) hydrogen bonds : bond 0.04027 / 2.71 ( 1449) hydrogen bonds : angle 5.06190 / 3.61 ( 4155) metal coordination : bond 0.01847 / 1.05 ( 37) metal coordination : angle 14.69956 / 10.28 ( 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 957 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 817 time to evaluate : 1.565 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 27 MET cc_start: 0.7268 (mtm) cc_final: 0.7042 (mpp) REVERT: A 90 MET cc_start: 0.8138 (mmm) cc_final: 0.7893 (mmt) REVERT: B 103 GLU cc_start: 0.8740 (tp30) cc_final: 0.8512 (mm-30) REVERT: B 113 ASP cc_start: 0.8454 (t0) cc_final: 0.8082 (t70) REVERT: B 122 ARG cc_start: 0.8806 (mmm160) cc_final: 0.7959 (mmm160) REVERT: B 129 ASP cc_start: 0.9032 (m-30) cc_final: 0.8676 (m-30) REVERT: B 141 MET cc_start: 0.9244 (mmm) cc_final: 0.8419 (tpp) REVERT: B 151 GLN cc_start: 0.8481 (mt0) cc_final: 0.7541 (mp10) REVERT: B 161 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: B 188 ASP cc_start: 0.8366 (m-30) cc_final: 0.7606 (m-30) REVERT: B 199 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 201 LEU cc_start: 0.9014 (tt) cc_final: 0.8509 (tt) REVERT: C 112 ASP cc_start: 0.8116 (t0) cc_final: 0.7834 (t0) REVERT: C 199 LYS cc_start: 0.9239 (tppt) cc_final: 0.8980 (mmtp) REVERT: D 214 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: D 406 GLU cc_start: 0.8197 (tt0) cc_final: 0.7988 (tt0) REVERT: E 47 ASN cc_start: 0.7967 (p0) cc_final: 0.7711 (p0) REVERT: E 59 TYR cc_start: 0.8614 (m-80) cc_final: 0.8364 (m-80) REVERT: E 140 MET cc_start: 0.8176 (ppp) cc_final: 0.7868 (ppp) REVERT: E 143 ASP cc_start: 0.9202 (OUTLIER) cc_final: 0.8969 (t70) REVERT: E 184 MET cc_start: 0.8361 (tmm) cc_final: 0.7881 (tmm) REVERT: F 135 PRO cc_start: 0.8944 (Cg_endo) cc_final: 0.8662 (Cg_exo) REVERT: F 244 ASN cc_start: 0.8384 (t0) cc_final: 0.7795 (t0) REVERT: F 246 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7729 (pt0) REVERT: F 315 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8612 (mt) REVERT: F 433 TRP cc_start: 0.8629 (m-10) cc_final: 0.8250 (m-10) REVERT: F 450 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8494 (mtp) REVERT: G 97 MET cc_start: 0.8099 (mtm) cc_final: 0.7796 (ptp) REVERT: G 100 TRP cc_start: 0.8741 (m-10) cc_final: 0.8494 (m-10) REVERT: G 154 LEU cc_start: 0.9274 (mp) cc_final: 0.8923 (pt) REVERT: G 360 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8748 (mtpp) REVERT: G 530 TYR cc_start: 0.8857 (m-80) cc_final: 0.8523 (m-80) REVERT: G 590 THR cc_start: 0.9317 (p) cc_final: 0.9040 (t) REVERT: G 618 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7549 (mt-10) REVERT: G 696 MET cc_start: 0.8603 (mtm) cc_final: 0.8106 (mtt) REVERT: H 33 LEU cc_start: 0.8682 (mp) cc_final: 0.7740 (mt) REVERT: H 34 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8382 (ptt-90) REVERT: H 35 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8371 (mmtt) REVERT: H 47 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8319 (tm-30) REVERT: H 54 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8507 (tttm) REVERT: H 61 MET cc_start: 0.6434 (tpt) cc_final: 0.6153 (tpt) REVERT: H 68 MET cc_start: 0.7202 (mmm) cc_final: 0.5550 (ttp) REVERT: H 110 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8838 (m) REVERT: H 127 TYR cc_start: 0.6926 (m-80) cc_final: 0.6591 (m-80) REVERT: H 195 ARG cc_start: 0.7968 (mmm-85) cc_final: 0.7531 (mmm-85) REVERT: H 289 LEU cc_start: 0.8813 (mt) cc_final: 0.8523 (mt) REVERT: I 36 TYR cc_start: 0.8780 (p90) cc_final: 0.7529 (p90) REVERT: I 37 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8736 (tttt) REVERT: I 50 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6770 (pmm) REVERT: I 76 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.8039 (t80) REVERT: I 149 MET cc_start: 0.8828 (mtp) cc_final: 0.8621 (mtp) REVERT: I 193 ASN cc_start: 0.8681 (m-40) cc_final: 0.8303 (m-40) REVERT: I 208 ASP cc_start: 0.8785 (t0) cc_final: 0.8007 (t70) REVERT: P 211 ASP cc_start: 0.8113 (p0) cc_final: 0.7083 (p0) REVERT: P 266 THR cc_start: 0.8591 (t) cc_final: 0.8335 (m) REVERT: P 291 TYR cc_start: 0.8931 (p90) cc_final: 0.8628 (p90) REVERT: Q 93 ASN cc_start: 0.8831 (m-40) cc_final: 0.8541 (m110) REVERT: Q 139 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7380 (mt-10) REVERT: Q 149 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7955 (pt0) REVERT: R 52 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7008 (pp30) REVERT: R 75 ARG cc_start: 0.8299 (mtp-110) cc_final: 0.7617 (mtp180) REVERT: R 96 ASP cc_start: 0.8035 (t0) cc_final: 0.7267 (t0) REVERT: S 71 PHE cc_start: 0.8963 (m-80) cc_final: 0.8753 (m-10) REVERT: T 90 TYR cc_start: 0.8331 (t80) cc_final: 0.8037 (t80) REVERT: V 44 TYR cc_start: 0.8792 (t80) cc_final: 0.8464 (t80) REVERT: W 19 SER cc_start: 0.8556 (m) cc_final: 0.8154 (p) REVERT: W 37 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8446 (mp0) REVERT: W 45 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: W 78 ASP cc_start: 0.8292 (t0) cc_final: 0.8036 (t0) REVERT: X 44 MET cc_start: 0.9031 (tpp) cc_final: 0.8758 (mmm) REVERT: X 101 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7633 (mmt180) REVERT: Z 51 MET cc_start: 0.8569 (tmm) cc_final: 0.8094 (tmm) REVERT: Z 132 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7354 (pt0) REVERT: Z 133 MET cc_start: 0.7293 (tmm) cc_final: 0.7090 (tmm) REVERT: a 2 TRP cc_start: 0.8357 (p-90) cc_final: 0.7956 (p-90) REVERT: q 8 LYS cc_start: 0.9175 (tmmt) cc_final: 0.8912 (tmmt) REVERT: q 13 GLN cc_start: 0.7548 (mm-40) cc_final: 0.6746 (mm-40) REVERT: q 49 TYR cc_start: 0.8560 (m-80) cc_final: 0.8336 (m-80) REVERT: q 51 ASP cc_start: 0.8293 (t0) cc_final: 0.7966 (t0) REVERT: q 96 ASP cc_start: 0.8685 (t0) cc_final: 0.8053 (t0) REVERT: q 133 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8564 (mmtp) REVERT: r 18 GLN cc_start: 0.9006 (mp10) cc_final: 0.8206 (mp10) REVERT: r 30 GLU cc_start: 0.7246 (pt0) cc_final: 0.6756 (pm20) REVERT: r 57 ARG cc_start: 0.7227 (ttp-110) cc_final: 0.6865 (ptt90) REVERT: r 109 ASP cc_start: 0.8116 (p0) cc_final: 0.7668 (p0) REVERT: r 112 TYR cc_start: 0.8116 (m-80) cc_final: 0.7830 (m-80) REVERT: s 44 THR cc_start: 0.8770 (m) cc_final: 0.8304 (p) outliers start: 140 outliers final: 104 residues processed: 895 average time/residue: 0.2108 time to fit residues: 314.4163 Evaluate side-chains 886 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 770 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 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 B residue 97 LEU Chi-restraints excluded: chain B residue 161 MET 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 D residue 101 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 241 THR Chi-restraints excluded: chain F residue 246 GLU 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 354 VAL 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 126 LEU Chi-restraints excluded: chain G residue 149 ASP 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 396 GLU Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 426 ASP Chi-restraints excluded: chain G residue 515 ILE Chi-restraints excluded: chain G residue 516 LEU Chi-restraints excluded: chain G residue 537 ILE Chi-restraints excluded: chain G residue 566 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 72 ILE 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 254 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 75 SER 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 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 207 PHE Chi-restraints excluded: chain P residue 224 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 91 VAL Chi-restraints excluded: chain S residue 61 VAL Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 37 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 39 THR 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 Z residue 121 ILE Chi-restraints excluded: chain a residue 18 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 18 VAL Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 34 MET 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 q residue 50 GLU Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain q residue 128 SER Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 43 VAL 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: 0.5980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 189 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 245 optimal weight: 0.9990 chunk 299 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 342 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** 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** 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 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 92 ASN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 HIS ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN q 54 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.079597 restraints weight = 104353.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082017 restraints weight = 47794.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.083561 restraints weight = 27620.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084665 restraints weight = 18771.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085460 restraints weight = 14099.593| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35541 Z= 0.140 Angle : 0.918 77.086 48210 Z= 0.347 Chirality : 0.044 0.324 5254 Planarity : 0.005 0.174 6117 Dihedral : 8.111 170.585 5011 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 3.31 % Allowed : 24.10 % Favored : 72.59 % 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: -0.06 (0.13), residues: 4234 helix: 1.02 (0.12), residues: 1858 sheet: -1.11 (0.27), residues: 370 loop : -0.79 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 40 TYR 0.033 0.002 TYR V 44 PHE 0.026 0.002 PHE H 223 TRP 0.028 0.001 TRP D 202 HIS 0.007 0.001 HIS H 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (35501) covalent geometry : angle 0.69949 / 0.34 (48120) SS BOND : bond 0.00261 / 0.13 ( 3) SS BOND : angle 2.39677 / 1.00 ( 6) hydrogen bonds : bond 0.03856 / 2.59 ( 1449) hydrogen bonds : angle 5.01077 / 3.57 ( 4155) metal coordination : bond 0.01397 / 0.91 ( 37) metal coordination : angle 14.23301 / 10.00 ( 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 964 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 841 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7203 (mtm) cc_final: 0.6983 (mpp) REVERT: A 112 GLU cc_start: 0.8815 (mm-30) cc_final: 0.7195 (mp0) REVERT: B 103 GLU cc_start: 0.8651 (tp30) cc_final: 0.7778 (mt-10) REVERT: B 122 ARG cc_start: 0.8835 (mmm160) cc_final: 0.8617 (mmm-85) REVERT: B 127 GLN cc_start: 0.7891 (mp10) cc_final: 0.7543 (mp10) REVERT: B 141 MET cc_start: 0.9198 (mmm) cc_final: 0.8377 (tpp) REVERT: B 151 GLN cc_start: 0.8424 (mt0) cc_final: 0.7502 (mp10) REVERT: B 161 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: B 188 ASP cc_start: 0.8132 (m-30) cc_final: 0.7473 (m-30) REVERT: B 199 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: B 215 GLU cc_start: 0.8761 (tt0) cc_final: 0.8475 (tt0) REVERT: C 112 ASP cc_start: 0.8009 (t0) cc_final: 0.7683 (t0) REVERT: C 114 THR cc_start: 0.8390 (m) cc_final: 0.7834 (m) REVERT: C 199 LYS cc_start: 0.9241 (tppt) cc_final: 0.9036 (mmtp) REVERT: D 144 MET cc_start: 0.7946 (mpp) cc_final: 0.7544 (mpp) REVERT: D 214 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: D 326 CYS cc_start: 0.8728 (m) cc_final: 0.8467 (m) REVERT: D 333 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7812 (mtt90) REVERT: E 47 ASN cc_start: 0.8062 (p0) cc_final: 0.7843 (p0) REVERT: E 59 TYR cc_start: 0.8677 (m-80) cc_final: 0.7800 (m-80) REVERT: E 140 MET cc_start: 0.8124 (ppp) cc_final: 0.7795 (ppp) REVERT: E 143 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8912 (t70) REVERT: E 184 MET cc_start: 0.8321 (tmm) cc_final: 0.7821 (tmm) REVERT: F 135 PRO cc_start: 0.8902 (Cg_endo) cc_final: 0.8630 (Cg_exo) REVERT: F 161 GLU cc_start: 0.8907 (mp0) cc_final: 0.8668 (mp0) REVERT: F 244 ASN cc_start: 0.8393 (t0) cc_final: 0.8125 (t0) REVERT: F 246 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: F 429 ASP cc_start: 0.8597 (t0) cc_final: 0.8253 (t0) REVERT: F 433 TRP cc_start: 0.8591 (m-10) cc_final: 0.8225 (m-10) REVERT: F 450 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8397 (mtp) REVERT: G 97 MET cc_start: 0.7994 (mtm) cc_final: 0.7737 (ptp) REVERT: G 100 TRP cc_start: 0.8717 (m-10) cc_final: 0.8406 (m-10) REVERT: G 144 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7412 (tmm) REVERT: G 154 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8914 (pt) REVERT: G 269 GLU cc_start: 0.8409 (pm20) cc_final: 0.7565 (pm20) REVERT: G 329 MET cc_start: 0.8676 (tpp) cc_final: 0.7865 (mmm) REVERT: G 360 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8709 (mtpp) REVERT: G 530 TYR cc_start: 0.8838 (m-80) cc_final: 0.8447 (m-80) REVERT: G 590 THR cc_start: 0.9298 (p) cc_final: 0.9058 (t) REVERT: G 618 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7504 (mt-10) REVERT: G 680 LEU cc_start: 0.7878 (tt) cc_final: 0.7146 (mp) REVERT: G 696 MET cc_start: 0.8582 (mtm) cc_final: 0.8115 (mtt) REVERT: H 1 MET cc_start: 0.7708 (ttm) cc_final: 0.7481 (ttm) REVERT: H 4 ILE cc_start: 0.8461 (mm) cc_final: 0.8258 (mt) REVERT: H 33 LEU cc_start: 0.8713 (mp) cc_final: 0.7615 (mt) REVERT: H 34 ARG cc_start: 0.8584 (ptt-90) cc_final: 0.8098 (ptt-90) REVERT: H 35 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8289 (mmtt) REVERT: H 47 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8189 (tm-30) REVERT: H 54 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8583 (tttm) REVERT: H 61 MET cc_start: 0.6085 (tpt) cc_final: 0.5697 (tpt) REVERT: H 68 MET cc_start: 0.6963 (mmm) cc_final: 0.5424 (ttp) REVERT: H 103 LEU cc_start: 0.8971 (mt) cc_final: 0.8729 (tt) REVERT: H 110 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8808 (m) REVERT: H 127 TYR cc_start: 0.6853 (m-80) cc_final: 0.6511 (m-80) REVERT: H 138 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7694 (tm-30) REVERT: H 159 SER cc_start: 0.8584 (t) cc_final: 0.8144 (p) REVERT: I 36 TYR cc_start: 0.8736 (p90) cc_final: 0.7571 (p90) REVERT: I 37 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8704 (tttt) REVERT: I 50 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6896 (pmm) REVERT: I 62 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6327 (tmm) REVERT: I 76 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.8038 (t80) REVERT: I 149 MET cc_start: 0.8612 (mtp) cc_final: 0.8405 (mtp) REVERT: I 188 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: I 193 ASN cc_start: 0.8716 (m-40) cc_final: 0.8467 (m-40) REVERT: I 208 ASP cc_start: 0.8750 (t0) cc_final: 0.8021 (t70) REVERT: P 291 TYR cc_start: 0.8891 (p90) cc_final: 0.8647 (p90) REVERT: Q 93 ASN cc_start: 0.8789 (m-40) cc_final: 0.8495 (m110) REVERT: Q 139 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7419 (mt-10) REVERT: R 52 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7221 (pp30) REVERT: R 75 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7562 (mtp180) REVERT: R 96 ASP cc_start: 0.8064 (t0) cc_final: 0.7479 (t0) REVERT: S 71 PHE cc_start: 0.8958 (m-80) cc_final: 0.8746 (m-10) REVERT: T 90 TYR cc_start: 0.8177 (t80) cc_final: 0.7930 (t80) REVERT: T 110 LEU cc_start: 0.8141 (mt) cc_final: 0.7936 (mt) REVERT: W 19 SER cc_start: 0.8558 (m) cc_final: 0.8156 (p) REVERT: W 30 GLU cc_start: 0.8441 (mp0) cc_final: 0.8238 (mp0) REVERT: W 37 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: W 45 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: W 93 LEU cc_start: 0.8528 (tp) cc_final: 0.8191 (tp) REVERT: X 42 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8027 (mt-10) REVERT: X 101 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7641 (mmt180) REVERT: Z 35 MET cc_start: 0.8255 (tpt) cc_final: 0.7784 (ttp) REVERT: Z 51 MET cc_start: 0.8611 (tmm) cc_final: 0.8192 (tmm) REVERT: Z 132 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7468 (pt0) REVERT: a 48 MET cc_start: 0.8087 (ttp) cc_final: 0.7722 (ttp) REVERT: b 81 LEU cc_start: 0.8019 (tt) cc_final: 0.7787 (tp) REVERT: q 8 LYS cc_start: 0.9156 (tmmt) cc_final: 0.8915 (tmmt) REVERT: q 13 GLN cc_start: 0.7567 (mm-40) cc_final: 0.6736 (mm-40) REVERT: q 51 ASP cc_start: 0.8373 (t0) cc_final: 0.8103 (t0) REVERT: q 96 ASP cc_start: 0.8706 (t0) cc_final: 0.8211 (t0) REVERT: q 127 TYR cc_start: 0.9279 (p90) cc_final: 0.9076 (p90) REVERT: q 133 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8583 (mmtp) REVERT: r 18 GLN cc_start: 0.9046 (mp10) cc_final: 0.8615 (mp10) REVERT: r 30 GLU cc_start: 0.7214 (pt0) cc_final: 0.6674 (pm20) REVERT: r 57 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6989 (ptt90) REVERT: r 105 GLU cc_start: 0.7450 (mp0) cc_final: 0.6940 (mp0) REVERT: r 109 ASP cc_start: 0.8090 (p0) cc_final: 0.7640 (p0) REVERT: r 112 TYR cc_start: 0.8123 (m-80) cc_final: 0.7843 (m-80) REVERT: s 44 THR cc_start: 0.8793 (m) cc_final: 0.8134 (p) outliers start: 123 outliers final: 82 residues processed: 906 average time/residue: 0.2095 time to fit residues: 317.5634 Evaluate side-chains 879 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 782 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 161 MET 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 236 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 116 ASN Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 251 SER 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 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 154 LEU 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 426 ASP Chi-restraints excluded: chain G residue 515 ILE 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 H residue 7 LEU Chi-restraints excluded: chain H residue 72 ILE 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 254 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 62 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 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 366 ILE 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 R residue 103 THR 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 W residue 37 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 95 GLU 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 b residue 20 VAL 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 q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 43 VAL 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: 0.9980 chunk 134 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 374 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 371 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** 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** ** 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 P 216 HIS Q 51 GLN Q 92 ASN ** 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** Z 135 ASN q 87 HIS ** q 123 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.091967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.079756 restraints weight = 104051.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.082127 restraints weight = 47514.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.083717 restraints weight = 27945.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084807 restraints weight = 18834.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085530 restraints weight = 14046.653| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35541 Z= 0.143 Angle : 0.931 77.545 48210 Z= 0.356 Chirality : 0.045 0.307 5254 Planarity : 0.005 0.155 6117 Dihedral : 8.031 171.930 5011 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 3.12 % Allowed : 24.47 % Favored : 72.40 % 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: -0.05 (0.13), residues: 4234 helix: 1.01 (0.12), residues: 1857 sheet: -1.09 (0.27), residues: 383 loop : -0.77 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 40 TYR 0.033 0.002 TYR T 147 PHE 0.056 0.002 PHE A 62 TRP 0.028 0.001 TRP D 202 HIS 0.006 0.001 HIS P 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (35501) covalent geometry : angle 0.72404 / 0.35 (48120) SS BOND : bond 0.00174 / 0.09 ( 3) SS BOND : angle 2.79442 / 1.20 ( 6) hydrogen bonds : bond 0.03810 / 2.57 ( 1449) hydrogen bonds : angle 4.99842 / 3.57 ( 4155) metal coordination : bond 0.01309 / 0.81 ( 37) metal coordination : angle 14.00727 / 9.76 ( 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 935 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 819 time to evaluate : 1.437 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: A 112 GLU cc_start: 0.8877 (mm-30) cc_final: 0.7042 (mt-10) REVERT: B 103 GLU cc_start: 0.8596 (tp30) cc_final: 0.7710 (mt-10) REVERT: B 122 ARG cc_start: 0.8851 (mmm160) cc_final: 0.8562 (mmm-85) REVERT: B 127 GLN cc_start: 0.7951 (mp10) cc_final: 0.7581 (mp10) REVERT: B 151 GLN cc_start: 0.8398 (mt0) cc_final: 0.7325 (mp10) REVERT: B 161 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7573 (ttt) REVERT: B 188 ASP cc_start: 0.7981 (m-30) cc_final: 0.7381 (m-30) REVERT: B 199 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: B 215 GLU cc_start: 0.8703 (tt0) cc_final: 0.8493 (tt0) REVERT: B 217 LYS cc_start: 0.8866 (mttp) cc_final: 0.8370 (mttp) REVERT: C 112 ASP cc_start: 0.8062 (t0) cc_final: 0.7778 (t0) REVERT: C 199 LYS cc_start: 0.9224 (tppt) cc_final: 0.8759 (mmtp) REVERT: D 140 ASP cc_start: 0.8496 (t0) cc_final: 0.8256 (t0) REVERT: D 144 MET cc_start: 0.7932 (mpp) cc_final: 0.7626 (mpp) REVERT: D 185 MET cc_start: 0.8362 (tpt) cc_final: 0.7978 (tpt) REVERT: D 214 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: D 326 CYS cc_start: 0.8748 (m) cc_final: 0.8326 (m) REVERT: D 371 MET cc_start: 0.8919 (ttp) cc_final: 0.8681 (ttp) REVERT: E 47 ASN cc_start: 0.8046 (p0) cc_final: 0.7822 (p0) REVERT: E 59 TYR cc_start: 0.8728 (m-80) cc_final: 0.8466 (m-80) REVERT: E 140 MET cc_start: 0.8101 (ppp) cc_final: 0.7764 (ppp) REVERT: E 143 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8903 (t70) REVERT: E 184 MET cc_start: 0.8352 (tmm) cc_final: 0.7843 (tmm) REVERT: F 135 PRO cc_start: 0.8913 (Cg_endo) cc_final: 0.8638 (Cg_exo) REVERT: F 161 GLU cc_start: 0.8899 (mp0) cc_final: 0.8681 (mp0) REVERT: F 244 ASN cc_start: 0.8546 (t0) cc_final: 0.8314 (t0) REVERT: F 429 ASP cc_start: 0.8602 (t0) cc_final: 0.8216 (t0) REVERT: F 433 TRP cc_start: 0.8577 (m-10) cc_final: 0.8203 (m-10) REVERT: F 450 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: G 97 MET cc_start: 0.7873 (mtm) cc_final: 0.7602 (ptp) REVERT: G 100 TRP cc_start: 0.8677 (m-10) cc_final: 0.8426 (m-10) REVERT: G 161 GLU cc_start: 0.7819 (tp30) cc_final: 0.7267 (tp30) REVERT: G 269 GLU cc_start: 0.8400 (pm20) cc_final: 0.7614 (pm20) REVERT: G 329 MET cc_start: 0.8651 (tpp) cc_final: 0.7850 (mmm) REVERT: G 360 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8794 (mmmm) REVERT: G 390 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8086 (p) REVERT: G 530 TYR cc_start: 0.8813 (m-80) cc_final: 0.8442 (m-80) REVERT: G 590 THR cc_start: 0.9322 (p) cc_final: 0.9000 (t) REVERT: G 618 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7511 (mt-10) REVERT: G 680 LEU cc_start: 0.7869 (tt) cc_final: 0.7156 (mp) REVERT: G 696 MET cc_start: 0.8649 (mtm) cc_final: 0.8192 (mtt) REVERT: H 30 TYR cc_start: 0.8964 (m-80) cc_final: 0.8756 (m-80) REVERT: H 34 ARG cc_start: 0.8704 (ptt-90) cc_final: 0.8178 (ptt-90) REVERT: H 35 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8325 (mmtt) REVERT: H 47 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8239 (tm-30) REVERT: H 54 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8624 (tttm) REVERT: H 68 MET cc_start: 0.6763 (mmm) cc_final: 0.5626 (ttp) REVERT: H 103 LEU cc_start: 0.8956 (mt) cc_final: 0.8717 (tt) REVERT: H 110 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8878 (m) REVERT: H 127 TYR cc_start: 0.6966 (m-80) cc_final: 0.6640 (m-80) REVERT: H 138 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7690 (tm-30) REVERT: H 159 SER cc_start: 0.8572 (t) cc_final: 0.8166 (p) REVERT: H 195 ARG cc_start: 0.8129 (mmm-85) cc_final: 0.7886 (mmm-85) REVERT: H 225 MET cc_start: 0.8315 (mtt) cc_final: 0.7928 (mtt) REVERT: H 287 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (m90) REVERT: I 36 TYR cc_start: 0.8719 (p90) cc_final: 0.7587 (p90) REVERT: I 37 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8652 (tttt) REVERT: I 50 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6996 (pmm) REVERT: I 62 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6355 (tmm) REVERT: I 181 GLU cc_start: 0.8553 (mp0) cc_final: 0.8024 (pm20) REVERT: I 188 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: I 208 ASP cc_start: 0.8741 (t0) cc_final: 0.8048 (t70) REVERT: Q 93 ASN cc_start: 0.8644 (m-40) cc_final: 0.8346 (m110) REVERT: Q 139 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7456 (mt-10) REVERT: R 52 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7320 (pp30) REVERT: R 75 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7577 (mtp180) REVERT: R 96 ASP cc_start: 0.8125 (t0) cc_final: 0.7520 (t0) REVERT: S 71 PHE cc_start: 0.8943 (m-80) cc_final: 0.8711 (m-10) REVERT: T 110 LEU cc_start: 0.8144 (mt) cc_final: 0.7887 (mt) REVERT: W 19 SER cc_start: 0.8587 (m) cc_final: 0.8185 (p) REVERT: W 30 GLU cc_start: 0.8391 (mp0) cc_final: 0.8138 (mp0) REVERT: W 37 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: W 45 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7623 (tp30) REVERT: W 114 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8205 (tp30) REVERT: X 42 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8087 (mt-10) REVERT: X 101 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7550 (mmt180) REVERT: Z 35 MET cc_start: 0.8292 (tpt) cc_final: 0.7892 (ttp) REVERT: Z 51 MET cc_start: 0.8554 (tmm) cc_final: 0.8093 (tmm) REVERT: Z 135 ASN cc_start: 0.7553 (m-40) cc_final: 0.7283 (t0) REVERT: a 43 TYR cc_start: 0.8270 (t80) cc_final: 0.8065 (t80) REVERT: a 48 MET cc_start: 0.8104 (ttp) cc_final: 0.7842 (ttp) REVERT: b 38 TYR cc_start: 0.7864 (m-80) cc_final: 0.7481 (m-80) REVERT: q 8 LYS cc_start: 0.9153 (tmmt) cc_final: 0.8911 (tmmt) REVERT: q 13 GLN cc_start: 0.7576 (mm-40) cc_final: 0.6816 (mm-40) REVERT: q 51 ASP cc_start: 0.8395 (t0) cc_final: 0.8120 (t0) REVERT: q 96 ASP cc_start: 0.8776 (t0) cc_final: 0.8371 (t0) REVERT: q 133 LYS cc_start: 0.8969 (mmtp) cc_final: 0.8559 (mmtp) REVERT: r 18 GLN cc_start: 0.9090 (mp10) cc_final: 0.8347 (mp10) REVERT: r 30 GLU cc_start: 0.7160 (pt0) cc_final: 0.6827 (pm20) REVERT: r 57 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7195 (ptt90) REVERT: r 109 ASP cc_start: 0.8090 (p0) cc_final: 0.7654 (p0) REVERT: r 112 TYR cc_start: 0.8205 (m-80) cc_final: 0.7905 (m-80) REVERT: r 113 LEU cc_start: 0.8204 (mm) cc_final: 0.7972 (mt) REVERT: s 44 THR cc_start: 0.8837 (m) cc_final: 0.8395 (p) outliers start: 116 outliers final: 87 residues processed: 882 average time/residue: 0.2119 time to fit residues: 311.4231 Evaluate side-chains 875 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 775 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 161 MET 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 D residue 101 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 246 GLU Chi-restraints excluded: chain F residue 251 SER 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 96 VAL 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 330 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 515 ILE 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 674 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 254 LEU Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 62 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 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 231 LEU Chi-restraints excluded: chain P residue 366 ILE 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 W residue 37 GLU Chi-restraints excluded: chain W residue 45 GLU Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 39 THR 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 b residue 20 VAL 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 14 VAL Chi-restraints excluded: chain q residue 114 LYS Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 49 LEU 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: 1.9990 chunk 100 optimal weight: 0.4980 chunk 360 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 305 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 268 optimal weight: 7.9990 chunk 341 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 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 71 ASN Q 51 GLN Q 92 ASN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079385 restraints weight = 105178.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081792 restraints weight = 48281.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083387 restraints weight = 28207.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084373 restraints weight = 18976.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085155 restraints weight = 14493.156| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35541 Z= 0.147 Angle : 0.927 77.910 48210 Z= 0.359 Chirality : 0.046 0.515 5254 Planarity : 0.005 0.142 6117 Dihedral : 7.954 173.342 5011 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 2.91 % Allowed : 24.91 % Favored : 72.19 % 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: -0.05 (0.13), residues: 4234 helix: 1.00 (0.12), residues: 1856 sheet: -1.06 (0.26), residues: 383 loop : -0.76 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 40 TYR 0.037 0.002 TYR T 147 PHE 0.029 0.002 PHE A 62 TRP 0.035 0.001 TRP I 197 HIS 0.006 0.001 HIS H 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (35501) covalent geometry : angle 0.72079 / 0.35 (48120) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 2.34357 / 0.99 ( 6) hydrogen bonds : bond 0.03811 / 2.55 ( 1449) hydrogen bonds : angle 5.04968 / 3.60 ( 4155) metal coordination : bond 0.01413 / 0.85 ( 37) metal coordination : angle 13.95615 / 9.66 ( 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 903 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 795 time to evaluate : 1.431 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: A 5 THR cc_start: 0.9073 (m) cc_final: 0.8782 (t) REVERT: A 55 PHE cc_start: 0.7235 (m-80) cc_final: 0.6215 (m-80) REVERT: A 112 GLU cc_start: 0.9007 (mm-30) cc_final: 0.7411 (mt-10) REVERT: B 103 GLU cc_start: 0.8548 (tp30) cc_final: 0.7666 (mt-10) REVERT: B 122 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8573 (mmm-85) REVERT: B 127 GLN cc_start: 0.7976 (mp10) cc_final: 0.7608 (mp10) REVERT: B 141 MET cc_start: 0.9299 (tpp) cc_final: 0.8340 (tpp) REVERT: B 151 GLN cc_start: 0.8382 (mt0) cc_final: 0.7333 (mp10) REVERT: B 161 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: B 188 ASP cc_start: 0.8343 (m-30) cc_final: 0.7671 (m-30) REVERT: B 199 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: C 112 ASP cc_start: 0.8082 (t0) cc_final: 0.7880 (t0) REVERT: C 199 LYS cc_start: 0.9217 (tppt) cc_final: 0.8759 (mmtp) REVERT: D 140 ASP cc_start: 0.8443 (t0) cc_final: 0.8205 (t0) REVERT: D 144 MET cc_start: 0.7768 (mpp) cc_final: 0.7568 (mpp) REVERT: D 214 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 371 MET cc_start: 0.8923 (ttp) cc_final: 0.8684 (ttp) REVERT: E 47 ASN cc_start: 0.7983 (p0) cc_final: 0.7765 (p0) REVERT: E 59 TYR cc_start: 0.8740 (m-80) cc_final: 0.8467 (m-80) REVERT: E 140 MET cc_start: 0.8079 (ppp) cc_final: 0.7762 (ppp) REVERT: E 143 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8911 (t70) REVERT: E 184 MET cc_start: 0.8294 (tmm) cc_final: 0.7781 (tmm) REVERT: F 135 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8663 (Cg_exo) REVERT: F 244 ASN cc_start: 0.8638 (t0) cc_final: 0.8381 (t0) REVERT: F 246 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7912 (pt0) REVERT: F 429 ASP cc_start: 0.8629 (t0) cc_final: 0.8252 (t0) REVERT: F 433 TRP cc_start: 0.8580 (m-10) cc_final: 0.8201 (m-10) REVERT: F 450 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: G 97 MET cc_start: 0.7856 (mtm) cc_final: 0.7575 (ptp) REVERT: G 100 TRP cc_start: 0.8692 (m-10) cc_final: 0.8448 (m-10) REVERT: G 161 GLU cc_start: 0.7835 (tp30) cc_final: 0.7273 (tp30) REVERT: G 269 GLU cc_start: 0.8337 (pm20) cc_final: 0.7522 (pm20) REVERT: G 329 MET cc_start: 0.8691 (tpp) cc_final: 0.7874 (mmm) REVERT: G 360 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8777 (mmmm) REVERT: G 530 TYR cc_start: 0.8833 (m-80) cc_final: 0.8456 (m-80) REVERT: G 590 THR cc_start: 0.9371 (p) cc_final: 0.9081 (t) REVERT: G 618 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7538 (mt-10) REVERT: G 680 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7167 (mp) REVERT: G 696 MET cc_start: 0.8695 (mtm) cc_final: 0.8271 (mtt) REVERT: H 34 ARG cc_start: 0.8752 (ptt-90) cc_final: 0.8281 (ptt-90) REVERT: H 47 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8197 (tm-30) REVERT: H 54 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8676 (tttm) REVERT: H 68 MET cc_start: 0.6809 (mmm) cc_final: 0.5719 (ttp) REVERT: H 103 LEU cc_start: 0.8941 (mt) cc_final: 0.8710 (tt) REVERT: H 110 SER cc_start: 0.9295 (OUTLIER) cc_final: 0.8848 (m) REVERT: H 127 TYR cc_start: 0.6954 (m-80) cc_final: 0.6607 (m-80) REVERT: H 138 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7787 (tm-30) REVERT: H 195 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: H 225 MET cc_start: 0.8268 (mtt) cc_final: 0.7920 (mtt) REVERT: H 287 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.8123 (m90) REVERT: I 36 TYR cc_start: 0.8719 (p90) cc_final: 0.7604 (p90) REVERT: I 50 MET cc_start: 0.7323 (ppp) cc_final: 0.7008 (pmm) REVERT: I 62 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6368 (tmm) REVERT: I 181 GLU cc_start: 0.8571 (mp0) cc_final: 0.8047 (pm20) REVERT: I 208 ASP cc_start: 0.8841 (t0) cc_final: 0.8182 (t70) REVERT: P 216 HIS cc_start: 0.8099 (t-90) cc_final: 0.7831 (t70) REVERT: Q 93 ASN cc_start: 0.8758 (m-40) cc_final: 0.8484 (m110) REVERT: Q 139 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7492 (mt-10) REVERT: R 52 GLN cc_start: 0.8262 (tm-30) cc_final: 0.8011 (pp30) REVERT: R 75 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7584 (mtp180) REVERT: R 96 ASP cc_start: 0.8102 (t0) cc_final: 0.7506 (t0) REVERT: S 71 PHE cc_start: 0.8952 (m-80) cc_final: 0.8728 (m-10) REVERT: T 110 LEU cc_start: 0.8148 (mt) cc_final: 0.7859 (mt) REVERT: T 143 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7493 (pt0) REVERT: W 19 SER cc_start: 0.8611 (m) cc_final: 0.8242 (p) REVERT: W 30 GLU cc_start: 0.8463 (mp0) cc_final: 0.8129 (mp0) REVERT: W 37 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: W 45 GLU cc_start: 0.8251 (tp30) cc_final: 0.7978 (tp30) REVERT: W 114 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8225 (tp30) REVERT: X 39 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8340 (p) REVERT: X 42 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8182 (mt-10) REVERT: X 101 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7574 (mmt180) REVERT: Z 35 MET cc_start: 0.8302 (tpt) cc_final: 0.7917 (ttp) REVERT: Z 51 MET cc_start: 0.8547 (tmm) cc_final: 0.8089 (tmm) REVERT: Z 98 MET cc_start: 0.3619 (mmp) cc_final: 0.3417 (mmp) REVERT: Z 133 MET cc_start: 0.7576 (tmm) cc_final: 0.6965 (tmm) REVERT: Z 135 ASN cc_start: 0.7586 (m-40) cc_final: 0.7253 (t0) REVERT: a 48 MET cc_start: 0.8226 (ttp) cc_final: 0.8009 (ttp) REVERT: b 38 TYR cc_start: 0.7904 (m-80) cc_final: 0.7530 (m-80) REVERT: q 8 LYS cc_start: 0.9152 (tmmt) cc_final: 0.8912 (tmmt) REVERT: q 13 GLN cc_start: 0.7632 (mm-40) cc_final: 0.6863 (mm-40) REVERT: q 51 ASP cc_start: 0.8363 (t0) cc_final: 0.8093 (t0) REVERT: q 68 MET cc_start: 0.7091 (ttt) cc_final: 0.6845 (ttt) REVERT: q 96 ASP cc_start: 0.8778 (t0) cc_final: 0.8404 (t0) REVERT: q 133 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8577 (mmtp) REVERT: r 18 GLN cc_start: 0.9016 (mp10) cc_final: 0.8643 (mp10) REVERT: r 57 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7199 (ptt90) REVERT: r 62 GLU cc_start: 0.5748 (mm-30) cc_final: 0.5446 (mm-30) REVERT: r 109 ASP cc_start: 0.8101 (p0) cc_final: 0.7669 (p0) REVERT: r 112 TYR cc_start: 0.8248 (m-80) cc_final: 0.7933 (m-80) REVERT: r 113 LEU cc_start: 0.8189 (mm) cc_final: 0.7947 (mt) REVERT: s 44 THR cc_start: 0.8769 (m) cc_final: 0.8348 (p) outliers start: 108 outliers final: 81 residues processed: 854 average time/residue: 0.2113 time to fit residues: 301.3568 Evaluate side-chains 868 residues out of total 3714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 775 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 161 MET 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 D residue 101 LEU Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 222 MET 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 180 VAL Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 251 SER 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 96 VAL 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 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 330 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 515 ILE 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 680 LEU Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 162 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 272 TRP Chi-restraints excluded: chain H residue 287 HIS Chi-restraints excluded: chain H residue 302 MET Chi-restraints excluded: chain I residue 62 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 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 366 ILE Chi-restraints excluded: chain Q residue 51 GLN 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 W residue 37 GLU Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain X residue 137 LEU Chi-restraints excluded: chain b residue 20 VAL 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 14 VAL Chi-restraints excluded: chain r residue 35 THR Chi-restraints excluded: chain r residue 43 VAL Chi-restraints excluded: chain r residue 49 LEU 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: 0.0010 chunk 328 optimal weight: 0.8980 chunk 250 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 333 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 260 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 ASN ** 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 163 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 Q 92 ASN ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.091692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079463 restraints weight = 104158.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081869 restraints weight = 47761.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083386 restraints weight = 27716.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084482 restraints weight = 18909.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.085220 restraints weight = 14158.339| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.271 35541 Z= 0.251 Angle : 1.067 77.911 48210 Z= 0.488 Chirality : 0.046 0.599 5254 Planarity : 0.006 0.144 6117 Dihedral : 7.966 173.353 5011 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 3.04 % Allowed : 24.99 % Favored : 71.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.39 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4234 helix: 1.01 (0.12), residues: 1855 sheet: -1.07 (0.26), residues: 383 loop : -0.76 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG F 159 TYR 0.040 0.002 TYR Z 125 PHE 0.070 0.002 PHE A 55 TRP 0.070 0.002 TRP A 113 HIS 0.006 0.001 HIS H 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (35501) covalent geometry : angle 0.89424 / 0.49 (48120) SS BOND : bond 0.00245 / 0.13 ( 3) SS BOND : angle 2.24954 / 0.96 ( 6) hydrogen bonds : bond 0.03834 / 2.57 ( 1449) hydrogen bonds : angle 5.05326 / 3.60 ( 4155) metal coordination : bond 0.01383 / 0.84 ( 37) metal coordination : angle 13.95758 / 9.66 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.70 seconds wall clock time: 131 minutes 22.95 seconds (7882.95 seconds total)