Starting phenix.real_space_refine on Tue May 5 18:51:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnt_38514/05_2026/8xnt_38514.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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 7 5.49 5 S 242 5.16 5 C 20738 2.51 5 N 5536 2.21 5 O 5882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32434 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1641 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3095 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 21, 'TRANS': 364} Chain: "E" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1635 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 21, 'TRANS': 188} Chain: "F" Number of atoms: 3288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3288 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 21, 'TRANS': 404} Chain: "G" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5287 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain: "H" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 22, 'TRANS': 293} Chain breaks: 2 Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1398 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 1 Chain: "P" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2730 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 19, 'TRANS': 320} Chain: "Q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 957 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 305 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1164 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 11, 'TRANS': 67} Chain: "q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 44 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "r" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 413 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "s" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 226 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1014 SG CYS B 99 80.934 58.820 105.542 1.00 29.52 S ATOM 1517 SG CYS B 164 78.180 55.433 110.608 1.00 28.96 S ATOM 1747 SG CYS B 194 83.328 55.262 109.825 1.00 29.28 S ATOM 1020 SG CYS B 100 79.612 54.847 104.802 1.00 30.11 S ATOM 7534 SG CYS E 134 140.909 50.788 151.853 1.00 56.01 S ATOM 7568 SG CYS E 139 143.395 52.392 151.081 1.00 56.50 S ATOM 7852 SG CYS E 175 138.553 54.313 154.441 1.00 54.42 S ATOM 7875 SG CYS E 179 141.860 55.976 154.511 1.00 57.95 S ATOM 11405 SG CYS F 425 122.255 60.133 154.650 1.00 45.60 S ATOM 11083 SG CYS F 385 122.251 57.544 148.906 1.00 39.95 S ATOM 11063 SG CYS F 382 118.002 58.768 151.175 1.00 40.29 S ATOM 11044 SG CYS F 379 119.964 54.750 154.106 1.00 43.09 S ATOM 12453 SG CYS G 131 101.688 47.429 137.943 1.00 31.31 S ATOM 12432 SG CYS G 128 103.691 51.177 133.270 1.00 30.26 S ATOM 12493 SG CYS G 137 101.387 53.358 139.263 1.00 33.13 S ATOM 13178 SG CYS G 226 103.265 47.579 146.522 1.00 34.31 S ATOM 12849 SG CYS G 182 106.431 45.991 152.289 1.00 36.31 S ATOM 12825 SG CYS G 179 105.822 51.528 149.652 1.00 35.62 S ATOM 12802 SG CYS G 176 109.234 47.202 147.240 1.00 34.05 S ATOM 11939 SG CYS G 64 107.269 57.596 151.553 1.00 35.53 S ATOM 12025 SG CYS G 75 107.996 59.606 149.849 1.00 36.47 S ATOM 12050 SG CYS G 78 106.919 64.096 151.889 1.00 36.76 S ATOM 12151 SG CYS G 92 106.705 62.248 155.103 1.00 39.04 S ATOM 20166 SG CYS I 123 87.275 50.265 118.989 1.00 27.30 S ATOM 20392 SG CYS I 152 87.022 49.013 113.897 1.00 27.39 S ATOM 20439 SG CYS I 158 92.685 49.191 115.997 1.00 26.60 S ATOM 20418 SG CYS I 155 89.592 53.615 115.604 1.00 27.04 S ATOM 20115 SG CYS I 116 97.112 46.312 126.435 1.00 29.24 S ATOM 20138 SG CYS I 119 92.743 45.944 123.088 1.00 28.85 S ATOM 20096 SG CYS I 113 95.948 41.125 123.256 1.00 28.61 S ATOM 20468 SG CYS I 162 98.853 45.684 121.075 1.00 28.07 S ATOM 24622 SG CYS R 79 112.342 39.007 125.805 1.00 32.60 S ATOM 24798 SG CYS R 104 109.883 37.611 127.278 1.00 32.49 S ATOM 24820 SG CYS R 107 109.211 38.204 123.843 1.00 30.78 S Time building chain proxies: 7.46, per 1000 atoms: 0.23 Number of scatterers: 32434 At special positions: 0 Unit cell: (168.3, 127.6, 202.4, 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 242 16.00 P 7 15.00 O 5882 8.00 N 5536 7.00 C 20738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 46 " - pdb=" SG CYS X 56 " distance=2.03 Simple disulfide: pdb=" SG CYS X 88 " - pdb=" SG CYS X 100 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 179 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 139 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 134 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 175 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 78 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 64 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 75 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 92 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 100 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 164 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 194 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 99 " pdb=" SF4 F 502 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 382 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 379 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 425 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 385 " pdb=" SF4 G 801 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 131 " pdb="FE1 SF4 G 801 " - pdb=" NE2 HIS G 124 " pdb="FE3 SF4 G 801 " - pdb=" SG CYS G 128 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 137 " pdb=" SF4 G 802 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 176 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 226 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 179 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 182 " pdb=" SF4 I 301 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 123 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 152 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 155 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 158 " pdb="FE2 SF4 I 301 " - pdb=" NE2 HIS I 101 " pdb=" SF4 I 302 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 113 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 162 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 116 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 119 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 107 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 104 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 79 " Number of angles added : 3 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7550 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 30 sheets defined 50.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 24 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.313A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 108 Processing helix chain 'B' and resid 70 through 89 Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.583A pdb=" N GLU B 103 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.588A pdb=" N TYR B 171 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'C' and resid 50 through 68 removed outlier: 3.602A pdb=" N HIS C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.321A pdb=" N GLN C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.117A pdb=" N TYR C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 167 " --> pdb=" O ASN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.966A pdb=" N GLU D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 6.296A pdb=" N LEU D 130 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 140 removed outlier: 3.770A pdb=" N PHE D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.861A pdb=" N ASN D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 195 Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.706A pdb=" N PHE D 201 " --> pdb=" O MET D 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 206 " --> pdb=" O TRP D 202 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 263 removed outlier: 3.691A pdb=" N ASP D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 248 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 Processing helix chain 'D' and resid 279 through 286 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.671A pdb=" N SER D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 325 through 350 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 428 through 439 removed outlier: 3.531A pdb=" N LEU D 435 " --> pdb=" O HIS D 431 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 453 Processing helix chain 'D' and resid 457 through 463 removed outlier: 3.621A pdb=" N ILE D 461 " --> pdb=" O VAL D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 107 through 118 removed outlier: 3.526A pdb=" N VAL E 111 " --> pdb=" O PRO E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 143 through 156 removed outlier: 3.684A pdb=" N THR E 150 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 209 removed outlier: 3.577A pdb=" N ILE E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 201 " --> pdb=" O PRO E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 72 removed outlier: 3.558A pdb=" N GLY F 72 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 84 Processing helix chain 'F' and resid 94 through 102 removed outlier: 4.294A pdb=" N MET F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 134 removed outlier: 3.553A pdb=" N GLU F 129 " --> pdb=" O CYS F 125 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 150 removed outlier: 3.920A pdb=" N LEU F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.516A pdb=" N ALA F 166 " --> pdb=" O PHE F 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.637A pdb=" N GLY F 188 " --> pdb=" O ASN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.831A pdb=" N ILE F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 245 through 266 removed outlier: 3.565A pdb=" N SER F 251 " --> pdb=" O THR F 247 " (cutoff:3.500A) Proline residue: F 252 - end of helix removed outlier: 5.534A pdb=" N GLY F 259 " --> pdb=" O CYS F 255 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TRP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.861A pdb=" N ILE F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.156A pdb=" N GLU F 333 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.506A pdb=" N VAL F 343 " --> pdb=" O PHE F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 376 removed outlier: 3.546A pdb=" N LEU F 370 " --> pdb=" O ALA F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 402 removed outlier: 3.662A pdb=" N ASP F 390 " --> pdb=" O ARG F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 423 removed outlier: 3.915A pdb=" N SER F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 457 removed outlier: 4.348A pdb=" N ASP F 429 " --> pdb=" O CYS F 425 " (cutoff:3.500A) Proline residue: F 434 - end of helix removed outlier: 3.518A pdb=" N ARG F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Proline residue: F 444 - end of helix Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.598A pdb=" N VAL G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 115 removed outlier: 3.774A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.714A pdb=" N ASN G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 200 through 204 removed outlier: 3.932A pdb=" N ASP G 203 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.671A pdb=" N GLU G 395 " --> pdb=" O ALA G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 411 through 424 removed outlier: 4.025A pdb=" N ARG G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 458 Processing helix chain 'G' and resid 461 through 468 removed outlier: 4.007A pdb=" N VAL G 465 " --> pdb=" O SER G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 482 removed outlier: 3.636A pdb=" N LEU G 481 " --> pdb=" O GLY G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 505 Processing helix chain 'G' and resid 522 through 528 Processing helix chain 'G' and resid 534 through 540 Processing helix chain 'G' and resid 618 through 631 Processing helix chain 'G' and resid 638 through 650 Processing helix chain 'G' and resid 651 through 655 Processing helix chain 'G' and resid 664 through 675 removed outlier: 3.523A pdb=" N ALA G 668 " --> pdb=" O TYR G 664 " (cutoff:3.500A) Processing helix chain 'G' and resid 690 through 696 removed outlier: 3.640A pdb=" N PHE G 694 " --> pdb=" O THR G 690 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET G 696 " --> pdb=" O LYS G 692 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 703 Processing helix chain 'G' and resid 704 through 715 Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 10 through 32 removed outlier: 3.750A pdb=" N THR H 21 " --> pdb=" O MET H 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY H 29 " --> pdb=" O ARG H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 58 removed outlier: 3.574A pdb=" N ASP H 51 " --> pdb=" O GLN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 85 removed outlier: 3.739A 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: 4.099A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN H 124 " --> pdb=" O GLY H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 156 removed outlier: 3.855A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.734A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.898A pdb=" N GLU H 214 " --> pdb=" O PHE H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 277 removed outlier: 3.538A pdb=" N SER H 256 " --> pdb=" O PRO H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 291 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 49 through 62 Processing helix chain 'I' and resid 63 through 78 removed outlier: 3.529A pdb=" N THR I 73 " --> pdb=" O GLY I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 123 Processing helix chain 'I' and resid 156 through 162 Processing helix chain 'I' and resid 179 through 183 removed outlier: 3.865A pdb=" N LEU I 183 " --> pdb=" O THR I 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 179 through 183' Processing helix chain 'I' and resid 186 through 209 removed outlier: 5.144A pdb=" N ALA I 199 " --> pdb=" O ASP I 195 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.804A pdb=" N TYR P 68 " --> pdb=" O PHE P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 96 removed outlier: 4.873A pdb=" N HIS P 93 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU P 94 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG P 95 " --> pdb=" O ILE P 91 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 removed outlier: 4.105A pdb=" N ILE P 116 " --> pdb=" O ASP P 112 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS P 122 " --> pdb=" O LYS P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'P' and resid 146 through 160 removed outlier: 3.624A pdb=" N ALA P 153 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 195 removed outlier: 3.755A pdb=" N ARG P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.612A 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 308 removed outlier: 3.621A pdb=" N TRP P 300 " --> pdb=" O PHE P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 324 Processing helix chain 'P' and resid 344 through 354 removed outlier: 4.033A pdb=" N LYS P 348 " --> pdb=" O PRO P 344 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE P 350 " --> pdb=" O GLU P 346 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU P 351 " --> pdb=" O LEU P 347 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 357 No H-bonds generated for 'chain 'P' and resid 355 through 357' Processing helix chain 'P' and resid 360 through 364 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.412A pdb=" N GLY Q 66 " --> pdb=" O THR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 130 through 142 Processing helix chain 'Q' and resid 159 through 164 removed outlier: 4.199A pdb=" N ASN Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE Q 164 " --> pdb=" O TYR Q 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 159 through 164' Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'S' and resid 30 through 48 removed outlier: 6.446A pdb=" N VAL S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLU S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 95 Processing helix chain 'T' and resid 77 through 90 removed outlier: 3.811A pdb=" N TYR T 90 " --> pdb=" O VAL T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 127 Processing helix chain 'T' and resid 133 through 138 removed outlier: 3.625A pdb=" N LYS T 137 " --> pdb=" O ILE T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 150 Processing helix chain 'V' and resid 19 through 36 Processing helix chain 'V' and resid 42 through 62 Processing helix chain 'V' and resid 64 through 72 Processing helix chain 'V' and resid 76 through 98 removed outlier: 3.676A pdb=" N VAL V 80 " --> pdb=" O GLU V 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 53 removed outlier: 3.586A 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: 3.616A pdb=" N ASN W 73 " --> pdb=" O MET W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 97 Processing helix chain 'W' and resid 98 through 100 No H-bonds generated for 'chain 'W' and resid 98 through 100' Processing helix chain 'W' and resid 102 through 108 removed outlier: 3.643A pdb=" N ARG W 108 " --> pdb=" O THR W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 109 through 111 No H-bonds generated for 'chain 'W' and resid 109 through 111' Processing helix chain 'W' and resid 120 through 128 Processing helix chain 'X' and resid 10 through 14 removed outlier: 3.529A pdb=" N LYS X 14 " --> pdb=" O GLU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 21 through 36 removed outlier: 4.625A pdb=" N HIS X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 51 Processing helix chain 'X' and resid 52 through 55 Processing helix chain 'X' and resid 56 through 77 Processing helix chain 'X' and resid 78 through 92 removed outlier: 3.945A pdb=" N SER X 92 " --> pdb=" O CYS X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 114 Processing helix chain 'X' and resid 140 through 144 removed outlier: 4.463A pdb=" N SER X 144 " --> pdb=" O PRO X 141 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 98 Proline residue: Z 73 - end of helix removed outlier: 3.905A pdb=" N MET Z 98 " --> pdb=" O GLU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 126 Processing helix chain 'Z' and resid 129 through 139 Processing helix chain 'a' and resid 4 through 31 removed outlier: 4.500A pdb=" N GLY a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS a 15 " --> pdb=" O ILE a 11 " (cutoff:3.500A) Proline residue: a 19 - end of helix removed outlier: 4.598A pdb=" N LYS a 28 " --> pdb=" O ALA a 24 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR a 30 " --> pdb=" O ILE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 55 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 18 through 32 Processing helix chain 'b' and resid 38 through 49 removed outlier: 3.759A pdb=" N ALA b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 Processing helix chain 's' and resid 43 through 54 removed outlier: 4.204A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.373A pdb=" N MET B 131 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET B 161 " --> pdb=" O MET B 131 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 133 " --> pdb=" O MET B 161 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 158 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 191 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER B 160 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 72 through 78 removed outlier: 3.523A pdb=" N GLN C 74 " --> pdb=" O CYS C 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 82 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU C 83 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LYS C 143 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 85 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL C 116 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 132 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU C 110 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.148A pdb=" N ILE C 152 " --> pdb=" O PHE C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 207 through 212 removed outlier: 3.564A pdb=" N ARG C 210 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.254A pdb=" N ARG D 96 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 100 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 108 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.373A pdb=" N VAL D 318 " --> pdb=" O LYS I 37 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 397 through 401 Processing sheet with id=AA9, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'F' and resid 195 through 199 removed outlier: 6.441A pdb=" N ALA F 154 " --> pdb=" O PHE F 196 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL F 198 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 156 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU F 113 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR F 157 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 115 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR F 241 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 286 through 288 removed outlier: 6.152A pdb=" N ASN F 277 " --> pdb=" O VAL F 354 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL F 356 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER F 279 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'G' and resid 89 through 90 removed outlier: 3.867A pdb=" N GLU G 81 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.312A 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=AB7, first strand: chain 'G' and resid 306 through 308 Processing sheet with id=AB8, first strand: chain 'G' and resid 531 through 532 removed outlier: 6.455A pdb=" N LEU G 366 " --> pdb=" O LYS G 531 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU G 545 " --> pdb=" O VAL G 567 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 442 through 446 removed outlier: 6.202A pdb=" N VAL G 400 " --> pdb=" O ALA G 430 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE G 432 " --> pdb=" O VAL G 400 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU G 402 " --> pdb=" O ILE G 432 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 595 through 597 Processing sheet with id=AC2, first strand: chain 'I' and resid 100 through 103 Processing sheet with id=AC3, first strand: chain 'I' and resid 128 through 134 removed outlier: 6.407A pdb=" N GLU I 133 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR I 142 " --> pdb=" O GLU I 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 103 through 107 removed outlier: 6.361A pdb=" N THR P 57 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 206 through 207 Processing sheet with id=AC6, first strand: chain 'P' and resid 226 through 227 removed outlier: 6.359A pdb=" N VAL P 226 " --> pdb=" O TYR P 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 128 Processing sheet with id=AC8, first strand: chain 'Q' and resid 106 through 108 Processing sheet with id=AC9, first strand: chain 'R' and resid 76 through 77 Processing sheet with id=AD1, first strand: chain 'R' and resid 102 through 103 removed outlier: 3.506A pdb=" N GLY R 102 " --> pdb=" O PHE R 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 53 through 56 removed outlier: 3.670A pdb=" N GLN S 73 " --> pdb=" O TYR S 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 129 through 130 1397 hydrogen bonds defined for protein. 4059 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: 7.22 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 11004 1.37 - 1.59: 21751 1.59 - 1.80: 246 1.80 - 2.02: 132 2.02 - 2.23: 80 Bond restraints: 33213 Sorted by residual: bond pdb=" O6 EHZ W 201 " pdb=" P1 EHZ W 201 " ideal model delta sigma weight residual 2.378 1.647 0.731 2.00e-02 2.50e+03 1.34e+03 bond pdb=" C20 EHZ W 201 " pdb=" O6 EHZ W 201 " ideal model delta sigma weight residual 1.191 1.399 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C15 EHZ W 201 " pdb=" O4 EHZ W 201 " ideal model delta sigma weight residual 1.356 1.179 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C VAL W 106 " pdb=" N MET W 107 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.35e-02 5.49e+03 7.42e+01 bond pdb=" C ILE Q 53 " pdb=" O ILE Q 53 " ideal model delta sigma weight residual 1.236 1.330 -0.094 1.20e-02 6.94e+03 6.11e+01 ... (remaining 33208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.66: 44327 6.66 - 13.33: 548 13.33 - 19.99: 156 19.99 - 26.65: 3 26.65 - 33.32: 2 Bond angle restraints: 45036 Sorted by residual: angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" CB VAL D 142 " ideal model delta sigma weight residual 110.65 132.46 -21.81 1.13e+00 7.83e-01 3.73e+02 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 110.42 92.53 17.89 9.40e-01 1.13e+00 3.62e+02 angle pdb=" N THR G 174 " pdb=" CA THR G 174 " pdb=" C THR G 174 " ideal model delta sigma weight residual 114.64 89.00 25.64 1.52e+00 4.33e-01 2.84e+02 angle pdb=" N CYS F 125 " pdb=" CA CYS F 125 " pdb=" C CYS F 125 " ideal model delta sigma weight residual 113.17 93.49 19.68 1.26e+00 6.30e-01 2.44e+02 angle pdb=" N ILE G 251 " pdb=" CA ILE G 251 " pdb=" C ILE G 251 " ideal model delta sigma weight residual 108.17 126.88 -18.71 1.40e+00 5.10e-01 1.79e+02 ... (remaining 45031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.71: 19319 26.71 - 53.42: 619 53.42 - 80.12: 77 80.12 - 106.83: 8 106.83 - 133.54: 3 Dihedral angle restraints: 20026 sinusoidal: 8321 harmonic: 11705 Sorted by residual: dihedral pdb=" C ASP D 140 " pdb=" N ASP D 140 " pdb=" CA ASP D 140 " pdb=" CB ASP D 140 " ideal model delta harmonic sigma weight residual -122.60 -101.23 -21.37 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" CB CYS X 88 " pdb=" SG CYS X 88 " pdb=" SG CYS X 100 " pdb=" CB CYS X 100 " ideal model delta sinusoidal sigma weight residual 93.00 161.51 -68.51 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" C LEU G 387 " pdb=" N LEU G 387 " pdb=" CA LEU G 387 " pdb=" CB LEU G 387 " ideal model delta harmonic sigma weight residual -122.60 -105.66 -16.94 0 2.50e+00 1.60e-01 4.59e+01 ... (remaining 20023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4382 0.182 - 0.364: 503 0.364 - 0.546: 47 0.546 - 0.728: 3 0.728 - 0.910: 24 Chirality restraints: 4959 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 2.07e+01 chirality pdb="FE3 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S4 SF4 I 302 " both_signs ideal model delta sigma weight residual False -10.55 -9.65 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb="FE2 SF4 I 301 " pdb=" S1 SF4 I 301 " pdb=" S3 SF4 I 301 " pdb=" S4 SF4 I 301 " both_signs ideal model delta sigma weight residual False 10.55 9.65 0.91 2.00e-01 2.50e+01 2.05e+01 ... (remaining 4956 not shown) Planarity restraints: 5728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET H 91 " -0.090 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO H 92 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO H 92 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO H 92 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 224 " 0.025 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLU C 224 " -0.086 2.00e-02 2.50e+03 pdb=" O GLU C 224 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU C 225 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 88 " -0.069 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO R 89 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " -0.065 5.00e-02 4.00e+02 ... (remaining 5725 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 74 2.38 - 3.01: 22018 3.01 - 3.64: 50739 3.64 - 4.27: 79698 4.27 - 4.90: 128784 Nonbonded interactions: 281313 Sorted by model distance: nonbonded pdb=" O ASP I 208 " pdb=" OD1 ASP I 208 " model vdw 1.755 3.040 nonbonded pdb=" O ASN F 116 " pdb=" OD1 ASN F 116 " model vdw 1.941 3.040 nonbonded pdb=" O ASP Q 146 " pdb=" OD1 ASP Q 146 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASN P 376 " pdb=" N TYR P 377 " model vdw 1.980 3.120 nonbonded pdb=" O ASN H 97 " pdb=" OD1 ASN H 97 " model vdw 1.982 3.040 ... (remaining 281308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 40.710 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:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5290 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 1.140 33253 Z= 1.041 Angle : 2.258 52.589 45126 Z= 1.505 Chirality : 0.131 0.910 4959 Planarity : 0.007 0.137 5728 Dihedral : 12.887 133.541 12467 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 43.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 0.26 % Allowed : 7.70 % Favored : 92.04 % Cbeta Deviations : 1.64 % 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: -2.14 (0.12), residues: 3981 helix: -0.80 (0.11), residues: 1757 sheet: -1.23 (0.29), residues: 321 loop : -2.05 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 333 TYR 0.045 0.003 TYR B 112 PHE 0.032 0.002 PHE G 462 TRP 0.034 0.002 TRP G 285 HIS 0.018 0.002 HIS H 93 Details of bonding type rmsd covalent geometry : bond 0.01449 (33213) covalent geometry : angle 2.12278 (45036) SS BOND : bond 0.00740 ( 3) SS BOND : angle 2.18317 ( 6) hydrogen bonds : bond 0.24675 ( 1397) hydrogen bonds : angle 8.96165 ( 4059) metal coordination : bond 0.52304 ( 37) metal coordination : angle 17.98820 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1267 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 TYR cc_start: 0.6680 (m-80) cc_final: 0.6126 (m-80) REVERT: B 220 ILE cc_start: 0.8208 (pt) cc_final: 0.7977 (tp) REVERT: C 83 LEU cc_start: 0.7076 (tp) cc_final: 0.6411 (tt) REVERT: C 132 LEU cc_start: 0.7326 (tp) cc_final: 0.7051 (tt) REVERT: D 255 ILE cc_start: 0.8297 (mt) cc_final: 0.8086 (mt) REVERT: D 344 ILE cc_start: 0.8617 (mt) cc_final: 0.8393 (tp) REVERT: D 400 ILE cc_start: 0.7288 (pt) cc_final: 0.6826 (pt) REVERT: D 447 VAL cc_start: 0.7157 (t) cc_final: 0.6824 (p) REVERT: F 149 MET cc_start: -0.2008 (ptp) cc_final: -0.2552 (ptm) REVERT: H 57 MET cc_start: 0.5330 (mtt) cc_final: 0.4397 (mtt) REVERT: H 96 ILE cc_start: 0.7693 (mt) cc_final: 0.7459 (mt) REVERT: H 154 LEU cc_start: 0.8458 (mt) cc_final: 0.8218 (mp) REVERT: H 192 GLU cc_start: 0.6372 (tp30) cc_final: 0.5963 (tp30) REVERT: H 233 LEU cc_start: 0.7850 (tp) cc_final: 0.7497 (tt) REVERT: H 271 LEU cc_start: 0.8330 (mp) cc_final: 0.8062 (mp) REVERT: H 288 LEU cc_start: 0.7322 (tt) cc_final: 0.6645 (tt) REVERT: H 311 THR cc_start: 0.6781 (p) cc_final: 0.6271 (p) REVERT: P 280 ILE cc_start: 0.8262 (mt) cc_final: 0.7944 (mm) REVERT: Q 53 ILE cc_start: 0.4607 (pt) cc_final: 0.4389 (pt) REVERT: Q 137 PHE cc_start: 0.5355 (t80) cc_final: 0.5060 (t80) REVERT: S 78 SER cc_start: 0.7577 (t) cc_final: 0.7289 (p) REVERT: T 118 ILE cc_start: 0.8068 (mm) cc_final: 0.7388 (mm) REVERT: V 88 LEU cc_start: 0.8244 (tp) cc_final: 0.8033 (tp) REVERT: W 66 VAL cc_start: 0.8696 (t) cc_final: 0.8447 (t) REVERT: Z 10 MET cc_start: 0.7653 (mtp) cc_final: 0.7200 (mtp) REVERT: Z 43 LEU cc_start: 0.7299 (mt) cc_final: 0.6464 (mt) outliers start: 9 outliers final: 2 residues processed: 1272 average time/residue: 0.2422 time to fit residues: 474.7288 Evaluate side-chains 711 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 709 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 GLN C 88 HIS ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS D 117 HIS D 131 GLN D 147 ASN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 346 GLN D 381 HIS E 68 ASN E 86 GLN E 152 GLN F 44 ASN F 281 HIS G 59 GLN G 74 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 444 HIS G 460 HIS G 495 ASN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 604 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 97 ASN H 169 GLN H 284 GLN ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 GLN P 251 ASN P 323 HIS P 341 GLN Q 51 GLN Q 86 ASN S 93 ASN V 21 HIS V 50 GLN V 83 GLN V 111 GLN ** W 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 30 HIS X 64 ASN X 77 HIS X 104 GLN X 109 GLN a 42 GLN ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 110 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.102470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.070704 restraints weight = 151455.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071904 restraints weight = 90720.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072812 restraints weight = 61441.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.073712 restraints weight = 47738.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.073921 restraints weight = 41511.960| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 33253 Z= 0.227 Angle : 1.071 69.707 45126 Z= 0.446 Chirality : 0.049 0.277 4959 Planarity : 0.007 0.114 5728 Dihedral : 7.634 133.473 4534 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 0.43 % Allowed : 3.86 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3981 helix: 0.05 (0.11), residues: 1843 sheet: -1.21 (0.27), residues: 349 loop : -1.40 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 25 TYR 0.063 0.003 TYR B 170 PHE 0.034 0.003 PHE H 310 TRP 0.045 0.003 TRP H 272 HIS 0.012 0.002 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00494 (33213) covalent geometry : angle 0.85483 (45036) SS BOND : bond 0.00572 ( 3) SS BOND : angle 1.49208 ( 6) hydrogen bonds : bond 0.06214 ( 1397) hydrogen bonds : angle 5.80461 ( 4059) metal coordination : bond 0.02879 ( 37) metal coordination : angle 14.95940 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 884 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9153 (mt) cc_final: 0.8842 (mt) REVERT: A 55 PHE cc_start: 0.8927 (m-80) cc_final: 0.8704 (m-80) REVERT: A 56 PHE cc_start: 0.9172 (t80) cc_final: 0.8762 (t80) REVERT: A 60 ILE cc_start: 0.9693 (mm) cc_final: 0.9436 (mm) REVERT: A 88 MET cc_start: 0.8617 (mpp) cc_final: 0.8401 (mpp) REVERT: A 92 PHE cc_start: 0.9307 (m-10) cc_final: 0.9034 (m-80) REVERT: B 91 TRP cc_start: 0.9156 (m100) cc_final: 0.8838 (m100) REVERT: B 103 GLU cc_start: 0.8730 (tp30) cc_final: 0.8153 (tp30) REVERT: B 107 MET cc_start: 0.9396 (ttm) cc_final: 0.9188 (ttm) REVERT: B 113 ASP cc_start: 0.8899 (t0) cc_final: 0.7316 (t0) REVERT: B 151 GLN cc_start: 0.9315 (mt0) cc_final: 0.9010 (mp10) REVERT: B 152 MET cc_start: 0.9020 (mtm) cc_final: 0.8385 (mtt) REVERT: B 175 TYR cc_start: 0.9153 (p90) cc_final: 0.8902 (p90) REVERT: C 96 LEU cc_start: 0.9525 (mt) cc_final: 0.9268 (mt) REVERT: C 104 ASN cc_start: 0.9258 (m-40) cc_final: 0.8336 (t0) REVERT: C 112 ASP cc_start: 0.8540 (p0) cc_final: 0.8321 (p0) REVERT: C 165 TYR cc_start: 0.8818 (m-80) cc_final: 0.8556 (m-80) REVERT: C 231 LYS cc_start: 0.9135 (tppt) cc_final: 0.8925 (tppt) REVERT: D 84 PHE cc_start: 0.8172 (t80) cc_final: 0.7581 (t80) REVERT: D 95 LEU cc_start: 0.9175 (tp) cc_final: 0.8870 (tp) REVERT: D 110 ASP cc_start: 0.8414 (t0) cc_final: 0.8069 (t0) REVERT: D 116 LEU cc_start: 0.9477 (tp) cc_final: 0.9275 (tp) REVERT: D 174 PHE cc_start: 0.9291 (m-80) cc_final: 0.9030 (m-80) REVERT: D 194 ILE cc_start: 0.9255 (mm) cc_final: 0.9037 (mm) REVERT: D 200 PHE cc_start: 0.9588 (t80) cc_final: 0.9313 (t80) REVERT: D 261 MET cc_start: 0.8876 (mmp) cc_final: 0.8533 (mmm) REVERT: D 288 PHE cc_start: 0.8479 (m-10) cc_final: 0.8137 (m-80) REVERT: D 323 ARG cc_start: 0.7779 (mpp-170) cc_final: 0.7332 (mpt180) REVERT: D 371 MET cc_start: 0.8472 (ptt) cc_final: 0.8213 (ptt) REVERT: D 432 LEU cc_start: 0.9511 (tp) cc_final: 0.9305 (tp) REVERT: E 116 THR cc_start: 0.6832 (p) cc_final: 0.6497 (p) REVERT: F 313 ASN cc_start: 0.5596 (m-40) cc_final: 0.5249 (t0) REVERT: F 357 MET cc_start: 0.2116 (ptp) cc_final: 0.1869 (ptp) REVERT: G 254 MET cc_start: 0.8114 (mtt) cc_final: 0.6910 (ppp) REVERT: G 271 MET cc_start: 0.7909 (mmp) cc_final: 0.7707 (mmm) REVERT: G 345 LEU cc_start: 0.8998 (mt) cc_final: 0.8751 (mt) REVERT: G 513 MET cc_start: 0.7842 (pmm) cc_final: 0.7455 (pmm) REVERT: G 544 MET cc_start: 0.8520 (tmm) cc_final: 0.8139 (tmm) REVERT: G 571 HIS cc_start: 0.8178 (p-80) cc_final: 0.7445 (p-80) REVERT: G 637 ASP cc_start: 0.8611 (p0) cc_final: 0.8364 (p0) REVERT: H 11 VAL cc_start: 0.9550 (t) cc_final: 0.9121 (t) REVERT: H 33 LEU cc_start: 0.9348 (mm) cc_final: 0.9138 (mp) REVERT: H 34 ARG cc_start: 0.9234 (ptt90) cc_final: 0.9017 (tmm-80) REVERT: H 47 GLN cc_start: 0.9284 (tp40) cc_final: 0.8725 (tp-100) REVERT: H 53 MET cc_start: 0.9191 (tpt) cc_final: 0.8917 (tpp) REVERT: H 54 LYS cc_start: 0.8974 (pttp) cc_final: 0.8770 (ptmm) REVERT: H 100 LEU cc_start: 0.8863 (mt) cc_final: 0.8407 (mm) REVERT: H 143 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8959 (mm-30) REVERT: H 146 MET cc_start: 0.9358 (ttp) cc_final: 0.8964 (ptp) REVERT: H 187 ILE cc_start: 0.9500 (OUTLIER) cc_final: 0.9272 (mm) REVERT: H 195 ARG cc_start: 0.8734 (tpt90) cc_final: 0.8425 (tpp-160) REVERT: H 234 MET cc_start: 0.9649 (mmp) cc_final: 0.9360 (mmp) REVERT: I 126 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8538 (mm-40) REVERT: I 128 ILE cc_start: 0.8692 (mt) cc_final: 0.8383 (mt) REVERT: I 185 TYR cc_start: 0.8615 (m-80) cc_final: 0.7912 (m-10) REVERT: I 190 LEU cc_start: 0.9458 (mt) cc_final: 0.9218 (mt) REVERT: P 148 ILE cc_start: 0.9156 (mm) cc_final: 0.8917 (mt) REVERT: P 201 ILE cc_start: 0.9534 (mt) cc_final: 0.9308 (tp) REVERT: P 251 ASN cc_start: 0.9153 (m-40) cc_final: 0.8927 (m110) REVERT: P 265 PHE cc_start: 0.7297 (m-10) cc_final: 0.7080 (m-10) REVERT: Q 101 PHE cc_start: 0.7621 (m-80) cc_final: 0.7050 (m-80) REVERT: Q 112 MET cc_start: 0.4131 (mmp) cc_final: 0.3301 (mmm) REVERT: Q 125 VAL cc_start: 0.8659 (m) cc_final: 0.8442 (m) REVERT: Q 149 GLU cc_start: 0.6696 (pp20) cc_final: 0.6303 (pp20) REVERT: T 125 GLU cc_start: 0.8764 (pp20) cc_final: 0.8467 (pp20) REVERT: W 45 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8929 (tm-30) REVERT: W 69 MET cc_start: 0.8287 (mpp) cc_final: 0.7997 (mtt) REVERT: W 91 MET cc_start: 0.9073 (mtp) cc_final: 0.8807 (mtm) REVERT: W 98 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8536 (pttm) REVERT: Z 43 LEU cc_start: 0.8981 (mt) cc_final: 0.8708 (mt) REVERT: Z 71 LEU cc_start: 0.9609 (mt) cc_final: 0.9133 (mp) REVERT: a 23 THR cc_start: 0.8447 (p) cc_final: 0.8120 (p) REVERT: q 93 MET cc_start: 0.7845 (ptt) cc_final: 0.7447 (ptt) REVERT: r 109 ASP cc_start: 0.8713 (p0) cc_final: 0.7628 (p0) REVERT: r 112 TYR cc_start: 0.8889 (m-80) cc_final: 0.8645 (m-80) outliers start: 15 outliers final: 3 residues processed: 893 average time/residue: 0.2089 time to fit residues: 298.9418 Evaluate side-chains 630 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 626 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 270 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 384 optimal weight: 40.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 453 GLN ** G 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN P 269 ASN Q 86 ASN Q 109 ASN S 81 ASN ** X 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 ASN b 69 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.101263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.070392 restraints weight = 156188.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.071647 restraints weight = 95841.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.072102 restraints weight = 63329.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.072396 restraints weight = 50382.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.072634 restraints weight = 44154.864| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33253 Z= 0.226 Angle : 1.025 71.971 45126 Z= 0.402 Chirality : 0.047 0.225 4959 Planarity : 0.006 0.117 5728 Dihedral : 7.408 140.823 4534 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 0.17 % Allowed : 3.95 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 3981 helix: 0.19 (0.11), residues: 1871 sheet: -1.07 (0.30), residues: 318 loop : -1.14 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG P 212 TYR 0.045 0.002 TYR H 142 PHE 0.036 0.003 PHE C 60 TRP 0.021 0.002 TRP Q 114 HIS 0.011 0.002 HIS P 72 Details of bonding type rmsd covalent geometry : bond 0.00478 (33213) covalent geometry : angle 0.78091 (45036) SS BOND : bond 0.00422 ( 3) SS BOND : angle 1.05511 ( 6) hydrogen bonds : bond 0.04961 ( 1397) hydrogen bonds : angle 5.45831 ( 4059) metal coordination : bond 0.02566 ( 37) metal coordination : angle 15.39665 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 763 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 8 PHE cc_start: 0.9067 (t80) cc_final: 0.8859 (t80) REVERT: A 24 LEU cc_start: 0.9729 (tp) cc_final: 0.9366 (tp) REVERT: A 68 GLU cc_start: 0.9489 (tt0) cc_final: 0.9287 (tt0) REVERT: A 92 PHE cc_start: 0.9256 (m-10) cc_final: 0.9014 (m-80) REVERT: B 91 TRP cc_start: 0.9368 (m100) cc_final: 0.8867 (m100) REVERT: B 93 MET cc_start: 0.8944 (tmm) cc_final: 0.8542 (tmm) REVERT: B 103 GLU cc_start: 0.8761 (tp30) cc_final: 0.8248 (tp30) REVERT: B 107 MET cc_start: 0.9363 (ttm) cc_final: 0.8881 (ttm) REVERT: B 114 MET cc_start: 0.8528 (ptm) cc_final: 0.8248 (ptm) REVERT: B 115 ASP cc_start: 0.9250 (m-30) cc_final: 0.8953 (m-30) REVERT: B 129 ASP cc_start: 0.9236 (m-30) cc_final: 0.8786 (m-30) REVERT: B 141 MET cc_start: 0.9156 (tpp) cc_final: 0.8839 (tpp) REVERT: B 151 GLN cc_start: 0.9311 (mt0) cc_final: 0.8879 (mt0) REVERT: B 158 VAL cc_start: 0.9516 (t) cc_final: 0.8104 (t) REVERT: B 161 MET cc_start: 0.8072 (ttp) cc_final: 0.7584 (ttp) REVERT: B 171 TYR cc_start: 0.9041 (m-80) cc_final: 0.8797 (m-10) REVERT: B 173 TYR cc_start: 0.7919 (m-10) cc_final: 0.7484 (m-10) REVERT: B 201 LEU cc_start: 0.9518 (tt) cc_final: 0.9082 (tt) REVERT: C 96 LEU cc_start: 0.9582 (mt) cc_final: 0.9381 (mt) REVERT: C 104 ASN cc_start: 0.9283 (m-40) cc_final: 0.8766 (t0) REVERT: C 172 MET cc_start: 0.8890 (mmm) cc_final: 0.8622 (mmm) REVERT: D 84 PHE cc_start: 0.8448 (t80) cc_final: 0.8124 (t80) REVERT: D 95 LEU cc_start: 0.9201 (tp) cc_final: 0.8968 (tp) REVERT: D 110 ASP cc_start: 0.8343 (t0) cc_final: 0.7980 (t0) REVERT: D 122 LYS cc_start: 0.9250 (tptp) cc_final: 0.8815 (tptm) REVERT: D 144 MET cc_start: 0.8984 (mpp) cc_final: 0.8478 (mmm) REVERT: D 194 ILE cc_start: 0.9306 (mm) cc_final: 0.9082 (mm) REVERT: D 203 MET cc_start: 0.9630 (mmm) cc_final: 0.9265 (mmm) REVERT: D 226 TYR cc_start: 0.8837 (t80) cc_final: 0.8390 (t80) REVERT: D 261 MET cc_start: 0.8888 (mmp) cc_final: 0.8620 (mmm) REVERT: D 288 PHE cc_start: 0.8545 (m-10) cc_final: 0.8086 (m-80) REVERT: D 337 MET cc_start: 0.9233 (tpp) cc_final: 0.8821 (tpp) REVERT: D 351 MET cc_start: 0.9649 (tpp) cc_final: 0.9293 (tpp) REVERT: D 432 LEU cc_start: 0.9589 (tp) cc_final: 0.9341 (tp) REVERT: F 62 TRP cc_start: 0.1260 (m-90) cc_final: 0.1006 (m-10) REVERT: F 255 CYS cc_start: -0.0237 (m) cc_final: -0.0628 (m) REVERT: F 313 ASN cc_start: 0.5436 (m-40) cc_final: 0.5174 (t0) REVERT: G 145 MET cc_start: 0.8367 (mpp) cc_final: 0.7930 (mtp) REVERT: G 173 MET cc_start: 0.8006 (ttt) cc_final: 0.7290 (tpt) REVERT: G 285 TRP cc_start: 0.8111 (m-90) cc_final: 0.7741 (m-90) REVERT: G 345 LEU cc_start: 0.8919 (mt) cc_final: 0.8635 (mt) REVERT: G 513 MET cc_start: 0.7852 (pmm) cc_final: 0.7144 (pmm) REVERT: G 544 MET cc_start: 0.8741 (tmm) cc_final: 0.8281 (tmm) REVERT: G 571 HIS cc_start: 0.8212 (p-80) cc_final: 0.7614 (p-80) REVERT: G 579 MET cc_start: 0.7507 (ptt) cc_final: 0.7269 (ppp) REVERT: G 707 MET cc_start: 0.7705 (mmt) cc_final: 0.6732 (tpp) REVERT: H 31 MET cc_start: 0.9339 (mtt) cc_final: 0.8773 (mmm) REVERT: H 47 GLN cc_start: 0.9277 (tp40) cc_final: 0.8669 (tp-100) REVERT: H 53 MET cc_start: 0.9150 (tpt) cc_final: 0.8511 (tpp) REVERT: H 54 LYS cc_start: 0.9221 (pttp) cc_final: 0.8993 (ptmm) REVERT: H 59 GLU cc_start: 0.8267 (tp30) cc_final: 0.7644 (tm-30) REVERT: H 100 LEU cc_start: 0.8717 (mt) cc_final: 0.8159 (mm) REVERT: H 118 TRP cc_start: 0.9189 (m-10) cc_final: 0.8980 (m-90) REVERT: H 138 GLN cc_start: 0.9237 (pm20) cc_final: 0.8973 (pm20) REVERT: H 143 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8290 (mm-30) REVERT: H 146 MET cc_start: 0.9422 (ttp) cc_final: 0.9042 (ptp) REVERT: H 187 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9334 (mp) REVERT: H 192 GLU cc_start: 0.8516 (tp30) cc_final: 0.8259 (tp30) REVERT: H 228 TYR cc_start: 0.9517 (m-80) cc_final: 0.9310 (m-80) REVERT: H 234 MET cc_start: 0.9631 (mmp) cc_final: 0.9312 (mmp) REVERT: H 284 GLN cc_start: 0.9520 (mm110) cc_final: 0.9308 (mp10) REVERT: H 285 LEU cc_start: 0.9262 (tt) cc_final: 0.9033 (mt) REVERT: H 286 MET cc_start: 0.8921 (ptt) cc_final: 0.8553 (ptt) REVERT: H 290 TRP cc_start: 0.9291 (m100) cc_final: 0.9066 (m100) REVERT: H 293 PHE cc_start: 0.9289 (m-80) cc_final: 0.8886 (m-80) REVERT: H 318 MET cc_start: 0.7135 (tpt) cc_final: 0.6836 (tmm) REVERT: I 185 TYR cc_start: 0.8966 (m-80) cc_final: 0.8013 (m-10) REVERT: P 92 MET cc_start: 0.8918 (mmp) cc_final: 0.8577 (tpp) REVERT: P 148 ILE cc_start: 0.9198 (mm) cc_final: 0.8984 (mt) REVERT: P 251 ASN cc_start: 0.9304 (m-40) cc_final: 0.9103 (m110) REVERT: P 269 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6201 (p0) REVERT: Q 101 PHE cc_start: 0.7530 (m-80) cc_final: 0.7242 (m-80) REVERT: Q 112 MET cc_start: 0.4451 (mmp) cc_final: 0.4055 (mmm) REVERT: Q 132 GLU cc_start: 0.8875 (pm20) cc_final: 0.8642 (pm20) REVERT: Q 133 ASP cc_start: 0.9222 (m-30) cc_final: 0.8883 (m-30) REVERT: T 88 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8757 (mmtt) REVERT: T 130 ILE cc_start: 0.6810 (tt) cc_final: 0.6489 (tt) REVERT: V 28 TYR cc_start: 0.9042 (m-80) cc_final: 0.8645 (m-80) REVERT: W 45 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8931 (tm-30) REVERT: W 91 MET cc_start: 0.9162 (mtp) cc_final: 0.8698 (mtp) REVERT: W 98 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8342 (pttt) REVERT: X 44 MET cc_start: 0.9202 (mmm) cc_final: 0.8693 (mmm) REVERT: Z 10 MET cc_start: 0.8690 (tpp) cc_final: 0.8477 (tpp) REVERT: Z 43 LEU cc_start: 0.9117 (mt) cc_final: 0.8822 (mt) REVERT: Z 51 MET cc_start: 0.8911 (tmm) cc_final: 0.8648 (tmm) REVERT: Z 75 PHE cc_start: 0.9183 (m-80) cc_final: 0.8709 (m-80) REVERT: a 23 THR cc_start: 0.8517 (p) cc_final: 0.7986 (p) REVERT: b 23 PHE cc_start: 0.8092 (t80) cc_final: 0.7685 (t80) REVERT: q 93 MET cc_start: 0.7993 (ptt) cc_final: 0.7628 (ptt) REVERT: r 96 THR cc_start: 0.8630 (p) cc_final: 0.8296 (p) REVERT: r 112 TYR cc_start: 0.8836 (m-80) cc_final: 0.8597 (m-80) outliers start: 6 outliers final: 0 residues processed: 765 average time/residue: 0.2055 time to fit residues: 254.4137 Evaluate side-chains 601 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 599 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 169 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 391 optimal weight: 0.6980 chunk 255 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 GLN ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 ASN Q 123 ASN V 50 GLN W 73 ASN ** a 31 ASN ** 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 = 0.4090 r_free = 0.4090 target = 0.099755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.068117 restraints weight = 154437.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.068786 restraints weight = 92462.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.070117 restraints weight = 63606.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.070653 restraints weight = 49784.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.071194 restraints weight = 43174.833| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33253 Z= 0.156 Angle : 0.975 71.831 45126 Z= 0.364 Chirality : 0.045 0.247 4959 Planarity : 0.005 0.118 5728 Dihedral : 7.220 148.568 4534 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 3981 helix: 0.40 (0.12), residues: 1849 sheet: -1.06 (0.29), residues: 319 loop : -0.98 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 230 TYR 0.040 0.002 TYR H 142 PHE 0.045 0.002 PHE C 197 TRP 0.022 0.002 TRP H 303 HIS 0.010 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00352 (33213) covalent geometry : angle 0.71714 (45036) SS BOND : bond 0.00502 ( 3) SS BOND : angle 1.44738 ( 6) hydrogen bonds : bond 0.04476 ( 1397) hydrogen bonds : angle 5.25097 ( 4059) metal coordination : bond 0.01556 ( 37) metal coordination : angle 15.34013 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 771 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.9538 (t80) cc_final: 0.9319 (t80) REVERT: A 88 MET cc_start: 0.9082 (mmt) cc_final: 0.8768 (mmp) REVERT: A 92 PHE cc_start: 0.9257 (m-10) cc_final: 0.8920 (m-80) REVERT: B 91 TRP cc_start: 0.9180 (m100) cc_final: 0.8950 (m100) REVERT: B 103 GLU cc_start: 0.8746 (tp30) cc_final: 0.8149 (tp30) REVERT: B 129 ASP cc_start: 0.9386 (m-30) cc_final: 0.8936 (m-30) REVERT: B 141 MET cc_start: 0.9309 (tpp) cc_final: 0.8882 (tpp) REVERT: B 151 GLN cc_start: 0.9357 (mt0) cc_final: 0.8938 (mt0) REVERT: B 152 MET cc_start: 0.9455 (mtm) cc_final: 0.9180 (mtt) REVERT: B 161 MET cc_start: 0.8401 (ttp) cc_final: 0.7872 (ttp) REVERT: B 171 TYR cc_start: 0.8996 (m-80) cc_final: 0.8477 (m-10) REVERT: B 176 SER cc_start: 0.9714 (m) cc_final: 0.9409 (p) REVERT: B 201 LEU cc_start: 0.9555 (tt) cc_final: 0.8947 (tt) REVERT: C 104 ASN cc_start: 0.9255 (m-40) cc_final: 0.8845 (t0) REVERT: C 164 TRP cc_start: 0.8603 (m-10) cc_final: 0.8228 (m-10) REVERT: C 231 LYS cc_start: 0.8585 (tppt) cc_final: 0.8328 (mmmm) REVERT: D 84 PHE cc_start: 0.8441 (t80) cc_final: 0.8060 (t80) REVERT: D 95 LEU cc_start: 0.9300 (tp) cc_final: 0.8819 (tp) REVERT: D 110 ASP cc_start: 0.8454 (t0) cc_final: 0.8057 (t0) REVERT: D 130 LEU cc_start: 0.9568 (tt) cc_final: 0.9340 (tt) REVERT: D 144 MET cc_start: 0.9059 (mpp) cc_final: 0.8725 (mpp) REVERT: D 156 GLU cc_start: 0.9190 (pt0) cc_final: 0.8785 (pt0) REVERT: D 194 ILE cc_start: 0.9281 (mm) cc_final: 0.8999 (mm) REVERT: D 226 TYR cc_start: 0.8892 (t80) cc_final: 0.8391 (t80) REVERT: D 282 ASP cc_start: 0.9496 (m-30) cc_final: 0.9153 (m-30) REVERT: D 288 PHE cc_start: 0.8680 (m-10) cc_final: 0.8182 (m-80) REVERT: D 323 ARG cc_start: 0.7909 (mpp-170) cc_final: 0.7389 (mpt180) REVERT: D 337 MET cc_start: 0.9263 (tpp) cc_final: 0.8785 (tpp) REVERT: D 348 LEU cc_start: 0.9514 (mt) cc_final: 0.9245 (mp) REVERT: D 371 MET cc_start: 0.8802 (ptp) cc_final: 0.8516 (mtm) REVERT: D 401 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8223 (tm-30) REVERT: D 432 LEU cc_start: 0.9598 (tp) cc_final: 0.9230 (tt) REVERT: F 62 TRP cc_start: 0.1151 (m-90) cc_final: 0.0892 (m-10) REVERT: F 131 MET cc_start: 0.5921 (tpt) cc_final: 0.4752 (ptm) REVERT: F 313 ASN cc_start: 0.5603 (m-40) cc_final: 0.5307 (t0) REVERT: F 357 MET cc_start: 0.2506 (ptp) cc_final: 0.1785 (ptm) REVERT: G 145 MET cc_start: 0.8234 (mpp) cc_final: 0.7800 (mtp) REVERT: G 150 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6708 (mpp80) REVERT: G 271 MET cc_start: 0.8315 (mmp) cc_final: 0.7874 (mmm) REVERT: G 277 MET cc_start: 0.8253 (tpp) cc_final: 0.7886 (tpp) REVERT: G 285 TRP cc_start: 0.7956 (m-90) cc_final: 0.7661 (m-90) REVERT: G 345 LEU cc_start: 0.8703 (mt) cc_final: 0.8436 (mt) REVERT: G 513 MET cc_start: 0.7846 (pmm) cc_final: 0.7115 (pmm) REVERT: G 544 MET cc_start: 0.8935 (tmm) cc_final: 0.8529 (tmm) REVERT: G 571 HIS cc_start: 0.8193 (p-80) cc_final: 0.7508 (p90) REVERT: G 696 MET cc_start: 0.8934 (mtt) cc_final: 0.8677 (mmm) REVERT: G 707 MET cc_start: 0.7414 (mmt) cc_final: 0.6560 (mmt) REVERT: H 17 MET cc_start: 0.9258 (ppp) cc_final: 0.8824 (ppp) REVERT: H 31 MET cc_start: 0.9419 (mtt) cc_final: 0.8885 (mmm) REVERT: H 47 GLN cc_start: 0.9256 (tp40) cc_final: 0.8605 (tp-100) REVERT: H 53 MET cc_start: 0.9074 (tpt) cc_final: 0.8633 (tpp) REVERT: H 56 PHE cc_start: 0.9178 (m-10) cc_final: 0.8941 (m-80) REVERT: H 57 MET cc_start: 0.9181 (mmp) cc_final: 0.8599 (mmm) REVERT: H 100 LEU cc_start: 0.8656 (mt) cc_final: 0.8196 (mm) REVERT: H 118 TRP cc_start: 0.9385 (m-10) cc_final: 0.8963 (m-90) REVERT: H 138 GLN cc_start: 0.9200 (pm20) cc_final: 0.8929 (pm20) REVERT: H 143 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8799 (mm-30) REVERT: H 183 MET cc_start: 0.9305 (mtm) cc_final: 0.9094 (mtm) REVERT: H 195 ARG cc_start: 0.9094 (tpm170) cc_final: 0.8607 (tpp-160) REVERT: H 234 MET cc_start: 0.9563 (mmp) cc_final: 0.9268 (mmp) REVERT: H 272 TRP cc_start: 0.8680 (t60) cc_final: 0.8296 (t60) REVERT: H 279 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8447 (ttm170) REVERT: H 284 GLN cc_start: 0.9544 (mm110) cc_final: 0.9234 (mp10) REVERT: H 285 LEU cc_start: 0.9267 (tt) cc_final: 0.8955 (mt) REVERT: H 290 TRP cc_start: 0.9413 (m100) cc_final: 0.9134 (m100) REVERT: I 60 ILE cc_start: 0.8814 (tt) cc_final: 0.8486 (mm) REVERT: I 128 ILE cc_start: 0.8731 (mt) cc_final: 0.8367 (mt) REVERT: I 185 TYR cc_start: 0.8955 (m-80) cc_final: 0.8154 (m-80) REVERT: I 190 LEU cc_start: 0.9578 (mt) cc_final: 0.9299 (mt) REVERT: P 84 TYR cc_start: 0.9074 (p90) cc_final: 0.8402 (p90) REVERT: P 91 ILE cc_start: 0.9520 (pt) cc_final: 0.9110 (pt) REVERT: P 148 ILE cc_start: 0.9250 (mm) cc_final: 0.9040 (mt) REVERT: P 269 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6512 (p0) REVERT: Q 99 MET cc_start: 0.9288 (ppp) cc_final: 0.8944 (ppp) REVERT: Q 100 GLU cc_start: 0.9506 (pm20) cc_final: 0.9245 (pm20) REVERT: Q 101 PHE cc_start: 0.7630 (m-80) cc_final: 0.7172 (m-80) REVERT: Q 125 VAL cc_start: 0.8854 (m) cc_final: 0.8653 (m) REVERT: Q 133 ASP cc_start: 0.9325 (m-30) cc_final: 0.8756 (t0) REVERT: T 77 ASP cc_start: 0.8162 (t0) cc_final: 0.7898 (t0) REVERT: T 81 ASP cc_start: 0.9425 (m-30) cc_final: 0.9188 (m-30) REVERT: T 92 LYS cc_start: 0.7678 (tppt) cc_final: 0.7213 (mmmm) REVERT: V 34 ILE cc_start: 0.9214 (tp) cc_final: 0.8995 (tt) REVERT: W 49 THR cc_start: 0.9649 (t) cc_final: 0.9391 (t) REVERT: W 91 MET cc_start: 0.9205 (mtp) cc_final: 0.8866 (mtm) REVERT: W 92 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8613 (tm-30) REVERT: X 44 MET cc_start: 0.9286 (mmm) cc_final: 0.8824 (mmm) REVERT: X 125 LEU cc_start: 0.9167 (mt) cc_final: 0.8903 (mm) REVERT: Z 43 LEU cc_start: 0.9172 (mt) cc_final: 0.8748 (mt) REVERT: Z 71 LEU cc_start: 0.9481 (mt) cc_final: 0.9237 (mt) REVERT: Z 75 PHE cc_start: 0.8880 (m-80) cc_final: 0.8618 (m-80) REVERT: b 23 PHE cc_start: 0.8212 (t80) cc_final: 0.7783 (t80) REVERT: b 32 MET cc_start: 0.8982 (tpt) cc_final: 0.8321 (tpt) REVERT: q 93 MET cc_start: 0.7991 (ptt) cc_final: 0.7570 (ptt) REVERT: r 96 THR cc_start: 0.8607 (p) cc_final: 0.8329 (p) REVERT: r 112 TYR cc_start: 0.8892 (m-80) cc_final: 0.8436 (m-80) REVERT: r 113 LEU cc_start: 0.8469 (mt) cc_final: 0.7815 (mt) outliers start: 3 outliers final: 0 residues processed: 772 average time/residue: 0.2038 time to fit residues: 255.4533 Evaluate side-chains 604 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 603 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 261 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 231 optimal weight: 0.0670 chunk 237 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 295 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 overall best weight: 1.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 605 GLN ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 ASN V 83 GLN ** a 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.099617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067456 restraints weight = 143027.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.068562 restraints weight = 92588.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.069552 restraints weight = 65190.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.070581 restraints weight = 52814.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.070900 restraints weight = 45222.263| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 33253 Z= 0.149 Angle : 0.959 72.982 45126 Z= 0.356 Chirality : 0.045 0.281 4959 Planarity : 0.005 0.121 5728 Dihedral : 7.150 150.654 4534 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 0.14 % Allowed : 2.63 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.44 (0.13), residues: 3981 helix: 0.47 (0.12), residues: 1841 sheet: -1.09 (0.30), residues: 312 loop : -0.86 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Q 104 TYR 0.036 0.002 TYR H 142 PHE 0.024 0.002 PHE H 130 TRP 0.033 0.002 TRP H 303 HIS 0.006 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00328 (33213) covalent geometry : angle 0.70189 (45036) SS BOND : bond 0.00579 ( 3) SS BOND : angle 2.13478 ( 6) hydrogen bonds : bond 0.04200 ( 1397) hydrogen bonds : angle 5.20461 ( 4059) metal coordination : bond 0.01469 ( 37) metal coordination : angle 15.15213 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 744 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8114 (ttt) cc_final: 0.7898 (tpt) REVERT: A 62 PHE cc_start: 0.9584 (t80) cc_final: 0.9334 (t80) REVERT: A 73 LEU cc_start: 0.9367 (mt) cc_final: 0.9161 (mt) REVERT: A 88 MET cc_start: 0.9013 (mmt) cc_final: 0.8665 (mmt) REVERT: A 92 PHE cc_start: 0.9220 (m-10) cc_final: 0.8997 (m-10) REVERT: A 102 LEU cc_start: 0.9409 (tp) cc_final: 0.9170 (tp) REVERT: B 91 TRP cc_start: 0.9347 (m100) cc_final: 0.8926 (m100) REVERT: B 103 GLU cc_start: 0.8791 (tp30) cc_final: 0.8241 (tp30) REVERT: B 107 MET cc_start: 0.9569 (ttm) cc_final: 0.9256 (ttp) REVERT: B 141 MET cc_start: 0.9316 (tpp) cc_final: 0.8870 (tpp) REVERT: B 147 LYS cc_start: 0.9333 (ptmt) cc_final: 0.9022 (pttt) REVERT: B 151 GLN cc_start: 0.9424 (mt0) cc_final: 0.9048 (mt0) REVERT: B 152 MET cc_start: 0.9436 (mtm) cc_final: 0.9186 (mtt) REVERT: B 158 VAL cc_start: 0.9658 (t) cc_final: 0.8887 (t) REVERT: B 161 MET cc_start: 0.8307 (ttp) cc_final: 0.7977 (ttp) REVERT: B 171 TYR cc_start: 0.8934 (m-80) cc_final: 0.8411 (m-10) REVERT: B 176 SER cc_start: 0.9748 (m) cc_final: 0.9443 (p) REVERT: B 201 LEU cc_start: 0.9555 (tt) cc_final: 0.9218 (tt) REVERT: C 104 ASN cc_start: 0.9251 (m-40) cc_final: 0.8884 (t0) REVERT: C 164 TRP cc_start: 0.8607 (m-10) cc_final: 0.8239 (m-10) REVERT: C 176 PHE cc_start: 0.8893 (t80) cc_final: 0.8317 (t80) REVERT: C 227 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 231 LYS cc_start: 0.8935 (tppt) cc_final: 0.8567 (mmmt) REVERT: D 84 PHE cc_start: 0.8317 (t80) cc_final: 0.7646 (t80) REVERT: D 95 LEU cc_start: 0.9339 (tp) cc_final: 0.8800 (tp) REVERT: D 110 ASP cc_start: 0.8382 (t0) cc_final: 0.7947 (t0) REVERT: D 127 LYS cc_start: 0.9264 (mmtp) cc_final: 0.9037 (mmmm) REVERT: D 135 TYR cc_start: 0.8704 (m-10) cc_final: 0.8264 (m-80) REVERT: D 144 MET cc_start: 0.9024 (mpp) cc_final: 0.8642 (mpp) REVERT: D 156 GLU cc_start: 0.9126 (pt0) cc_final: 0.8640 (pt0) REVERT: D 190 HIS cc_start: 0.9086 (t-170) cc_final: 0.8874 (t70) REVERT: D 222 MET cc_start: 0.8366 (ppp) cc_final: 0.8013 (ppp) REVERT: D 226 TYR cc_start: 0.8795 (t80) cc_final: 0.8450 (t80) REVERT: D 265 ASN cc_start: 0.8943 (t0) cc_final: 0.8721 (t0) REVERT: D 288 PHE cc_start: 0.8509 (m-10) cc_final: 0.8001 (m-80) REVERT: D 323 ARG cc_start: 0.7937 (mpp-170) cc_final: 0.7428 (mpt180) REVERT: D 336 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8839 (tm-30) REVERT: D 348 LEU cc_start: 0.9439 (mt) cc_final: 0.9191 (mp) REVERT: D 371 MET cc_start: 0.8850 (ptp) cc_final: 0.8519 (ptp) REVERT: D 401 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8434 (mm-30) REVERT: D 432 LEU cc_start: 0.9622 (tp) cc_final: 0.9211 (tt) REVERT: E 120 MET cc_start: 0.1224 (tmm) cc_final: 0.0946 (tmm) REVERT: F 62 TRP cc_start: 0.1036 (m-90) cc_final: 0.0753 (m-10) REVERT: F 131 MET cc_start: 0.6068 (tpt) cc_final: 0.4884 (ptm) REVERT: F 313 ASN cc_start: 0.5679 (m-40) cc_final: 0.5376 (t0) REVERT: F 357 MET cc_start: 0.2801 (ptp) cc_final: 0.2175 (ptm) REVERT: G 145 MET cc_start: 0.8102 (mpp) cc_final: 0.7565 (mtp) REVERT: G 215 MET cc_start: 0.4943 (tpt) cc_final: 0.4106 (tpt) REVERT: G 513 MET cc_start: 0.7658 (pmm) cc_final: 0.7217 (pmm) REVERT: G 544 MET cc_start: 0.8848 (tmm) cc_final: 0.8530 (tmm) REVERT: G 571 HIS cc_start: 0.8164 (p-80) cc_final: 0.7409 (p-80) REVERT: G 696 MET cc_start: 0.8954 (mtt) cc_final: 0.8741 (mmm) REVERT: G 707 MET cc_start: 0.7788 (mmt) cc_final: 0.7233 (mmm) REVERT: H 31 MET cc_start: 0.9453 (mtt) cc_final: 0.8874 (mmm) REVERT: H 34 ARG cc_start: 0.9408 (ptt90) cc_final: 0.9073 (ptt90) REVERT: H 47 GLN cc_start: 0.9268 (tp40) cc_final: 0.8614 (tp-100) REVERT: H 53 MET cc_start: 0.9146 (tpt) cc_final: 0.8715 (tpp) REVERT: H 56 PHE cc_start: 0.9195 (m-10) cc_final: 0.8954 (m-80) REVERT: H 57 MET cc_start: 0.9140 (mmp) cc_final: 0.8493 (mmm) REVERT: H 71 PHE cc_start: 0.9026 (t80) cc_final: 0.8702 (t80) REVERT: H 118 TRP cc_start: 0.9324 (m-10) cc_final: 0.8976 (m-90) REVERT: H 143 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8797 (mm-30) REVERT: H 146 MET cc_start: 0.9341 (ttm) cc_final: 0.8698 (mtt) REVERT: H 183 MET cc_start: 0.9244 (mtm) cc_final: 0.8886 (mtt) REVERT: H 187 ILE cc_start: 0.9654 (mp) cc_final: 0.9371 (mp) REVERT: H 192 GLU cc_start: 0.8646 (tp30) cc_final: 0.8399 (tp30) REVERT: H 195 ARG cc_start: 0.9243 (tpm170) cc_final: 0.8536 (tpp-160) REVERT: H 215 TYR cc_start: 0.4796 (m-10) cc_final: 0.4570 (m-10) REVERT: H 234 MET cc_start: 0.9504 (mmp) cc_final: 0.9182 (mmp) REVERT: H 272 TRP cc_start: 0.8726 (t60) cc_final: 0.8401 (t60) REVERT: H 274 ARG cc_start: 0.9426 (ttt180) cc_final: 0.8891 (ttm-80) REVERT: H 279 ARG cc_start: 0.8975 (ttm170) cc_final: 0.8618 (ttm170) REVERT: H 283 ASP cc_start: 0.8768 (p0) cc_final: 0.7991 (p0) REVERT: H 284 GLN cc_start: 0.9553 (mm110) cc_final: 0.9283 (mp10) REVERT: H 285 LEU cc_start: 0.9321 (tt) cc_final: 0.8977 (mt) REVERT: H 303 TRP cc_start: 0.8603 (t60) cc_final: 0.8339 (t60) REVERT: I 148 ASP cc_start: 0.8605 (t70) cc_final: 0.8345 (t0) REVERT: I 149 MET cc_start: 0.8555 (mmm) cc_final: 0.7869 (mmm) REVERT: I 185 TYR cc_start: 0.8987 (m-80) cc_final: 0.8179 (m-80) REVERT: I 190 LEU cc_start: 0.9603 (mt) cc_final: 0.9342 (mt) REVERT: P 84 TYR cc_start: 0.9019 (p90) cc_final: 0.8474 (p90) REVERT: P 92 MET cc_start: 0.8887 (tpt) cc_final: 0.8641 (tpp) REVERT: P 97 MET cc_start: 0.7252 (pmm) cc_final: 0.7015 (pmm) REVERT: P 129 LEU cc_start: 0.9036 (tt) cc_final: 0.8830 (tt) REVERT: P 148 ILE cc_start: 0.9262 (mm) cc_final: 0.9060 (mt) REVERT: P 366 ILE cc_start: 0.5464 (OUTLIER) cc_final: 0.5187 (pt) REVERT: Q 88 GLN cc_start: 0.6489 (mm-40) cc_final: 0.6061 (mm110) REVERT: Q 100 GLU cc_start: 0.9465 (pm20) cc_final: 0.9179 (pm20) REVERT: Q 112 MET cc_start: 0.4782 (mmt) cc_final: 0.4476 (mmp) REVERT: Q 128 PHE cc_start: 0.8717 (m-10) cc_final: 0.8093 (m-80) REVERT: Q 133 ASP cc_start: 0.9411 (m-30) cc_final: 0.9026 (m-30) REVERT: Q 141 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7762 (p0) REVERT: Q 148 GLU cc_start: 0.6415 (pp20) cc_final: 0.6204 (pp20) REVERT: Q 149 GLU cc_start: 0.7342 (pm20) cc_final: 0.7095 (pm20) REVERT: T 77 ASP cc_start: 0.8270 (t0) cc_final: 0.7971 (t0) REVERT: T 81 ASP cc_start: 0.9403 (m-30) cc_final: 0.9152 (m-30) REVERT: T 92 LYS cc_start: 0.7630 (tppt) cc_final: 0.7249 (mmmm) REVERT: T 130 ILE cc_start: 0.7265 (tt) cc_final: 0.6819 (tt) REVERT: T 139 MET cc_start: 0.5468 (mmp) cc_final: 0.5197 (mmm) REVERT: W 34 ARG cc_start: 0.9234 (mtt-85) cc_final: 0.8720 (mtt180) REVERT: W 45 GLU cc_start: 0.9435 (tp30) cc_final: 0.9041 (tp30) REVERT: W 90 LYS cc_start: 0.9481 (mtmm) cc_final: 0.9107 (mttm) REVERT: W 91 MET cc_start: 0.9247 (mtp) cc_final: 0.8729 (mtm) REVERT: W 96 THR cc_start: 0.9599 (p) cc_final: 0.9386 (p) REVERT: W 100 TRP cc_start: 0.7927 (m-10) cc_final: 0.7537 (m-10) REVERT: X 44 MET cc_start: 0.9259 (mmm) cc_final: 0.8928 (mmm) REVERT: X 125 LEU cc_start: 0.9178 (mt) cc_final: 0.8933 (mm) REVERT: a 17 VAL cc_start: 0.9097 (p) cc_final: 0.8872 (m) REVERT: b 23 PHE cc_start: 0.8243 (t80) cc_final: 0.7827 (t80) REVERT: b 28 LEU cc_start: 0.8625 (pp) cc_final: 0.8411 (pp) REVERT: b 32 MET cc_start: 0.8986 (tpt) cc_final: 0.8432 (tpt) REVERT: q 93 MET cc_start: 0.8005 (ptt) cc_final: 0.7551 (ptt) REVERT: r 96 THR cc_start: 0.8442 (p) cc_final: 0.7999 (p) REVERT: r 112 TYR cc_start: 0.8889 (m-80) cc_final: 0.8471 (m-80) outliers start: 5 outliers final: 1 residues processed: 747 average time/residue: 0.2113 time to fit residues: 256.2596 Evaluate side-chains 592 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 589 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 205 optimal weight: 10.0000 chunk 313 optimal weight: 30.0000 chunk 308 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 HIS ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 HIS ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 569 GLN G 605 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** V 111 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 = 0.4024 r_free = 0.4024 target = 0.095056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.063477 restraints weight = 144755.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.065032 restraints weight = 97206.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065875 restraints weight = 69413.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066949 restraints weight = 57314.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.067226 restraints weight = 49254.024| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 33253 Z= 0.230 Angle : 1.031 77.472 45126 Z= 0.386 Chirality : 0.046 0.284 4959 Planarity : 0.005 0.118 5728 Dihedral : 7.315 153.628 4534 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.45 (0.13), residues: 3981 helix: 0.41 (0.12), residues: 1865 sheet: -1.03 (0.29), residues: 340 loop : -0.83 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 100 TYR 0.037 0.002 TYR B 170 PHE 0.027 0.002 PHE Q 80 TRP 0.040 0.002 TRP Q 143 HIS 0.018 0.002 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00497 (33213) covalent geometry : angle 0.75665 (45036) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.32561 ( 6) hydrogen bonds : bond 0.04228 ( 1397) hydrogen bonds : angle 5.34088 ( 4059) metal coordination : bond 0.02566 ( 37) metal coordination : angle 16.23447 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 698 time to evaluate : 1.252 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: A 17 LEU cc_start: 0.9588 (mt) cc_final: 0.9381 (mt) REVERT: A 62 PHE cc_start: 0.9643 (t80) cc_final: 0.9423 (t80) REVERT: A 73 LEU cc_start: 0.9365 (mt) cc_final: 0.9162 (mt) REVERT: A 102 LEU cc_start: 0.9481 (tp) cc_final: 0.9212 (tp) REVERT: B 90 LEU cc_start: 0.9733 (mt) cc_final: 0.9306 (mt) REVERT: B 91 TRP cc_start: 0.9472 (m100) cc_final: 0.9095 (m100) REVERT: B 103 GLU cc_start: 0.9001 (tp30) cc_final: 0.8474 (tp30) REVERT: B 107 MET cc_start: 0.9562 (ttm) cc_final: 0.9249 (ttm) REVERT: B 141 MET cc_start: 0.9376 (tpp) cc_final: 0.8762 (tpp) REVERT: B 147 LYS cc_start: 0.9340 (ptmt) cc_final: 0.9006 (pttt) REVERT: B 151 GLN cc_start: 0.9418 (mt0) cc_final: 0.9014 (mt0) REVERT: B 152 MET cc_start: 0.9494 (mtm) cc_final: 0.9165 (mtt) REVERT: B 161 MET cc_start: 0.8467 (ttp) cc_final: 0.8156 (ttp) REVERT: B 171 TYR cc_start: 0.8944 (m-80) cc_final: 0.8361 (m-10) REVERT: B 173 TYR cc_start: 0.7707 (m-10) cc_final: 0.7375 (m-10) REVERT: B 201 LEU cc_start: 0.9587 (tt) cc_final: 0.9333 (tp) REVERT: C 104 ASN cc_start: 0.9276 (m-40) cc_final: 0.8891 (t0) REVERT: C 227 GLN cc_start: 0.8792 (tm-30) cc_final: 0.7926 (tm-30) REVERT: D 84 PHE cc_start: 0.8444 (t80) cc_final: 0.8136 (t80) REVERT: D 110 ASP cc_start: 0.8517 (t0) cc_final: 0.8115 (t0) REVERT: D 135 TYR cc_start: 0.9009 (m-10) cc_final: 0.8475 (m-80) REVERT: D 144 MET cc_start: 0.9044 (mpp) cc_final: 0.8792 (mpp) REVERT: D 156 GLU cc_start: 0.9179 (pt0) cc_final: 0.8784 (pt0) REVERT: D 194 ILE cc_start: 0.9432 (mm) cc_final: 0.9168 (mm) REVERT: D 205 GLU cc_start: 0.9382 (tp30) cc_final: 0.8892 (tp30) REVERT: D 258 VAL cc_start: 0.9799 (t) cc_final: 0.9559 (m) REVERT: D 261 MET cc_start: 0.8868 (mmp) cc_final: 0.8585 (mmm) REVERT: D 336 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8830 (tm-30) REVERT: D 348 LEU cc_start: 0.9417 (mt) cc_final: 0.9165 (mp) REVERT: D 371 MET cc_start: 0.8922 (ptp) cc_final: 0.8654 (ptt) REVERT: D 401 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8233 (mm-30) REVERT: D 432 LEU cc_start: 0.9682 (tp) cc_final: 0.9439 (tp) REVERT: E 120 MET cc_start: 0.0594 (tmm) cc_final: 0.0237 (tmm) REVERT: F 131 MET cc_start: 0.6136 (tpt) cc_final: 0.5093 (ptm) REVERT: F 217 GLU cc_start: 0.3697 (mt-10) cc_final: 0.3278 (pt0) REVERT: F 313 ASN cc_start: 0.5894 (m-40) cc_final: 0.5592 (t0) REVERT: F 357 MET cc_start: 0.2957 (ptp) cc_final: 0.2129 (ttm) REVERT: G 144 MET cc_start: 0.8574 (tpp) cc_final: 0.8171 (tpp) REVERT: G 271 MET cc_start: 0.8267 (mmp) cc_final: 0.7723 (mmm) REVERT: G 294 TYR cc_start: 0.8761 (p90) cc_final: 0.8535 (p90) REVERT: G 473 MET cc_start: 0.7768 (mtt) cc_final: 0.7021 (tpp) REVERT: G 513 MET cc_start: 0.7863 (pmm) cc_final: 0.7177 (pmm) REVERT: G 544 MET cc_start: 0.8840 (tmm) cc_final: 0.7971 (tmm) REVERT: G 571 HIS cc_start: 0.8161 (p-80) cc_final: 0.7692 (p-80) REVERT: G 696 MET cc_start: 0.8940 (mtt) cc_final: 0.8730 (mmm) REVERT: G 707 MET cc_start: 0.7835 (mmt) cc_final: 0.7289 (mmm) REVERT: H 31 MET cc_start: 0.9497 (mtt) cc_final: 0.8849 (mmm) REVERT: H 47 GLN cc_start: 0.9310 (tp40) cc_final: 0.8735 (tp-100) REVERT: H 53 MET cc_start: 0.9227 (tpt) cc_final: 0.8635 (tpp) REVERT: H 56 PHE cc_start: 0.9239 (m-10) cc_final: 0.8930 (m-80) REVERT: H 57 MET cc_start: 0.9093 (mmp) cc_final: 0.8494 (mmp) REVERT: H 71 PHE cc_start: 0.9157 (t80) cc_final: 0.8835 (t80) REVERT: H 118 TRP cc_start: 0.9377 (m-10) cc_final: 0.9045 (m-90) REVERT: H 143 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9044 (mm-30) REVERT: H 146 MET cc_start: 0.9395 (ttm) cc_final: 0.8769 (mtt) REVERT: H 155 LEU cc_start: 0.9585 (mm) cc_final: 0.9372 (tp) REVERT: H 183 MET cc_start: 0.9339 (mtm) cc_final: 0.9034 (mtt) REVERT: H 187 ILE cc_start: 0.9684 (mp) cc_final: 0.9379 (mp) REVERT: H 195 ARG cc_start: 0.9290 (tpm170) cc_final: 0.8715 (tpp-160) REVERT: H 215 TYR cc_start: 0.5715 (m-10) cc_final: 0.5151 (m-10) REVERT: H 234 MET cc_start: 0.9530 (mmp) cc_final: 0.9215 (mmp) REVERT: H 272 TRP cc_start: 0.8759 (t60) cc_final: 0.8400 (t60) REVERT: H 274 ARG cc_start: 0.9368 (ttt180) cc_final: 0.9116 (ttt180) REVERT: H 279 ARG cc_start: 0.8845 (ttm170) cc_final: 0.8208 (tpp80) REVERT: H 285 LEU cc_start: 0.9180 (tt) cc_final: 0.8727 (mt) REVERT: H 293 PHE cc_start: 0.9390 (m-80) cc_final: 0.9104 (m-80) REVERT: I 185 TYR cc_start: 0.9147 (m-80) cc_final: 0.8322 (m-80) REVERT: P 65 LEU cc_start: 0.9347 (mm) cc_final: 0.9139 (mm) REVERT: P 68 TYR cc_start: 0.9092 (m-80) cc_final: 0.8856 (m-80) REVERT: P 84 TYR cc_start: 0.9141 (p90) cc_final: 0.8724 (p90) REVERT: P 92 MET cc_start: 0.8942 (tpt) cc_final: 0.8609 (tpp) REVERT: P 97 MET cc_start: 0.7573 (pmm) cc_final: 0.7342 (pmm) REVERT: P 148 ILE cc_start: 0.9377 (mm) cc_final: 0.9171 (mt) REVERT: P 251 ASN cc_start: 0.9364 (m-40) cc_final: 0.9107 (m-40) REVERT: Q 88 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6224 (mm110) REVERT: Q 133 ASP cc_start: 0.9385 (m-30) cc_final: 0.9027 (m-30) REVERT: Q 149 GLU cc_start: 0.7348 (pm20) cc_final: 0.7122 (pm20) REVERT: S 68 ARG cc_start: 0.7147 (tmt170) cc_final: 0.6836 (tmt170) REVERT: S 71 PHE cc_start: 0.8464 (t80) cc_final: 0.8256 (t80) REVERT: T 92 LYS cc_start: 0.7736 (tppt) cc_final: 0.7452 (mmmm) REVERT: T 139 MET cc_start: 0.5720 (mmp) cc_final: 0.5489 (mmm) REVERT: T 148 ILE cc_start: 0.7940 (mt) cc_final: 0.7694 (mt) REVERT: W 24 PHE cc_start: 0.8139 (m-10) cc_final: 0.7930 (m-10) REVERT: W 45 GLU cc_start: 0.9454 (tp30) cc_final: 0.9117 (tp30) REVERT: W 91 MET cc_start: 0.9250 (mtp) cc_final: 0.8882 (mtp) REVERT: W 92 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8697 (tm-30) REVERT: X 44 MET cc_start: 0.9265 (mmm) cc_final: 0.8915 (mmm) REVERT: a 35 GLU cc_start: 0.8314 (pt0) cc_final: 0.7429 (tp30) REVERT: b 23 PHE cc_start: 0.8341 (t80) cc_final: 0.7889 (t80) REVERT: b 28 LEU cc_start: 0.8679 (pp) cc_final: 0.8475 (pp) REVERT: b 32 MET cc_start: 0.8866 (tpt) cc_final: 0.8433 (tpt) REVERT: q 93 MET cc_start: 0.8099 (ptt) cc_final: 0.7642 (ptt) REVERT: r 96 THR cc_start: 0.8409 (p) cc_final: 0.8137 (p) REVERT: r 112 TYR cc_start: 0.8859 (m-80) cc_final: 0.8564 (m-80) outliers start: 0 outliers final: 0 residues processed: 698 average time/residue: 0.2135 time to fit residues: 241.8596 Evaluate side-chains 559 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 142 optimal weight: 30.0000 chunk 202 optimal weight: 0.0770 chunk 253 optimal weight: 6.9990 chunk 385 optimal weight: 10.0000 chunk 302 optimal weight: 5.9990 chunk 218 optimal weight: 0.5980 chunk 127 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN C 130 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 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 = 0.4055 r_free = 0.4055 target = 0.097446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.065331 restraints weight = 139371.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.066526 restraints weight = 90470.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.066953 restraints weight = 66519.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.067444 restraints weight = 58870.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.068210 restraints weight = 53804.703| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 33253 Z= 0.149 Angle : 0.983 77.020 45126 Z= 0.359 Chirality : 0.045 0.297 4959 Planarity : 0.006 0.167 5728 Dihedral : 7.143 154.892 4534 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.01 % Rotamer: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.38 (0.13), residues: 3981 helix: 0.52 (0.12), residues: 1859 sheet: -1.06 (0.29), residues: 340 loop : -0.82 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 110 TYR 0.032 0.002 TYR B 157 PHE 0.031 0.002 PHE C 60 TRP 0.033 0.002 TRP Q 143 HIS 0.009 0.001 HIS T 103 Details of bonding type rmsd covalent geometry : bond 0.00335 (33213) covalent geometry : angle 0.71750 (45036) SS BOND : bond 0.00411 ( 3) SS BOND : angle 1.27750 ( 6) hydrogen bonds : bond 0.04066 ( 1397) hydrogen bonds : angle 5.19944 ( 4059) metal coordination : bond 0.01543 ( 37) metal coordination : angle 15.58002 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 24 LEU cc_start: 0.9573 (tp) cc_final: 0.9353 (tp) REVERT: A 62 PHE cc_start: 0.9620 (t80) cc_final: 0.9417 (t80) REVERT: A 87 MET cc_start: 0.8141 (tpp) cc_final: 0.7919 (mmt) REVERT: B 80 ASP cc_start: 0.9270 (t0) cc_final: 0.9003 (t0) REVERT: B 91 TRP cc_start: 0.9475 (m100) cc_final: 0.8854 (m100) REVERT: B 103 GLU cc_start: 0.8898 (tp30) cc_final: 0.8150 (tp30) REVERT: B 129 ASP cc_start: 0.9337 (m-30) cc_final: 0.9039 (m-30) REVERT: B 147 LYS cc_start: 0.9323 (ptmt) cc_final: 0.9025 (pttt) REVERT: B 151 GLN cc_start: 0.9401 (mt0) cc_final: 0.8980 (mt0) REVERT: B 152 MET cc_start: 0.9486 (mtm) cc_final: 0.9163 (mtt) REVERT: B 161 MET cc_start: 0.8479 (ttp) cc_final: 0.8126 (ttp) REVERT: B 171 TYR cc_start: 0.8915 (m-80) cc_final: 0.8140 (m-10) REVERT: B 173 TYR cc_start: 0.7622 (m-10) cc_final: 0.7283 (m-10) REVERT: B 174 SER cc_start: 0.9309 (t) cc_final: 0.8873 (p) REVERT: B 201 LEU cc_start: 0.9549 (tt) cc_final: 0.9295 (tp) REVERT: B 207 GLN cc_start: 0.9177 (mm110) cc_final: 0.8867 (mm110) REVERT: C 225 LEU cc_start: 0.8050 (tp) cc_final: 0.7794 (tp) REVERT: C 227 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 84 PHE cc_start: 0.8349 (t80) cc_final: 0.7987 (t80) REVERT: D 110 ASP cc_start: 0.8452 (t0) cc_final: 0.8031 (t0) REVERT: D 135 TYR cc_start: 0.9000 (m-80) cc_final: 0.8420 (m-80) REVERT: D 144 MET cc_start: 0.8890 (mpp) cc_final: 0.8186 (mpp) REVERT: D 156 GLU cc_start: 0.9066 (pt0) cc_final: 0.8690 (pt0) REVERT: D 194 ILE cc_start: 0.9408 (mm) cc_final: 0.9199 (mm) REVERT: D 222 MET cc_start: 0.8405 (ppp) cc_final: 0.7990 (ppp) REVERT: D 226 TYR cc_start: 0.8779 (t80) cc_final: 0.8187 (t80) REVERT: D 261 MET cc_start: 0.8811 (mmp) cc_final: 0.8529 (mmm) REVERT: D 323 ARG cc_start: 0.7889 (mpp-170) cc_final: 0.7351 (mpt180) REVERT: D 336 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8942 (tm-30) REVERT: D 348 LEU cc_start: 0.9427 (mt) cc_final: 0.9159 (mp) REVERT: D 371 MET cc_start: 0.8891 (ptp) cc_final: 0.8683 (ptt) REVERT: D 401 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8256 (mt-10) REVERT: D 443 MET cc_start: 0.8373 (mmp) cc_final: 0.8160 (mmp) REVERT: E 109 MET cc_start: 0.0952 (mmm) cc_final: 0.0581 (tpp) REVERT: E 120 MET cc_start: 0.0575 (tmm) cc_final: 0.0181 (tmm) REVERT: F 131 MET cc_start: 0.6169 (tpt) cc_final: 0.4889 (ptm) REVERT: F 313 ASN cc_start: 0.6581 (m-40) cc_final: 0.6227 (t0) REVERT: F 357 MET cc_start: 0.2972 (ptp) cc_final: 0.1998 (ttm) REVERT: F 436 GLN cc_start: 0.7394 (tp-100) cc_final: 0.6944 (mm110) REVERT: G 145 MET cc_start: 0.8305 (tpp) cc_final: 0.7957 (tpp) REVERT: G 271 MET cc_start: 0.8120 (mmp) cc_final: 0.7746 (mmm) REVERT: G 277 MET cc_start: 0.7742 (tpp) cc_final: 0.7515 (tpp) REVERT: G 294 TYR cc_start: 0.8666 (p90) cc_final: 0.8455 (p90) REVERT: G 345 LEU cc_start: 0.8978 (mt) cc_final: 0.8766 (mt) REVERT: G 473 MET cc_start: 0.7758 (mtt) cc_final: 0.6917 (tpp) REVERT: G 513 MET cc_start: 0.7946 (pmm) cc_final: 0.7227 (pmm) REVERT: G 696 MET cc_start: 0.8968 (mtt) cc_final: 0.8734 (mmm) REVERT: G 707 MET cc_start: 0.7846 (mmt) cc_final: 0.7335 (mmm) REVERT: H 31 MET cc_start: 0.9528 (mtt) cc_final: 0.9065 (mmm) REVERT: H 47 GLN cc_start: 0.9295 (tp40) cc_final: 0.8712 (tp-100) REVERT: H 53 MET cc_start: 0.9278 (tpt) cc_final: 0.8804 (tpp) REVERT: H 56 PHE cc_start: 0.9232 (m-10) cc_final: 0.8968 (m-80) REVERT: H 57 MET cc_start: 0.9063 (mmp) cc_final: 0.8503 (mmp) REVERT: H 71 PHE cc_start: 0.9196 (t80) cc_final: 0.8896 (t80) REVERT: H 98 LEU cc_start: 0.9116 (mm) cc_final: 0.8901 (mm) REVERT: H 118 TRP cc_start: 0.9335 (m-10) cc_final: 0.8965 (m-90) REVERT: H 130 PHE cc_start: 0.9259 (m-10) cc_final: 0.9034 (m-80) REVERT: H 143 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8928 (mm-30) REVERT: H 146 MET cc_start: 0.9515 (ttm) cc_final: 0.9095 (mtt) REVERT: H 183 MET cc_start: 0.9279 (mtm) cc_final: 0.8936 (mtt) REVERT: H 185 TRP cc_start: 0.9709 (t-100) cc_final: 0.9443 (t-100) REVERT: H 215 TYR cc_start: 0.5228 (m-10) cc_final: 0.4803 (m-10) REVERT: H 222 LEU cc_start: 0.9633 (mt) cc_final: 0.9389 (tp) REVERT: H 234 MET cc_start: 0.9463 (mmp) cc_final: 0.9140 (mmp) REVERT: H 272 TRP cc_start: 0.8749 (t60) cc_final: 0.8449 (t60) REVERT: H 274 ARG cc_start: 0.9321 (ttt180) cc_final: 0.9011 (ttm-80) REVERT: H 279 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8639 (ttm170) REVERT: H 285 LEU cc_start: 0.9178 (tt) cc_final: 0.8749 (mt) REVERT: H 293 PHE cc_start: 0.9423 (m-80) cc_final: 0.9048 (m-80) REVERT: H 303 TRP cc_start: 0.8700 (t60) cc_final: 0.8369 (t60) REVERT: H 318 MET cc_start: 0.7488 (tpt) cc_final: 0.7247 (tpt) REVERT: I 140 ARG cc_start: 0.8181 (ttt180) cc_final: 0.7281 (ttp-170) REVERT: I 185 TYR cc_start: 0.9041 (m-80) cc_final: 0.8356 (m-80) REVERT: P 68 TYR cc_start: 0.9091 (m-80) cc_final: 0.8793 (m-80) REVERT: P 84 TYR cc_start: 0.9080 (p90) cc_final: 0.8612 (p90) REVERT: P 92 MET cc_start: 0.8902 (tpt) cc_final: 0.8645 (tpp) REVERT: P 97 MET cc_start: 0.7624 (pmm) cc_final: 0.7372 (pmm) REVERT: P 148 ILE cc_start: 0.9330 (mm) cc_final: 0.9110 (mt) REVERT: P 251 ASN cc_start: 0.9382 (m-40) cc_final: 0.9129 (m-40) REVERT: Q 88 GLN cc_start: 0.6561 (mm-40) cc_final: 0.6219 (mm110) REVERT: Q 99 MET cc_start: 0.9314 (ppp) cc_final: 0.9100 (ppp) REVERT: Q 133 ASP cc_start: 0.9400 (m-30) cc_final: 0.8761 (t0) REVERT: Q 149 GLU cc_start: 0.7629 (pm20) cc_final: 0.7405 (pm20) REVERT: Q 150 LYS cc_start: 0.2403 (tttt) cc_final: 0.2178 (tmtt) REVERT: R 86 LEU cc_start: 0.9372 (mp) cc_final: 0.9165 (mp) REVERT: S 71 PHE cc_start: 0.8440 (t80) cc_final: 0.8218 (t80) REVERT: T 92 LYS cc_start: 0.7761 (tppt) cc_final: 0.7491 (mmmm) REVERT: T 139 MET cc_start: 0.6168 (mmp) cc_final: 0.5669 (mmm) REVERT: V 93 LYS cc_start: 0.9294 (mtpt) cc_final: 0.8843 (mmmm) REVERT: W 24 PHE cc_start: 0.8191 (m-10) cc_final: 0.7957 (m-10) REVERT: W 45 GLU cc_start: 0.9430 (tp30) cc_final: 0.9071 (tp30) REVERT: W 49 THR cc_start: 0.9784 (t) cc_final: 0.9358 (t) REVERT: W 91 MET cc_start: 0.9248 (mtp) cc_final: 0.8863 (mtm) REVERT: W 92 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8639 (tm-30) REVERT: X 44 MET cc_start: 0.9270 (mmm) cc_final: 0.8948 (mmm) REVERT: a 12 MET cc_start: 0.9230 (mmm) cc_final: 0.9028 (mmp) REVERT: a 35 GLU cc_start: 0.8552 (pt0) cc_final: 0.7333 (tp30) REVERT: b 23 PHE cc_start: 0.8318 (t80) cc_final: 0.7903 (t80) REVERT: b 32 MET cc_start: 0.8847 (tpt) cc_final: 0.8398 (tpt) REVERT: q 93 MET cc_start: 0.8073 (ptt) cc_final: 0.7726 (ptt) REVERT: r 96 THR cc_start: 0.8234 (p) cc_final: 0.7649 (p) outliers start: 1 outliers final: 0 residues processed: 694 average time/residue: 0.2027 time to fit residues: 229.2387 Evaluate side-chains 563 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 168 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 131 optimal weight: 40.0000 chunk 122 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 ASN Q 141 ASN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.094022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.062689 restraints weight = 145345.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.064216 restraints weight = 96716.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064971 restraints weight = 69728.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065927 restraints weight = 58350.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.066159 restraints weight = 50365.950| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 33253 Z= 0.220 Angle : 1.050 80.059 45126 Z= 0.388 Chirality : 0.046 0.324 4959 Planarity : 0.006 0.120 5728 Dihedral : 7.192 155.984 4534 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.63 % Rotamer: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.49 (0.13), residues: 3981 helix: 0.38 (0.12), residues: 1856 sheet: -1.07 (0.28), residues: 347 loop : -0.83 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 159 TYR 0.034 0.002 TYR B 170 PHE 0.043 0.002 PHE C 60 TRP 0.034 0.002 TRP Q 114 HIS 0.009 0.002 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00470 (33213) covalent geometry : angle 0.76124 (45036) SS BOND : bond 0.00387 ( 3) SS BOND : angle 1.08179 ( 6) hydrogen bonds : bond 0.04209 ( 1397) hydrogen bonds : angle 5.41436 ( 4059) metal coordination : bond 0.02381 ( 37) metal coordination : angle 16.76351 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 651 time to evaluate : 1.954 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: A 92 PHE cc_start: 0.9294 (m-80) cc_final: 0.8981 (m-80) REVERT: B 80 ASP cc_start: 0.9290 (t0) cc_final: 0.9035 (t0) REVERT: B 91 TRP cc_start: 0.9508 (m100) cc_final: 0.9219 (m100) REVERT: B 103 GLU cc_start: 0.8910 (tp30) cc_final: 0.8340 (tp30) REVERT: B 104 MET cc_start: 0.9526 (tmm) cc_final: 0.9052 (tmm) REVERT: B 147 LYS cc_start: 0.9314 (ptmt) cc_final: 0.9079 (pttt) REVERT: B 152 MET cc_start: 0.9557 (mtm) cc_final: 0.9269 (mtt) REVERT: B 161 MET cc_start: 0.8566 (ttp) cc_final: 0.8250 (ttp) REVERT: B 207 GLN cc_start: 0.9204 (mm110) cc_final: 0.8887 (mm110) REVERT: C 225 LEU cc_start: 0.7984 (tp) cc_final: 0.7747 (tp) REVERT: D 80 MET cc_start: 0.4005 (mtp) cc_final: 0.3664 (mmm) REVERT: D 110 ASP cc_start: 0.8587 (t0) cc_final: 0.8240 (t0) REVERT: D 135 TYR cc_start: 0.9177 (m-80) cc_final: 0.8714 (m-80) REVERT: D 145 MET cc_start: 0.8380 (mpp) cc_final: 0.7380 (mpp) REVERT: D 156 GLU cc_start: 0.9127 (pt0) cc_final: 0.8768 (pt0) REVERT: D 194 ILE cc_start: 0.9503 (mm) cc_final: 0.9243 (mm) REVERT: D 214 TYR cc_start: 0.9187 (m-80) cc_final: 0.8815 (m-80) REVERT: D 323 ARG cc_start: 0.8068 (mpp-170) cc_final: 0.7548 (mpt180) REVERT: D 335 GLU cc_start: 0.9427 (tp30) cc_final: 0.8734 (tp30) REVERT: D 337 MET cc_start: 0.9109 (tpp) cc_final: 0.8829 (tpp) REVERT: D 348 LEU cc_start: 0.9400 (mt) cc_final: 0.9174 (mp) REVERT: D 432 LEU cc_start: 0.9618 (tp) cc_final: 0.9378 (tt) REVERT: E 109 MET cc_start: 0.1082 (mmm) cc_final: 0.0630 (tpp) REVERT: E 120 MET cc_start: 0.0558 (tmm) cc_final: 0.0162 (tmm) REVERT: F 131 MET cc_start: 0.6178 (tpt) cc_final: 0.5219 (ptm) REVERT: F 313 ASN cc_start: 0.6463 (m-40) cc_final: 0.6145 (t0) REVERT: F 357 MET cc_start: 0.2971 (ptp) cc_final: 0.2071 (ttm) REVERT: G 33 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8451 (tp30) REVERT: G 144 MET cc_start: 0.8237 (tpp) cc_final: 0.7969 (tpp) REVERT: G 145 MET cc_start: 0.8295 (tpp) cc_final: 0.7857 (tpp) REVERT: G 173 MET cc_start: 0.7695 (tpt) cc_final: 0.7291 (tpt) REVERT: G 213 MET cc_start: 0.2621 (ppp) cc_final: 0.2386 (ppp) REVERT: G 271 MET cc_start: 0.8210 (mmp) cc_final: 0.7834 (mmm) REVERT: G 277 MET cc_start: 0.7728 (tpp) cc_final: 0.7455 (tpp) REVERT: G 294 TYR cc_start: 0.8773 (p90) cc_final: 0.8489 (p90) REVERT: G 345 LEU cc_start: 0.8953 (mt) cc_final: 0.8713 (mt) REVERT: G 473 MET cc_start: 0.7762 (mtt) cc_final: 0.6877 (tpp) REVERT: G 513 MET cc_start: 0.7875 (pmm) cc_final: 0.7125 (pmm) REVERT: G 544 MET cc_start: 0.8476 (tpt) cc_final: 0.8254 (tpp) REVERT: G 571 HIS cc_start: 0.8212 (p-80) cc_final: 0.7751 (p-80) REVERT: G 696 MET cc_start: 0.8947 (mtt) cc_final: 0.8717 (mmm) REVERT: G 707 MET cc_start: 0.7879 (mmt) cc_final: 0.7344 (mmm) REVERT: H 17 MET cc_start: 0.9317 (ppp) cc_final: 0.9048 (ppp) REVERT: H 31 MET cc_start: 0.9483 (mtt) cc_final: 0.8993 (mmm) REVERT: H 47 GLN cc_start: 0.9346 (tp40) cc_final: 0.8805 (tp-100) REVERT: H 53 MET cc_start: 0.9260 (tpt) cc_final: 0.8895 (tpp) REVERT: H 56 PHE cc_start: 0.9289 (m-10) cc_final: 0.8990 (m-80) REVERT: H 57 MET cc_start: 0.9100 (mmp) cc_final: 0.8497 (mmm) REVERT: H 98 LEU cc_start: 0.9151 (mm) cc_final: 0.8635 (mm) REVERT: H 118 TRP cc_start: 0.9396 (m-10) cc_final: 0.9051 (m-90) REVERT: H 138 GLN cc_start: 0.9360 (pm20) cc_final: 0.9104 (pm20) REVERT: H 143 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8951 (mm-30) REVERT: H 146 MET cc_start: 0.9524 (ttm) cc_final: 0.9054 (mtt) REVERT: H 155 LEU cc_start: 0.9611 (mm) cc_final: 0.9083 (tt) REVERT: H 183 MET cc_start: 0.9324 (mtm) cc_final: 0.9008 (mtt) REVERT: H 234 MET cc_start: 0.9472 (mmp) cc_final: 0.9187 (mmp) REVERT: H 272 TRP cc_start: 0.8757 (t60) cc_final: 0.8539 (t60) REVERT: H 274 ARG cc_start: 0.9373 (ttt180) cc_final: 0.8928 (ttm-80) REVERT: H 300 LEU cc_start: 0.9625 (mt) cc_final: 0.9215 (mp) REVERT: I 159 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9193 (tm-30) REVERT: I 185 TYR cc_start: 0.9160 (m-80) cc_final: 0.8428 (m-80) REVERT: P 68 TYR cc_start: 0.9144 (m-80) cc_final: 0.8771 (m-80) REVERT: P 84 TYR cc_start: 0.9157 (p90) cc_final: 0.8760 (p90) REVERT: P 92 MET cc_start: 0.8977 (tpt) cc_final: 0.8581 (tpp) REVERT: P 251 ASN cc_start: 0.9418 (m-40) cc_final: 0.9174 (m-40) REVERT: P 283 MET cc_start: 0.6628 (tpt) cc_final: 0.6413 (tpt) REVERT: Q 88 GLN cc_start: 0.6514 (mm-40) cc_final: 0.6094 (mm110) REVERT: Q 141 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.7796 (p0) REVERT: Q 150 LYS cc_start: 0.2491 (tttt) cc_final: 0.2144 (tmtt) REVERT: S 71 PHE cc_start: 0.8400 (t80) cc_final: 0.8188 (t80) REVERT: T 92 LYS cc_start: 0.7796 (tppt) cc_final: 0.7570 (mmmm) REVERT: T 130 ILE cc_start: 0.6582 (tt) cc_final: 0.6186 (tt) REVERT: T 139 MET cc_start: 0.6145 (mmp) cc_final: 0.5766 (mmm) REVERT: V 93 LYS cc_start: 0.9408 (mtpt) cc_final: 0.8964 (mmmm) REVERT: W 45 GLU cc_start: 0.9451 (tp30) cc_final: 0.9091 (tp30) REVERT: W 49 THR cc_start: 0.9748 (t) cc_final: 0.9310 (t) REVERT: W 69 MET cc_start: 0.8128 (mtt) cc_final: 0.7579 (mtp) REVERT: W 91 MET cc_start: 0.9183 (mtp) cc_final: 0.8332 (mtp) REVERT: W 92 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8651 (tm-30) REVERT: W 93 LEU cc_start: 0.9830 (pp) cc_final: 0.9620 (pp) REVERT: W 94 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8978 (tm-30) REVERT: X 32 TYR cc_start: 0.8640 (t80) cc_final: 0.8267 (t80) REVERT: X 44 MET cc_start: 0.9278 (mmm) cc_final: 0.8981 (mmm) REVERT: Z 57 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8751 (mtp85) REVERT: a 12 MET cc_start: 0.9246 (mmm) cc_final: 0.9042 (mmp) REVERT: a 35 GLU cc_start: 0.8418 (pt0) cc_final: 0.7509 (tp30) REVERT: b 23 PHE cc_start: 0.8361 (t80) cc_final: 0.7867 (t80) REVERT: b 32 MET cc_start: 0.8811 (tpt) cc_final: 0.8481 (tpp) REVERT: q 93 MET cc_start: 0.8115 (ptt) cc_final: 0.7770 (ptt) outliers start: 1 outliers final: 0 residues processed: 652 average time/residue: 0.1958 time to fit residues: 206.3405 Evaluate side-chains 537 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 148 optimal weight: 20.0000 chunk 254 optimal weight: 0.6980 chunk 155 optimal weight: 0.0050 chunk 222 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 389 optimal weight: 30.0000 chunk 368 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 325 optimal weight: 0.4980 chunk 165 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN D 131 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 HIS V 111 GLN X 95 GLN a 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.097811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.065861 restraints weight = 137898.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.067187 restraints weight = 93147.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.067996 restraints weight = 66925.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.069163 restraints weight = 55384.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.069397 restraints weight = 47770.394| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 33253 Z= 0.138 Angle : 0.968 76.521 45126 Z= 0.361 Chirality : 0.045 0.251 4959 Planarity : 0.005 0.120 5728 Dihedral : 7.019 155.200 4534 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.35 (0.13), residues: 3981 helix: 0.53 (0.12), residues: 1854 sheet: -0.83 (0.28), residues: 356 loop : -0.84 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 68 TYR 0.040 0.002 TYR I 145 PHE 0.031 0.002 PHE C 60 TRP 0.048 0.002 TRP H 303 HIS 0.016 0.001 HIS H 304 Details of bonding type rmsd covalent geometry : bond 0.00312 (33213) covalent geometry : angle 0.72503 (45036) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.21652 ( 6) hydrogen bonds : bond 0.04010 ( 1397) hydrogen bonds : angle 5.18408 ( 4059) metal coordination : bond 0.01166 ( 37) metal coordination : angle 14.87352 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 699 time to evaluate : 2.058 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: B 80 ASP cc_start: 0.9302 (t0) cc_final: 0.9044 (t0) REVERT: B 91 TRP cc_start: 0.9495 (m100) cc_final: 0.8928 (m100) REVERT: B 103 GLU cc_start: 0.8764 (tp30) cc_final: 0.8197 (tp30) REVERT: B 129 ASP cc_start: 0.9176 (m-30) cc_final: 0.8873 (m-30) REVERT: B 147 LYS cc_start: 0.9290 (ptmt) cc_final: 0.9044 (pttt) REVERT: B 152 MET cc_start: 0.9474 (mtm) cc_final: 0.9216 (mtt) REVERT: B 161 MET cc_start: 0.8603 (ttp) cc_final: 0.8257 (ttp) REVERT: B 171 TYR cc_start: 0.8803 (m-80) cc_final: 0.8050 (m-10) REVERT: B 176 SER cc_start: 0.9726 (m) cc_final: 0.9512 (p) REVERT: B 207 GLN cc_start: 0.9176 (mm110) cc_final: 0.8805 (mm110) REVERT: B 209 GLN cc_start: 0.9598 (mm-40) cc_final: 0.9102 (mm110) REVERT: C 113 LEU cc_start: 0.8767 (mt) cc_final: 0.8546 (mt) REVERT: C 176 PHE cc_start: 0.8903 (t80) cc_final: 0.8206 (t80) REVERT: C 227 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8468 (tm-30) REVERT: C 231 LYS cc_start: 0.9165 (tppt) cc_final: 0.8502 (mmmm) REVERT: D 84 PHE cc_start: 0.8309 (t80) cc_final: 0.7986 (t80) REVERT: D 110 ASP cc_start: 0.8445 (t0) cc_final: 0.8084 (t0) REVERT: D 116 LEU cc_start: 0.9388 (tp) cc_final: 0.9185 (tp) REVERT: D 127 LYS cc_start: 0.9374 (mmtp) cc_final: 0.9139 (mmmm) REVERT: D 135 TYR cc_start: 0.9029 (m-80) cc_final: 0.8385 (m-80) REVERT: D 156 GLU cc_start: 0.8961 (pt0) cc_final: 0.8543 (pt0) REVERT: D 185 MET cc_start: 0.9466 (mmm) cc_final: 0.9117 (mmm) REVERT: D 205 GLU cc_start: 0.9311 (tp30) cc_final: 0.9071 (tp30) REVERT: D 261 MET cc_start: 0.8586 (mmp) cc_final: 0.8083 (mmt) REVERT: D 336 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8879 (tm-30) REVERT: D 348 LEU cc_start: 0.9395 (mt) cc_final: 0.9112 (mp) REVERT: D 371 MET cc_start: 0.8931 (ptp) cc_final: 0.8716 (ptt) REVERT: D 401 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8251 (mt-10) REVERT: D 443 MET cc_start: 0.8192 (mmp) cc_final: 0.7929 (mmp) REVERT: E 109 MET cc_start: 0.1217 (mmm) cc_final: 0.0392 (tpp) REVERT: E 120 MET cc_start: 0.0586 (tmm) cc_final: 0.0097 (tmm) REVERT: F 131 MET cc_start: 0.6095 (tpt) cc_final: 0.4733 (ptm) REVERT: F 157 TYR cc_start: 0.5169 (t80) cc_final: 0.4745 (t80) REVERT: F 313 ASN cc_start: 0.6716 (m-40) cc_final: 0.6419 (t0) REVERT: F 357 MET cc_start: 0.3264 (ptp) cc_final: 0.2449 (ttt) REVERT: G 33 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8401 (tp30) REVERT: G 145 MET cc_start: 0.8531 (tpp) cc_final: 0.7936 (tpp) REVERT: G 146 PHE cc_start: 0.5753 (m-10) cc_final: 0.5464 (m-10) REVERT: G 213 MET cc_start: 0.2610 (ppp) cc_final: 0.2324 (ppp) REVERT: G 271 MET cc_start: 0.8227 (mmp) cc_final: 0.7821 (mmm) REVERT: G 294 TYR cc_start: 0.8687 (p90) cc_final: 0.8414 (p90) REVERT: G 345 LEU cc_start: 0.8878 (mt) cc_final: 0.8607 (mt) REVERT: G 473 MET cc_start: 0.7682 (mtt) cc_final: 0.6760 (tpp) REVERT: G 513 MET cc_start: 0.7938 (pmm) cc_final: 0.7164 (pmm) REVERT: G 544 MET cc_start: 0.7990 (tpt) cc_final: 0.7651 (tpp) REVERT: G 571 HIS cc_start: 0.8129 (p-80) cc_final: 0.7683 (p-80) REVERT: G 707 MET cc_start: 0.7850 (mmt) cc_final: 0.7439 (mmm) REVERT: H 31 MET cc_start: 0.9481 (mtt) cc_final: 0.9015 (mmm) REVERT: H 47 GLN cc_start: 0.9324 (tp40) cc_final: 0.8745 (tp-100) REVERT: H 53 MET cc_start: 0.9312 (tpt) cc_final: 0.8794 (tpp) REVERT: H 56 PHE cc_start: 0.9204 (m-10) cc_final: 0.8998 (m-80) REVERT: H 57 MET cc_start: 0.8995 (mmp) cc_final: 0.8537 (mmp) REVERT: H 71 PHE cc_start: 0.9117 (t80) cc_final: 0.8744 (t80) REVERT: H 118 TRP cc_start: 0.9306 (m-10) cc_final: 0.8966 (m-90) REVERT: H 143 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8893 (mt-10) REVERT: H 146 MET cc_start: 0.9478 (ttm) cc_final: 0.8962 (mtt) REVERT: H 183 MET cc_start: 0.9291 (mtm) cc_final: 0.8974 (mtt) REVERT: H 222 LEU cc_start: 0.9660 (mt) cc_final: 0.9218 (tp) REVERT: H 234 MET cc_start: 0.9422 (mmp) cc_final: 0.9134 (mmp) REVERT: H 272 TRP cc_start: 0.8846 (t60) cc_final: 0.8466 (t60) REVERT: H 274 ARG cc_start: 0.9287 (ttt180) cc_final: 0.8919 (ttm-80) REVERT: H 284 GLN cc_start: 0.9530 (mm-40) cc_final: 0.9083 (tm-30) REVERT: H 285 LEU cc_start: 0.9088 (mt) cc_final: 0.8426 (mt) REVERT: H 300 LEU cc_start: 0.9535 (mt) cc_final: 0.9330 (mp) REVERT: I 74 LEU cc_start: 0.9482 (tt) cc_final: 0.9239 (tp) REVERT: I 148 ASP cc_start: 0.8708 (t70) cc_final: 0.8443 (t0) REVERT: I 149 MET cc_start: 0.8700 (mmm) cc_final: 0.7974 (mmm) REVERT: I 185 TYR cc_start: 0.9099 (m-80) cc_final: 0.8211 (m-80) REVERT: P 68 TYR cc_start: 0.9108 (m-80) cc_final: 0.8753 (m-80) REVERT: P 84 TYR cc_start: 0.9064 (p90) cc_final: 0.8602 (p90) REVERT: P 92 MET cc_start: 0.8841 (tpt) cc_final: 0.8556 (tpp) REVERT: P 251 ASN cc_start: 0.9386 (m-40) cc_final: 0.9134 (m-40) REVERT: Q 88 GLN cc_start: 0.6401 (mm-40) cc_final: 0.5826 (mm110) REVERT: Q 99 MET cc_start: 0.9210 (ppp) cc_final: 0.8762 (ppp) REVERT: Q 126 LEU cc_start: 0.9164 (mt) cc_final: 0.8905 (mp) REVERT: Q 128 PHE cc_start: 0.8579 (m-80) cc_final: 0.8318 (m-10) REVERT: Q 133 ASP cc_start: 0.9370 (m-30) cc_final: 0.9039 (t0) REVERT: Q 150 LYS cc_start: 0.2413 (tttt) cc_final: 0.2121 (tmtt) REVERT: S 71 PHE cc_start: 0.8475 (t80) cc_final: 0.8177 (t80) REVERT: T 130 ILE cc_start: 0.6720 (tt) cc_final: 0.6338 (tt) REVERT: T 139 MET cc_start: 0.5360 (mmp) cc_final: 0.5122 (mmm) REVERT: V 93 LYS cc_start: 0.9297 (mtpt) cc_final: 0.8848 (mmmm) REVERT: W 45 GLU cc_start: 0.9374 (tp30) cc_final: 0.9011 (tp30) REVERT: W 49 THR cc_start: 0.9704 (t) cc_final: 0.9312 (t) REVERT: W 69 MET cc_start: 0.8054 (mtt) cc_final: 0.7519 (mtp) REVERT: W 80 ARG cc_start: 0.8977 (mtm180) cc_final: 0.8428 (mpp80) REVERT: W 91 MET cc_start: 0.9229 (mtp) cc_final: 0.8793 (mtm) REVERT: W 92 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8631 (tm-30) REVERT: W 95 GLU cc_start: 0.9607 (mt-10) cc_final: 0.9344 (mt-10) REVERT: X 44 MET cc_start: 0.9251 (mmm) cc_final: 0.9042 (mmm) REVERT: Z 10 MET cc_start: 0.8678 (tpp) cc_final: 0.8446 (tpp) REVERT: Z 43 LEU cc_start: 0.9054 (mt) cc_final: 0.8815 (mt) REVERT: a 35 GLU cc_start: 0.8553 (pt0) cc_final: 0.7440 (tp30) REVERT: b 23 PHE cc_start: 0.8123 (t80) cc_final: 0.7619 (t80) REVERT: b 32 MET cc_start: 0.8936 (tpt) cc_final: 0.8501 (tpt) REVERT: b 44 MET cc_start: 0.8725 (ptp) cc_final: 0.8427 (ptp) REVERT: q 93 MET cc_start: 0.7975 (ptt) cc_final: 0.7672 (ptt) outliers start: 0 outliers final: 0 residues processed: 699 average time/residue: 0.2042 time to fit residues: 231.9083 Evaluate side-chains 558 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 209 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 367 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 390 optimal weight: 0.1980 chunk 221 optimal weight: 5.9990 chunk 365 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.097544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.065118 restraints weight = 140444.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.067026 restraints weight = 93137.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.067901 restraints weight = 66709.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.069190 restraints weight = 54504.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.069461 restraints weight = 46634.130| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 33253 Z= 0.139 Angle : 0.963 75.884 45126 Z= 0.361 Chirality : 0.045 0.276 4959 Planarity : 0.005 0.117 5728 Dihedral : 6.975 155.295 4534 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % 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: -0.35 (0.13), residues: 3981 helix: 0.56 (0.12), residues: 1849 sheet: -0.90 (0.28), residues: 364 loop : -0.85 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 68 TYR 0.034 0.002 TYR D 151 PHE 0.035 0.002 PHE H 130 TRP 0.055 0.002 TRP F 62 HIS 0.006 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00320 (33213) covalent geometry : angle 0.72438 (45036) SS BOND : bond 0.00305 ( 3) SS BOND : angle 1.10686 ( 6) hydrogen bonds : bond 0.03937 ( 1397) hydrogen bonds : angle 5.17075 ( 4059) metal coordination : bond 0.01120 ( 37) metal coordination : angle 14.71594 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7962 Ramachandran restraints generated. 3981 Oldfield, 0 Emsley, 3981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.342 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: A 17 LEU cc_start: 0.9466 (mt) cc_final: 0.9257 (mt) REVERT: A 92 PHE cc_start: 0.9307 (m-10) cc_final: 0.8997 (m-80) REVERT: A 102 LEU cc_start: 0.9396 (tp) cc_final: 0.9104 (tp) REVERT: B 80 ASP cc_start: 0.9309 (t0) cc_final: 0.9048 (t0) REVERT: B 91 TRP cc_start: 0.9495 (m100) cc_final: 0.8929 (m100) REVERT: B 93 MET cc_start: 0.8251 (tmm) cc_final: 0.7838 (tmm) REVERT: B 103 GLU cc_start: 0.8759 (tp30) cc_final: 0.8204 (tp30) REVERT: B 129 ASP cc_start: 0.9140 (m-30) cc_final: 0.8835 (m-30) REVERT: B 147 LYS cc_start: 0.9262 (ptmt) cc_final: 0.8984 (pttt) REVERT: B 152 MET cc_start: 0.9440 (mtm) cc_final: 0.8927 (mtt) REVERT: B 207 GLN cc_start: 0.9202 (mm110) cc_final: 0.8857 (mm110) REVERT: B 209 GLN cc_start: 0.9595 (mm-40) cc_final: 0.9095 (mm110) REVERT: C 108 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8761 (mmtm) REVERT: C 176 PHE cc_start: 0.8945 (t80) cc_final: 0.8196 (t80) REVERT: C 225 LEU cc_start: 0.8357 (tp) cc_final: 0.8082 (tp) REVERT: C 231 LYS cc_start: 0.9187 (tppt) cc_final: 0.8876 (tppt) REVERT: D 84 PHE cc_start: 0.8309 (t80) cc_final: 0.8008 (t80) REVERT: D 110 ASP cc_start: 0.8447 (t0) cc_final: 0.8124 (t0) REVERT: D 116 LEU cc_start: 0.9335 (tp) cc_final: 0.9131 (tp) REVERT: D 127 LYS cc_start: 0.9344 (mmtp) cc_final: 0.9140 (mmmm) REVERT: D 135 TYR cc_start: 0.9075 (m-80) cc_final: 0.8495 (m-80) REVERT: D 138 ARG cc_start: 0.9321 (mtt90) cc_final: 0.9035 (mtt90) REVERT: D 145 MET cc_start: 0.8542 (mpp) cc_final: 0.7645 (mpp) REVERT: D 156 GLU cc_start: 0.8951 (pt0) cc_final: 0.8522 (pt0) REVERT: D 185 MET cc_start: 0.9477 (mmm) cc_final: 0.9118 (mmm) REVERT: D 194 ILE cc_start: 0.9434 (mm) cc_final: 0.9217 (mm) REVERT: D 205 GLU cc_start: 0.9378 (tp30) cc_final: 0.9141 (tp30) REVERT: D 210 MET cc_start: 0.9341 (pmm) cc_final: 0.9041 (pmm) REVERT: D 214 TYR cc_start: 0.8879 (m-80) cc_final: 0.8481 (m-10) REVERT: D 261 MET cc_start: 0.8632 (mmp) cc_final: 0.8139 (mmt) REVERT: D 323 ARG cc_start: 0.8040 (mpp-170) cc_final: 0.7523 (mpt180) REVERT: D 336 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8917 (tm-30) REVERT: D 348 LEU cc_start: 0.9362 (mt) cc_final: 0.9092 (mp) REVERT: D 371 MET cc_start: 0.8912 (ptp) cc_final: 0.8483 (mtm) REVERT: D 401 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8278 (mm-30) REVERT: D 443 MET cc_start: 0.8131 (mmp) cc_final: 0.7822 (mmp) REVERT: E 109 MET cc_start: 0.0942 (mmm) cc_final: 0.0349 (tpp) REVERT: E 120 MET cc_start: 0.0403 (tmm) cc_final: -0.0080 (tmm) REVERT: F 131 MET cc_start: 0.6158 (tpt) cc_final: 0.4828 (ptm) REVERT: F 313 ASN cc_start: 0.6901 (m-40) cc_final: 0.6616 (t0) REVERT: F 357 MET cc_start: 0.3298 (ptp) cc_final: 0.2574 (ttt) REVERT: G 33 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8389 (tp30) REVERT: G 145 MET cc_start: 0.8546 (tpp) cc_final: 0.8276 (tpp) REVERT: G 173 MET cc_start: 0.8365 (tpt) cc_final: 0.7876 (tpt) REVERT: G 215 MET cc_start: 0.6208 (tpt) cc_final: 0.5478 (tpt) REVERT: G 271 MET cc_start: 0.8319 (mmp) cc_final: 0.7898 (mmm) REVERT: G 345 LEU cc_start: 0.8806 (mt) cc_final: 0.8478 (mt) REVERT: G 473 MET cc_start: 0.7709 (mtt) cc_final: 0.6714 (tpp) REVERT: G 513 MET cc_start: 0.7893 (pmm) cc_final: 0.7118 (pmm) REVERT: G 544 MET cc_start: 0.7946 (tpt) cc_final: 0.7715 (tpp) REVERT: G 571 HIS cc_start: 0.8056 (p-80) cc_final: 0.7176 (t-90) REVERT: H 17 MET cc_start: 0.9227 (ppp) cc_final: 0.8980 (ppp) REVERT: H 31 MET cc_start: 0.9448 (mtt) cc_final: 0.8974 (mmm) REVERT: H 47 GLN cc_start: 0.9346 (tp40) cc_final: 0.8758 (tp-100) REVERT: H 53 MET cc_start: 0.9299 (tpt) cc_final: 0.8813 (tpp) REVERT: H 56 PHE cc_start: 0.9220 (m-10) cc_final: 0.9001 (m-80) REVERT: H 57 MET cc_start: 0.8996 (mmp) cc_final: 0.8587 (mmp) REVERT: H 91 MET cc_start: 0.8723 (ttp) cc_final: 0.8264 (tmm) REVERT: H 118 TRP cc_start: 0.9294 (m-10) cc_final: 0.8917 (m-90) REVERT: H 143 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8879 (mt-10) REVERT: H 146 MET cc_start: 0.9493 (ttm) cc_final: 0.9061 (mtt) REVERT: H 183 MET cc_start: 0.9291 (mtm) cc_final: 0.8888 (mtt) REVERT: H 234 MET cc_start: 0.9438 (mmp) cc_final: 0.9151 (mmp) REVERT: H 272 TRP cc_start: 0.8787 (t60) cc_final: 0.8365 (t60) REVERT: H 274 ARG cc_start: 0.9224 (ttt180) cc_final: 0.9016 (ttm-80) REVERT: H 284 GLN cc_start: 0.9469 (mm-40) cc_final: 0.9092 (tm-30) REVERT: H 285 LEU cc_start: 0.9100 (mt) cc_final: 0.8424 (mt) REVERT: H 294 LEU cc_start: 0.9782 (tt) cc_final: 0.9538 (tt) REVERT: H 300 LEU cc_start: 0.9557 (mt) cc_final: 0.9140 (mp) REVERT: H 304 HIS cc_start: 0.8738 (m-70) cc_final: 0.8526 (m90) REVERT: I 74 LEU cc_start: 0.9491 (tt) cc_final: 0.9238 (tp) REVERT: I 148 ASP cc_start: 0.8584 (t70) cc_final: 0.8346 (t0) REVERT: I 149 MET cc_start: 0.8716 (mmm) cc_final: 0.7961 (mmm) REVERT: I 185 TYR cc_start: 0.9089 (m-80) cc_final: 0.8160 (m-80) REVERT: P 68 TYR cc_start: 0.9028 (m-80) cc_final: 0.8707 (m-80) REVERT: P 84 TYR cc_start: 0.9043 (p90) cc_final: 0.8575 (p90) REVERT: P 92 MET cc_start: 0.8821 (tpt) cc_final: 0.8569 (tpp) REVERT: P 251 ASN cc_start: 0.9372 (m-40) cc_final: 0.9111 (m-40) REVERT: Q 88 GLN cc_start: 0.6363 (mm-40) cc_final: 0.5959 (mm110) REVERT: Q 99 MET cc_start: 0.9220 (ppp) cc_final: 0.8825 (ppp) REVERT: Q 126 LEU cc_start: 0.9128 (mt) cc_final: 0.8830 (mp) REVERT: Q 128 PHE cc_start: 0.8474 (m-80) cc_final: 0.8092 (m-80) REVERT: Q 133 ASP cc_start: 0.9359 (m-30) cc_final: 0.8920 (t0) REVERT: Q 150 LYS cc_start: 0.2154 (tttt) cc_final: 0.1837 (tmtt) REVERT: Q 164 PHE cc_start: 0.7991 (m-10) cc_final: 0.7741 (m-80) REVERT: S 71 PHE cc_start: 0.8463 (t80) cc_final: 0.8242 (t80) REVERT: T 104 PHE cc_start: 0.9077 (m-10) cc_final: 0.8826 (m-80) REVERT: T 117 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8402 (mt-10) REVERT: T 130 ILE cc_start: 0.6622 (tt) cc_final: 0.6242 (tt) REVERT: T 139 MET cc_start: 0.5640 (mmp) cc_final: 0.5169 (mmm) REVERT: V 93 LYS cc_start: 0.9299 (mtpt) cc_final: 0.8852 (mmmm) REVERT: W 45 GLU cc_start: 0.9354 (tp30) cc_final: 0.8966 (tp30) REVERT: W 49 THR cc_start: 0.9657 (t) cc_final: 0.9233 (t) REVERT: W 69 MET cc_start: 0.8081 (mtt) cc_final: 0.7450 (mtp) REVERT: W 80 ARG cc_start: 0.8951 (mtm180) cc_final: 0.8235 (mpp80) REVERT: W 87 ILE cc_start: 0.9509 (mt) cc_final: 0.9228 (mt) REVERT: W 91 MET cc_start: 0.9244 (mtp) cc_final: 0.8887 (mtm) REVERT: W 92 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8551 (tm-30) REVERT: W 93 LEU cc_start: 0.9794 (pp) cc_final: 0.9580 (pp) REVERT: W 94 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8979 (tm-30) REVERT: X 44 MET cc_start: 0.9226 (mmm) cc_final: 0.8944 (mmm) REVERT: Z 10 MET cc_start: 0.8654 (tpp) cc_final: 0.8432 (tpp) REVERT: a 35 GLU cc_start: 0.8637 (pt0) cc_final: 0.7503 (tp30) REVERT: a 48 MET cc_start: 0.8599 (mmt) cc_final: 0.8046 (mmp) REVERT: b 23 PHE cc_start: 0.8060 (t80) cc_final: 0.7513 (t80) REVERT: b 30 ILE cc_start: 0.9376 (mm) cc_final: 0.9073 (mm) REVERT: b 32 MET cc_start: 0.8933 (tpt) cc_final: 0.8556 (tpt) REVERT: q 93 MET cc_start: 0.7932 (ptt) cc_final: 0.7655 (ptt) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.2132 time to fit residues: 235.1390 Evaluate side-chains 554 residues out of total 3493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 339 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 370 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 21 optimal weight: 0.0170 chunk 262 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 106 GLN C 130 ASN D 131 GLN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** G 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 81 ASN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.095190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064063 restraints weight = 143323.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.065595 restraints weight = 95306.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.066192 restraints weight = 68432.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.066775 restraints weight = 58996.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.067612 restraints weight = 53062.402| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.7522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33253 Z= 0.175 Angle : 0.975 78.096 45126 Z= 0.366 Chirality : 0.045 0.269 4959 Planarity : 0.005 0.118 5728 Dihedral : 7.019 155.812 4534 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 3981 helix: 0.52 (0.12), residues: 1847 sheet: -0.91 (0.28), residues: 361 loop : -0.82 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 68 TYR 0.030 0.002 TYR I 145 PHE 0.099 0.002 PHE X 107 TRP 0.047 0.002 TRP H 303 HIS 0.006 0.001 HIS G 124 Details of bonding type rmsd covalent geometry : bond 0.00394 (33213) covalent geometry : angle 0.72576 (45036) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.98612 ( 6) hydrogen bonds : bond 0.03946 ( 1397) hydrogen bonds : angle 5.24824 ( 4059) metal coordination : bond 0.01704 ( 37) metal coordination : angle 15.12039 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8659.67 seconds wall clock time: 149 minutes 42.31 seconds (8982.31 seconds total)