Starting phenix.real_space_refine on Fri Mar 6 05:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.map" model { file = "/net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vlk_32023/03_2026/7vlk_32023.cif" } resolution = 2.27 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= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 158 5.16 5 C 18288 2.51 5 N 4998 2.21 5 O 5330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28774 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2279 Classifications: {'peptide': 294} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2279 Classifications: {'peptide': 294} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "D" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "H" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "I" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 5.60, per 1000 atoms: 0.19 Number of scatterers: 28774 At special positions: 0 Unit cell: (174.09, 140.93, 125.179, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 158 16.00 O 5330 8.00 N 4998 7.00 C 18288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 33 sheets defined 47.6% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.623A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.710A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 116 removed outlier: 3.990A pdb=" N LYS A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.669A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.630A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.278A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.601A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.652A pdb=" N ARG B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.745A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 removed outlier: 3.854A pdb=" N LEU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.526A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.672A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 188 removed outlier: 4.585A pdb=" N GLU B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.592A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.573A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 292 through 304 removed outlier: 4.138A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.522A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.414A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.674A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.791A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.545A pdb=" N LEU C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.652A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.534A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.362A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.648A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 210 Processing helix chain 'D' and resid 221 through 227 removed outlier: 4.143A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.825A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.664A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.614A pdb=" N ILE E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 114 through 124 removed outlier: 4.543A pdb=" N LEU E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.640A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.723A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.700A pdb=" N LEU F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.624A pdb=" N ILE F 93 " --> pdb=" O SER F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.381A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.656A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 280 through 292 removed outlier: 4.184A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.850A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.159A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 325 removed outlier: 4.168A pdb=" N LEU G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 368 through 379 removed outlier: 3.888A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.580A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 398 No H-bonds generated for 'chain 'G' and resid 396 through 398' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.663A pdb=" N SER G 520 " --> pdb=" O LEU G 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 3.703A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 325 removed outlier: 4.168A pdb=" N LEU H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 353 removed outlier: 3.637A pdb=" N GLY H 353 " --> pdb=" O ALA H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 379 removed outlier: 3.893A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.565A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 521 removed outlier: 3.613A pdb=" N SER H 520 " --> pdb=" O LEU H 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.894A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.556A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.637A pdb=" N CYS I 112 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.681A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 322 through 326 removed outlier: 3.636A pdb=" N ASN I 326 " --> pdb=" O PRO I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.574A pdb=" N GLN I 333 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 330 through 334' Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.883A pdb=" N ASP J 62 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 98 through 108 removed outlier: 3.517A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.557A pdb=" N CYS J 112 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.507A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.653A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 322 through 326 removed outlier: 3.640A pdb=" N ASN J 326 " --> pdb=" O PRO J 323 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 334 removed outlier: 3.543A pdb=" N SER J 334 " --> pdb=" O THR J 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 1 through 3 No H-bonds generated for 'chain 'K' and resid 1 through 3' Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.219A pdb=" N TRP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.918A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 158 through 177 Processing helix chain 'K' and resid 180 through 184 removed outlier: 3.572A pdb=" N HIS K 183 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'L' and resid 1 through 3 No H-bonds generated for 'chain 'L' and resid 1 through 3' Processing helix chain 'L' and resid 61 through 66 Processing helix chain 'L' and resid 90 through 98 Processing helix chain 'L' and resid 112 through 118 Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.848A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 154 Processing helix chain 'L' and resid 158 through 178 Processing helix chain 'L' and resid 188 through 204 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 8.801A pdb=" N THR A 176 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 192 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 178 removed outlier: 8.786A pdb=" N THR B 176 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY B 196 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.673A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.558A pdb=" N SER C 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N LEU H 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLY H 404 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR H 336 " --> pdb=" O GLY H 404 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.663A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR D 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.441A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 332 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU G 402 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLY G 404 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR G 336 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL G 401 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N CYS G 437 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 403 " --> pdb=" O CYS G 437 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.105A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER E 105 " --> pdb=" O HIS E 203 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS E 203 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 172 removed outlier: 6.302A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE E 157 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE I 249 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS I 186 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS I 247 " --> pdb=" O LYS I 186 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 180 through 183 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 79 removed outlier: 6.469A pdb=" N ALA F 5 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL F 54 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL F 7 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU F 131 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU F 204 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA F 129 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.345A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N MET F 170 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE F 157 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL J 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE J 287 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE J 249 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LYS J 186 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS J 247 " --> pdb=" O LYS J 186 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE J 123 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'G' and resid 466 through 467 removed outlier: 3.538A pdb=" N ARG G 467 " --> pdb=" O HIS G 470 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS G 470 " --> pdb=" O ARG G 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC3, first strand: chain 'I' and resid 336 through 338 removed outlier: 6.228A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.535A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR I 424 " --> pdb=" O ILE I 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 384 through 385 removed outlier: 6.474A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AC7, first strand: chain 'J' and resid 336 through 338 removed outlier: 6.184A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.497A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.447A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 5 through 13 removed outlier: 4.870A pdb=" N TYR K 5 " --> pdb=" O LYS K 32 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS K 32 " --> pdb=" O TYR K 5 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE K 7 " --> pdb=" O TYR K 30 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 38 through 41 Processing sheet with id=AD3, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 13 removed outlier: 4.859A pdb=" N TYR L 5 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS L 32 " --> pdb=" O TYR L 5 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE L 7 " --> pdb=" O TYR L 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 38 through 41 Processing sheet with id=AD6, first strand: chain 'L' and resid 52 through 54 removed outlier: 6.156A pdb=" N ARG L 52 " --> pdb=" O LEU L 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 1307 hydrogen bonds defined for protein. 3621 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: 5.52 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9532 1.35 - 1.46: 6425 1.46 - 1.58: 13119 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 29316 Sorted by residual: bond pdb=" CB ASP E 177 " pdb=" CG ASP E 177 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 2.00e+00 bond pdb=" CG LYS B 38 " pdb=" CD LYS B 38 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C TYR F 38 " pdb=" N PRO F 39 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.38e-02 5.25e+03 1.68e+00 bond pdb=" CB LYS B 38 " pdb=" CG LYS B 38 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C GLN B 156 " pdb=" N PRO B 157 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.45e+00 ... (remaining 29311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 39442 2.34 - 4.67: 254 4.67 - 7.01: 25 7.01 - 9.34: 8 9.34 - 11.68: 5 Bond angle restraints: 39734 Sorted by residual: angle pdb=" CB LYS B 38 " pdb=" CG LYS B 38 " pdb=" CD LYS B 38 " ideal model delta sigma weight residual 111.30 120.56 -9.26 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CB MET K 87 " pdb=" CG MET K 87 " pdb=" SD MET K 87 " ideal model delta sigma weight residual 112.70 124.33 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA LEU L 97 " pdb=" CB LEU L 97 " pdb=" CG LEU L 97 " ideal model delta sigma weight residual 116.30 127.98 -11.68 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CB MET F 8 " pdb=" CG MET F 8 " pdb=" SD MET F 8 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" CB MET F 216 " pdb=" CG MET F 216 " pdb=" SD MET F 216 " ideal model delta sigma weight residual 112.70 121.52 -8.82 3.00e+00 1.11e-01 8.64e+00 ... (remaining 39729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15480 17.96 - 35.92: 1690 35.92 - 53.88: 489 53.88 - 71.84: 96 71.84 - 89.80: 43 Dihedral angle restraints: 17798 sinusoidal: 6996 harmonic: 10802 Sorted by residual: dihedral pdb=" CA THR I 432 " pdb=" C THR I 432 " pdb=" N SER I 433 " pdb=" CA SER I 433 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA THR J 432 " pdb=" C THR J 432 " pdb=" N SER J 433 " pdb=" CA SER J 433 " ideal model delta harmonic sigma weight residual 180.00 160.89 19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU C 245 " pdb=" C LEU C 245 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 17795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3031 0.030 - 0.061: 979 0.061 - 0.091: 312 0.091 - 0.122: 281 0.122 - 0.152: 33 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CB ILE H 388 " pdb=" CA ILE H 388 " pdb=" CG1 ILE H 388 " pdb=" CG2 ILE H 388 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ILE L 123 " pdb=" N ILE L 123 " pdb=" C ILE L 123 " pdb=" CB ILE L 123 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE E 158 " pdb=" N ILE E 158 " pdb=" C ILE E 158 " pdb=" CB ILE E 158 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 4633 not shown) Planarity restraints: 5078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 177 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.93e+00 pdb=" C ASP E 177 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP E 177 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU E 178 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.28e+00 pdb=" N PRO H 396 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO G 396 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.032 5.00e-02 4.00e+02 ... (remaining 5075 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1632 2.74 - 3.28: 28261 3.28 - 3.82: 49136 3.82 - 4.36: 59366 4.36 - 4.90: 100568 Nonbonded interactions: 238963 Sorted by model distance: nonbonded pdb=" O SER A 61 " pdb=" OG SER A 61 " model vdw 2.195 3.040 nonbonded pdb=" OD2 ASP A 245 " pdb=" NZ LYS G 326 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASP I 206 " pdb=" OG1 THR I 208 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU B 154 " pdb=" NE2 GLN B 156 " model vdw 2.239 3.120 nonbonded pdb=" OG SER K 39 " pdb=" O PRO K 71 " model vdw 2.247 3.040 ... (remaining 238958 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.440 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.002 0.039 29316 Z= 0.094 Angle : 0.497 11.676 39734 Z= 0.254 Chirality : 0.041 0.152 4636 Planarity : 0.004 0.057 5078 Dihedral : 17.005 89.800 10782 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.51 % Allowed : 22.19 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.38 (0.14), residues: 3646 helix: 1.86 (0.14), residues: 1460 sheet: 0.22 (0.25), residues: 438 loop : 0.41 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 185 TYR 0.016 0.001 TYR L 65 PHE 0.016 0.001 PHE C 272 TRP 0.014 0.001 TRP L 74 HIS 0.005 0.000 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00197 (29316) covalent geometry : angle 0.49676 (39734) hydrogen bonds : bond 0.14645 ( 1307) hydrogen bonds : angle 5.39755 ( 3621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 308 time to evaluate : 1.094 Fit side-chains REVERT: A 171 LEU cc_start: 0.8094 (mp) cc_final: 0.7636 (tt) REVERT: B 171 LEU cc_start: 0.8126 (mp) cc_final: 0.7662 (tt) REVERT: D 199 GLN cc_start: 0.7739 (mt0) cc_final: 0.7522 (mt0) REVERT: F 45 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7484 (ttp-110) REVERT: F 116 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6868 (tt0) REVERT: F 225 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7237 (ttt90) REVERT: G 295 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6917 (mt-10) REVERT: J 149 LEU cc_start: 0.8457 (mp) cc_final: 0.8196 (tt) REVERT: J 176 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7975 (mmmm) REVERT: K 42 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7058 (tm-30) REVERT: L 42 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7187 (tm-30) REVERT: L 50 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8243 (mmtp) REVERT: L 93 MET cc_start: 0.6998 (ttt) cc_final: 0.5944 (mmt) outliers start: 79 outliers final: 73 residues processed: 382 average time/residue: 0.6186 time to fit residues: 276.1800 Evaluate side-chains 352 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 175 ASP Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 429 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 65 TYR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS A 208 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN H 347 GLN H 422 GLN I 302 ASN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.147636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.108318 restraints weight = 38508.195| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.18 r_work: 0.3393 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29316 Z= 0.110 Angle : 0.490 9.207 39734 Z= 0.253 Chirality : 0.042 0.155 4636 Planarity : 0.004 0.058 5078 Dihedral : 5.653 58.532 4102 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.98 % Allowed : 21.05 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.57 (0.14), residues: 3646 helix: 2.05 (0.14), residues: 1480 sheet: 0.23 (0.25), residues: 428 loop : 0.49 (0.16), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 185 TYR 0.017 0.001 TYR K 65 PHE 0.015 0.001 PHE D 272 TRP 0.011 0.001 TRP L 74 HIS 0.006 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00238 (29316) covalent geometry : angle 0.49032 (39734) hydrogen bonds : bond 0.03868 ( 1307) hydrogen bonds : angle 4.23125 ( 3621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 285 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8114 (t0) REVERT: B 54 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7139 (tp30) REVERT: C 53 ASN cc_start: 0.8148 (p0) cc_final: 0.7833 (p0) REVERT: D 59 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: F 1 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6660 (mmt) REVERT: F 45 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7633 (ttp-110) REVERT: F 194 ARG cc_start: 0.7215 (tmt170) cc_final: 0.6795 (tmt170) REVERT: F 225 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7048 (ttt90) REVERT: G 295 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7243 (mt-10) REVERT: H 347 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7459 (mp-120) REVERT: H 506 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8115 (mmt) REVERT: J 411 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8581 (m) REVERT: K 42 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7161 (tm-30) REVERT: L 42 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7233 (tm-30) outliers start: 94 outliers final: 35 residues processed: 361 average time/residue: 0.6801 time to fit residues: 283.4235 Evaluate side-chains 314 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 318 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 308 optimal weight: 0.9990 chunk 325 optimal weight: 0.0970 chunk 312 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 ASN B 214 GLN C 44 GLN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 GLN H 422 GLN I 302 ASN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.104928 restraints weight = 38502.468| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.18 r_work: 0.3342 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29316 Z= 0.162 Angle : 0.532 10.595 39734 Z= 0.276 Chirality : 0.045 0.153 4636 Planarity : 0.004 0.058 5078 Dihedral : 5.043 58.171 4029 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.92 % Allowed : 20.67 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.37 (0.14), residues: 3646 helix: 1.88 (0.13), residues: 1492 sheet: 0.23 (0.24), residues: 448 loop : 0.33 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 223 TYR 0.017 0.001 TYR A 304 PHE 0.017 0.001 PHE C 272 TRP 0.012 0.001 TRP L 74 HIS 0.007 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00388 (29316) covalent geometry : angle 0.53234 (39734) hydrogen bonds : bond 0.04441 ( 1307) hydrogen bonds : angle 4.19081 ( 3621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 0.951 Fit side-chains REVERT: B 54 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: B 151 TYR cc_start: 0.8595 (m-80) cc_final: 0.8385 (m-80) REVERT: C 49 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.6911 (m-70) REVERT: D 14 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7373 (mtm180) REVERT: D 59 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: E 194 ARG cc_start: 0.6963 (tmt170) cc_final: 0.6637 (tmt170) REVERT: F 45 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7684 (ttp-110) REVERT: F 177 ASP cc_start: 0.7471 (t0) cc_final: 0.7239 (m-30) REVERT: F 225 ARG cc_start: 0.7602 (ttp80) cc_final: 0.7127 (ttt90) REVERT: G 194 GLN cc_start: 0.8538 (pt0) cc_final: 0.8314 (pt0) REVERT: G 295 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7281 (mt-10) REVERT: H 506 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8290 (mmt) REVERT: J 411 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8639 (m) REVERT: K 42 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7175 (tm-30) REVERT: L 42 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7285 (tm-30) outliers start: 92 outliers final: 48 residues processed: 349 average time/residue: 0.6579 time to fit residues: 266.2773 Evaluate side-chains 330 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 276 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 163 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 134 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 136 optimal weight: 0.3980 chunk 254 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 166 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 294 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 125 HIS D 44 GLN H 347 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107233 restraints weight = 38323.875| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.17 r_work: 0.3378 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29316 Z= 0.102 Angle : 0.482 11.292 39734 Z= 0.247 Chirality : 0.042 0.147 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.817 58.022 4027 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.54 % Allowed : 21.08 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.53 (0.14), residues: 3646 helix: 2.09 (0.14), residues: 1468 sheet: 0.14 (0.25), residues: 434 loop : 0.42 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 223 TYR 0.016 0.001 TYR K 65 PHE 0.018 0.001 PHE D 272 TRP 0.010 0.001 TRP L 74 HIS 0.005 0.001 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00233 (29316) covalent geometry : angle 0.48215 (39734) hydrogen bonds : bond 0.03481 ( 1307) hydrogen bonds : angle 4.01304 ( 3621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.6390 (tp30) cc_final: 0.6190 (tp30) REVERT: B 88 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7524 (mtpp) REVERT: C 49 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: C 53 ASN cc_start: 0.8164 (p0) cc_final: 0.7848 (p0) REVERT: D 14 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7388 (mtm180) REVERT: D 59 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: F 45 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7626 (ttp-110) REVERT: F 116 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7013 (tp30) REVERT: F 177 ASP cc_start: 0.7469 (t0) cc_final: 0.7194 (m-30) REVERT: F 225 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7122 (ttt90) REVERT: G 194 GLN cc_start: 0.8549 (pt0) cc_final: 0.8323 (pt0) REVERT: G 295 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7265 (mt-10) REVERT: J 411 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8617 (m) REVERT: K 42 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7158 (tm-30) REVERT: K 86 MET cc_start: 0.7366 (ttm) cc_final: 0.7047 (ttm) REVERT: L 42 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7254 (tm-30) REVERT: L 93 MET cc_start: 0.7107 (ttt) cc_final: 0.6021 (mmt) outliers start: 80 outliers final: 44 residues processed: 362 average time/residue: 0.6594 time to fit residues: 276.3937 Evaluate side-chains 334 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 274 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 215 optimal weight: 0.1980 chunk 243 optimal weight: 0.4980 chunk 325 optimal weight: 0.9980 chunk 323 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 chunk 361 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 44 GLN H 347 GLN H 422 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.148637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110197 restraints weight = 38346.103| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.10 r_work: 0.3470 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29316 Z= 0.095 Angle : 0.476 11.749 39734 Z= 0.243 Chirality : 0.042 0.224 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.636 58.247 4022 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.51 % Allowed : 21.21 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.60 (0.14), residues: 3646 helix: 2.19 (0.14), residues: 1468 sheet: 0.14 (0.25), residues: 434 loop : 0.44 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 223 TYR 0.021 0.001 TYR L 65 PHE 0.017 0.001 PHE D 272 TRP 0.012 0.001 TRP L 74 HIS 0.005 0.001 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00215 (29316) covalent geometry : angle 0.47610 (39734) hydrogen bonds : bond 0.03284 ( 1307) hydrogen bonds : angle 3.90545 ( 3621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 303 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 GLU cc_start: 0.7123 (pm20) cc_final: 0.6432 (pt0) REVERT: B 88 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7583 (mtpp) REVERT: C 49 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.6853 (m-70) REVERT: C 53 ASN cc_start: 0.8211 (p0) cc_final: 0.7800 (p0) REVERT: D 59 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: F 45 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7618 (ttp-110) REVERT: F 116 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7486 (mm-30) REVERT: F 177 ASP cc_start: 0.7489 (t0) cc_final: 0.7250 (t0) REVERT: F 225 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7166 (ttt90) REVERT: G 194 GLN cc_start: 0.8577 (pt0) cc_final: 0.8353 (pt0) REVERT: G 295 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7294 (mt-10) REVERT: H 344 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7529 (ttp80) REVERT: H 347 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7681 (mp-120) REVERT: H 506 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8816 (mmt) REVERT: J 411 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8650 (m) REVERT: K 42 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7209 (tm-30) REVERT: K 86 MET cc_start: 0.7407 (ttm) cc_final: 0.7079 (ttm) REVERT: L 42 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7306 (tm-30) REVERT: L 93 MET cc_start: 0.7106 (ttt) cc_final: 0.6023 (mmt) outliers start: 79 outliers final: 44 residues processed: 361 average time/residue: 0.6303 time to fit residues: 264.8586 Evaluate side-chains 333 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 123 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 36 optimal weight: 4.9990 chunk 338 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 294 optimal weight: 0.8980 chunk 270 optimal weight: 0.9990 chunk 355 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 44 GLN H 422 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108968 restraints weight = 38471.408| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.11 r_work: 0.3452 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29316 Z= 0.116 Angle : 0.498 12.441 39734 Z= 0.255 Chirality : 0.043 0.354 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.681 58.056 4021 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.79 % Allowed : 21.17 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.56 (0.14), residues: 3646 helix: 2.15 (0.14), residues: 1468 sheet: 0.10 (0.25), residues: 434 loop : 0.43 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 172 TYR 0.022 0.001 TYR L 65 PHE 0.016 0.001 PHE D 272 TRP 0.014 0.001 TRP L 74 HIS 0.007 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00273 (29316) covalent geometry : angle 0.49816 (39734) hydrogen bonds : bond 0.03584 ( 1307) hydrogen bonds : angle 3.93253 ( 3621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 283 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7808 (t0) cc_final: 0.7506 (t70) REVERT: B 40 GLU cc_start: 0.7128 (pm20) cc_final: 0.6423 (pt0) REVERT: B 54 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: B 88 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: C 49 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.6879 (m-70) REVERT: C 53 ASN cc_start: 0.8243 (p0) cc_final: 0.7903 (p0) REVERT: D 59 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: E 194 ARG cc_start: 0.7014 (tmt170) cc_final: 0.6756 (tmt170) REVERT: F 45 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7865 (mtp-110) REVERT: F 177 ASP cc_start: 0.7530 (t0) cc_final: 0.7295 (t0) REVERT: F 225 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7079 (ttt90) REVERT: G 194 GLN cc_start: 0.8584 (pt0) cc_final: 0.8361 (pt0) REVERT: H 344 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7585 (ttp80) REVERT: H 347 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: J 411 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8669 (m) REVERT: K 42 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7217 (tm-30) REVERT: K 86 MET cc_start: 0.7400 (ttm) cc_final: 0.7040 (ttm) REVERT: L 42 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7325 (tm-30) outliers start: 88 outliers final: 53 residues processed: 352 average time/residue: 0.6364 time to fit residues: 260.6651 Evaluate side-chains 337 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 153 optimal weight: 20.0000 chunk 240 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 285 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 354 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 44 GLN D 44 GLN F 115 HIS F 172 ASN H 347 GLN I 177 ASN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.147396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108972 restraints weight = 38446.428| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.09 r_work: 0.3452 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29316 Z= 0.115 Angle : 0.502 12.657 39734 Z= 0.256 Chirality : 0.043 0.362 4636 Planarity : 0.004 0.056 5078 Dihedral : 4.691 59.298 4020 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.70 % Allowed : 21.30 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.56 (0.14), residues: 3646 helix: 2.16 (0.14), residues: 1468 sheet: 0.08 (0.25), residues: 434 loop : 0.42 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.021 0.001 TYR L 65 PHE 0.017 0.001 PHE C 272 TRP 0.013 0.001 TRP L 74 HIS 0.007 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00270 (29316) covalent geometry : angle 0.50163 (39734) hydrogen bonds : bond 0.03578 ( 1307) hydrogen bonds : angle 3.93042 ( 3621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 293 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7804 (t0) cc_final: 0.7509 (t70) REVERT: B 54 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: B 88 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7569 (mtpp) REVERT: B 223 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8169 (t0) REVERT: C 37 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: C 49 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6881 (m-70) REVERT: C 53 ASN cc_start: 0.8255 (p0) cc_final: 0.7906 (p0) REVERT: D 59 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: F 45 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (mtp-110) REVERT: F 49 GLU cc_start: 0.7276 (pp20) cc_final: 0.6859 (pp20) REVERT: F 177 ASP cc_start: 0.7549 (t0) cc_final: 0.7319 (t0) REVERT: F 216 MET cc_start: 0.8122 (tpt) cc_final: 0.7582 (mmm) REVERT: F 225 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7111 (ttt90) REVERT: J 411 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8682 (m) REVERT: K 42 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7221 (tm-30) REVERT: K 86 MET cc_start: 0.7405 (ttm) cc_final: 0.6922 (ttm) REVERT: L 42 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7321 (tm-30) REVERT: L 93 MET cc_start: 0.7115 (ttt) cc_final: 0.6029 (mmt) outliers start: 85 outliers final: 59 residues processed: 358 average time/residue: 0.6483 time to fit residues: 270.0452 Evaluate side-chains 347 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 259 optimal weight: 0.0000 chunk 248 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 87 optimal weight: 0.0170 chunk 276 optimal weight: 1.9990 overall best weight: 0.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 44 GLN D 44 GLN H 347 GLN H 422 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.109365 restraints weight = 38544.339| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.11 r_work: 0.3456 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29316 Z= 0.107 Angle : 0.500 12.800 39734 Z= 0.254 Chirality : 0.043 0.306 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.651 57.569 4020 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.60 % Allowed : 21.46 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.60 (0.14), residues: 3646 helix: 2.19 (0.14), residues: 1468 sheet: 0.10 (0.25), residues: 434 loop : 0.44 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.020 0.001 TYR L 65 PHE 0.018 0.001 PHE D 272 TRP 0.015 0.001 TRP L 74 HIS 0.007 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00250 (29316) covalent geometry : angle 0.50046 (39734) hydrogen bonds : bond 0.03444 ( 1307) hydrogen bonds : angle 3.90251 ( 3621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7818 (t0) cc_final: 0.7535 (t70) REVERT: B 40 GLU cc_start: 0.7106 (pm20) cc_final: 0.6490 (pt0) REVERT: B 54 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: B 88 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7640 (mtpp) REVERT: B 223 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (t0) REVERT: C 37 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: C 49 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.6853 (m-70) REVERT: C 53 ASN cc_start: 0.8246 (p0) cc_final: 0.7788 (p0) REVERT: D 59 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 8 MET cc_start: 0.7640 (mmp) cc_final: 0.7392 (mmm) REVERT: F 45 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7867 (mtp-110) REVERT: F 49 GLU cc_start: 0.7323 (pp20) cc_final: 0.6847 (pp20) REVERT: F 177 ASP cc_start: 0.7555 (t0) cc_final: 0.7326 (t0) REVERT: F 225 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7029 (ttt90) REVERT: H 347 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7744 (mp-120) REVERT: J 411 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8667 (m) REVERT: K 42 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7215 (tm-30) REVERT: L 42 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7319 (tm-30) REVERT: L 93 MET cc_start: 0.7113 (ttt) cc_final: 0.6030 (mmt) outliers start: 82 outliers final: 59 residues processed: 355 average time/residue: 0.6316 time to fit residues: 261.9101 Evaluate side-chains 346 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 347 GLN Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 4 optimal weight: 0.9980 chunk 122 optimal weight: 0.0570 chunk 292 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 44 GLN H 422 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.147976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109687 restraints weight = 38449.466| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.09 r_work: 0.3462 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29316 Z= 0.104 Angle : 0.500 12.943 39734 Z= 0.254 Chirality : 0.043 0.291 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.636 57.679 4020 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.35 % Allowed : 21.78 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.61 (0.14), residues: 3646 helix: 2.20 (0.14), residues: 1468 sheet: 0.11 (0.25), residues: 434 loop : 0.45 (0.16), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.022 0.001 TYR L 65 PHE 0.017 0.001 PHE D 272 TRP 0.016 0.001 TRP L 74 HIS 0.007 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00242 (29316) covalent geometry : angle 0.50002 (39734) hydrogen bonds : bond 0.03386 ( 1307) hydrogen bonds : angle 3.88530 ( 3621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7815 (t0) cc_final: 0.7517 (t70) REVERT: B 40 GLU cc_start: 0.7125 (pm20) cc_final: 0.6508 (pt0) REVERT: B 88 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7600 (mtpp) REVERT: C 37 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: C 49 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: C 53 ASN cc_start: 0.8249 (p0) cc_final: 0.7787 (p0) REVERT: D 59 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: E 8 MET cc_start: 0.7664 (mmp) cc_final: 0.7434 (mmm) REVERT: F 45 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7869 (mtp-110) REVERT: F 49 GLU cc_start: 0.7275 (pp20) cc_final: 0.6807 (pp20) REVERT: F 177 ASP cc_start: 0.7573 (t0) cc_final: 0.7352 (t0) REVERT: F 225 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7130 (ttt90) REVERT: G 295 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7299 (mt-10) REVERT: J 411 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8665 (m) REVERT: K 42 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7205 (tm-30) REVERT: L 42 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7330 (tm-30) REVERT: L 93 MET cc_start: 0.7118 (ttt) cc_final: 0.6033 (mmt) outliers start: 74 outliers final: 61 residues processed: 345 average time/residue: 0.6344 time to fit residues: 255.1740 Evaluate side-chains 350 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 283 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 222 SER Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 520 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 28 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Chi-restraints excluded: chain L residue 114 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 165 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 154 optimal weight: 0.0050 chunk 104 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 241 optimal weight: 0.1980 chunk 321 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 162 ASN D 44 GLN H 347 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111437 restraints weight = 38356.963| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.10 r_work: 0.3488 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29316 Z= 0.091 Angle : 0.485 12.338 39734 Z= 0.245 Chirality : 0.042 0.275 4636 Planarity : 0.004 0.056 5078 Dihedral : 4.451 59.114 4019 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.78 % Allowed : 22.29 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.71 (0.14), residues: 3646 helix: 2.30 (0.14), residues: 1466 sheet: 0.19 (0.26), residues: 424 loop : 0.47 (0.16), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.021 0.001 TYR L 65 PHE 0.016 0.001 PHE D 272 TRP 0.015 0.001 TRP L 74 HIS 0.007 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00206 (29316) covalent geometry : angle 0.48491 (39734) hydrogen bonds : bond 0.03016 ( 1307) hydrogen bonds : angle 3.78995 ( 3621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7816 (t0) cc_final: 0.7422 (p0) REVERT: A 171 LEU cc_start: 0.8012 (mp) cc_final: 0.7505 (tt) REVERT: B 40 GLU cc_start: 0.7114 (pm20) cc_final: 0.6464 (pt0) REVERT: B 88 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7624 (mtpp) REVERT: B 171 LEU cc_start: 0.8017 (mp) cc_final: 0.7462 (tt) REVERT: C 37 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: C 49 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.6749 (m-70) REVERT: C 53 ASN cc_start: 0.8237 (p0) cc_final: 0.7856 (p0) REVERT: D 59 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: E 8 MET cc_start: 0.7634 (mmp) cc_final: 0.7428 (mmm) REVERT: F 49 GLU cc_start: 0.7285 (pp20) cc_final: 0.6868 (pp20) REVERT: F 91 ARG cc_start: 0.7588 (ptp90) cc_final: 0.7275 (ttp-110) REVERT: F 177 ASP cc_start: 0.7574 (t0) cc_final: 0.7352 (t0) REVERT: F 194 ARG cc_start: 0.7051 (tmt170) cc_final: 0.6729 (tmt170) REVERT: F 225 ARG cc_start: 0.7619 (ttp80) cc_final: 0.7080 (ttt90) REVERT: G 295 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7296 (mt-10) REVERT: H 344 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7710 (ttp80) REVERT: J 411 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8662 (m) REVERT: K 42 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7170 (tm-30) REVERT: L 42 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7320 (tm-30) REVERT: L 93 MET cc_start: 0.7088 (ttt) cc_final: 0.6016 (mmt) outliers start: 56 outliers final: 39 residues processed: 335 average time/residue: 0.6394 time to fit residues: 249.4684 Evaluate side-chains 322 residues out of total 3238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 260 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 399 SER Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 411 SER Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 99 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 221 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 GLN C 44 GLN D 44 GLN F 172 ASN H 347 GLN H 422 GLN K 13 ASN L 13 ASN L 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.145149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106153 restraints weight = 38463.564| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.11 r_work: 0.3410 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 29316 Z= 0.199 Angle : 0.579 12.634 39734 Z= 0.299 Chirality : 0.047 0.274 4636 Planarity : 0.004 0.057 5078 Dihedral : 4.841 57.810 4016 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.29 % Allowed : 22.00 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.79 % 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: 1.32 (0.14), residues: 3646 helix: 1.90 (0.13), residues: 1474 sheet: 0.04 (0.24), residues: 468 loop : 0.31 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.019 0.002 TYR A 304 PHE 0.019 0.002 PHE D 272 TRP 0.024 0.002 TRP L 74 HIS 0.008 0.001 HIS I 168 Details of bonding type rmsd covalent geometry : bond 0.00479 (29316) covalent geometry : angle 0.57894 (39734) hydrogen bonds : bond 0.04604 ( 1307) hydrogen bonds : angle 4.10368 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12648.54 seconds wall clock time: 215 minutes 8.81 seconds (12908.81 seconds total)