Starting phenix.real_space_refine on Thu Mar 5 07:43:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dn0_30776/03_2026/7dn0_30776.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 4 5.21 5 S 134 5.16 5 C 12822 2.51 5 N 3460 2.21 5 O 3918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s 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: 20356 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3346 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'G2P': 1, 'TAJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.15, per 1000 atoms: 0.20 Number of scatterers: 20356 At special positions: 0 Unit cell: (124.2, 103.95, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 18 15.00 Mg 4 11.99 O 3918 8.00 N 3460 7.00 C 12822 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 934.5 milliseconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 17 sheets defined 49.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.614A pdb=" N HIS D 28 " --> pdb=" O TYR D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 Processing helix chain 'D' and resid 74 through 81 removed outlier: 3.894A pdb=" N VAL D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 114 through 126 Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.377A pdb=" N THR D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.698A pdb=" N ASN D 186 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.149A pdb=" N LEU D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 removed outlier: 4.234A pdb=" N THR D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.553A pdb=" N GLN D 301 " --> pdb=" O PRO D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.522A pdb=" N GLY D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.711A pdb=" N VAL D 328 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 398 removed outlier: 4.068A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.188A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 437 removed outlier: 4.461A pdb=" N SER D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.713A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.723A pdb=" N ASP A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 77' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.444A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.613A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.949A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 4.592A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.798A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.566A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.604A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 4.000A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.103A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 71 through 79 removed outlier: 4.566A pdb=" N ILE B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.733A pdb=" N GLU B 113 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.589A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.701A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.008A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B 241 " --> pdb=" O SER B 237 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.201A pdb=" N PHE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 3.727A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.771A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.518A pdb=" N VAL B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 401 removed outlier: 3.888A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.296A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 removed outlier: 4.169A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.536A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.646A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.571A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.933A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 4.085A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 296 through 301 removed outlier: 6.519A pdb=" N ALA C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.598A pdb=" N GLY C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.623A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.977A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.149A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 437 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 41 through 48 removed outlier: 3.534A pdb=" N GLU E 47 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG E 48 " --> pdb=" O LEU E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 48' Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.570A pdb=" N MET E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 128 removed outlier: 5.152A pdb=" N ASP E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N SER E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 161 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.653A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 removed outlier: 3.693A pdb=" N LEU E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.916A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.077A pdb=" N VAL E 260 " --> pdb=" O ALA E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.512A pdb=" N GLY E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 339 removed outlier: 4.318A pdb=" N ASN E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 343 removed outlier: 3.778A pdb=" N PHE E 343 " --> pdb=" O SER E 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 340 through 343' Processing helix chain 'E' and resid 384 through 401 removed outlier: 4.446A pdb=" N GLN E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.446A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 435 removed outlier: 3.922A pdb=" N PHE E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 Processing helix chain 'F' and resid 48 through 51 removed outlier: 4.038A pdb=" N VAL F 51 " --> pdb=" O ARG F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 51' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.629A pdb=" N GLY F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 110 through 129 removed outlier: 4.974A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.572A pdb=" N ASN F 186 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 240 removed outlier: 4.247A pdb=" N LEU F 227 " --> pdb=" O THR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 251 through 260 removed outlier: 3.576A pdb=" N VAL F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.608A pdb=" N TYR F 283 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 284 " --> pdb=" O GLN F 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 284' Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.548A pdb=" N ASN F 300 " --> pdb=" O ASP F 297 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET F 301 " --> pdb=" O ALA F 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 301' Processing helix chain 'F' and resid 306 through 310 removed outlier: 3.995A pdb=" N GLY F 310 " --> pdb=" O PRO F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 339 removed outlier: 4.330A pdb=" N ASN F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 400 removed outlier: 4.008A pdb=" N GLN F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 Processing helix chain 'F' and resid 414 through 435 removed outlier: 4.060A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 92 through 93 removed outlier: 8.155A pdb=" N ILE D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE D 67 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL D 137 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 7 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLN D 133 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE D 135 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE D 171 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS D 139 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 200 " --> pdb=" O LYS D 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'D' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.172A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.680A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.950A pdb=" N ILE B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 67 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N VAL B 66 " --> pdb=" O CYS B 4 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 5 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 137 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 170 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 204 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 273 Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.163A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 202 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.642A pdb=" N VAL E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 67 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE E 66 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS E 6 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL E 68 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 9 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER E 140 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.642A pdb=" N VAL E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU E 67 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE E 66 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS E 6 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL E 68 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA E 9 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER E 140 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL E 171 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N HIS E 139 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR E 201 " --> pdb=" O PHE E 268 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N CYS E 203 " --> pdb=" O PRO E 270 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N PHE E 272 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N PHE E 267 " --> pdb=" O SER E 381 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER E 381 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.559A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ILE F 165 " --> pdb=" O CYS F 131 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.578A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER F 374 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE F 319 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR F 376 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 317 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 378 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL F 315 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN F 380 " --> pdb=" O LEU F 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.582A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2640 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: 3.00 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3428 1.31 - 1.43: 5598 1.43 - 1.56: 11565 1.56 - 1.69: 35 1.69 - 1.81: 208 Bond restraints: 20834 Sorted by residual: bond pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP C 501 " pdb=" C2' GTP C 501 " ideal model delta sigma weight residual 1.524 1.277 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP B 501 " pdb=" C2' GTP B 501 " ideal model delta sigma weight residual 1.524 1.278 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C1' GTP D 501 " pdb=" C2' GTP D 501 " ideal model delta sigma weight residual 1.524 1.284 0.240 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1' GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sigma weight residual 1.410 1.615 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 20829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 28223 4.25 - 8.49: 134 8.49 - 12.74: 4 12.74 - 16.99: 2 16.99 - 21.24: 1 Bond angle restraints: 28364 Sorted by residual: angle pdb=" C PRO F 173 " pdb=" N SER F 174 " pdb=" CA SER F 174 " ideal model delta sigma weight residual 120.69 141.93 -21.24 2.95e+00 1.15e-01 5.18e+01 angle pdb=" C THR F 287 " pdb=" N VAL F 288 " pdb=" CA VAL F 288 " ideal model delta sigma weight residual 120.24 123.59 -3.35 6.30e-01 2.52e+00 2.83e+01 angle pdb=" PA G2P E 501 " pdb=" C3A G2P E 501 " pdb=" PB G2P E 501 " ideal model delta sigma weight residual 120.83 106.17 14.66 3.00e+00 1.11e-01 2.39e+01 angle pdb=" N SER B 340 " pdb=" CA SER B 340 " pdb=" C SER B 340 " ideal model delta sigma weight residual 111.28 105.97 5.31 1.09e+00 8.42e-01 2.37e+01 angle pdb=" C PHE A 87 " pdb=" N HIS A 88 " pdb=" CA HIS A 88 " ideal model delta sigma weight residual 120.67 126.76 -6.09 1.34e+00 5.57e-01 2.06e+01 ... (remaining 28359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.30: 12220 33.30 - 66.59: 348 66.59 - 99.89: 38 99.89 - 133.18: 4 133.18 - 166.48: 8 Dihedral angle restraints: 12618 sinusoidal: 5204 harmonic: 7414 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -124.25 -166.48 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP C 501 " pdb=" C1' GTP C 501 " pdb=" N9 GTP C 501 " pdb=" O4' GTP C 501 " ideal model delta sinusoidal sigma weight residual 104.59 -55.83 160.42 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -134.98 -155.75 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 12615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2970 0.118 - 0.237: 147 0.237 - 0.355: 11 0.355 - 0.474: 0 0.474 - 0.592: 2 Chirality restraints: 3130 Sorted by residual: chirality pdb=" CBB TAJ E 502 " pdb=" CBA TAJ E 502 " pdb=" CBC TAJ E 502 " pdb=" CBD TAJ E 502 " both_signs ideal model delta sigma weight residual False 2.06 2.65 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CBB TAJ F 502 " pdb=" CBA TAJ F 502 " pdb=" CBC TAJ F 502 " pdb=" CBD TAJ F 502 " both_signs ideal model delta sigma weight residual False 2.06 2.65 -0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CAV TAJ F 502 " pdb=" CAQ TAJ F 502 " pdb=" CAU TAJ F 502 " pdb=" CAZ TAJ F 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 3127 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 397 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ALA E 397 " 0.056 2.00e-02 2.50e+03 pdb=" O ALA E 397 " -0.021 2.00e-02 2.50e+03 pdb=" N MET E 398 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 397 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C LEU C 397 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU C 397 " -0.020 2.00e-02 2.50e+03 pdb=" N MET C 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 397 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C LEU A 397 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 397 " -0.020 2.00e-02 2.50e+03 pdb=" N MET A 398 " -0.018 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 240 2.64 - 3.21: 16824 3.21 - 3.77: 29598 3.77 - 4.34: 39966 4.34 - 4.90: 69716 Nonbonded interactions: 156344 Sorted by model distance: nonbonded pdb=" O1G GTP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 2.126 2.170 nonbonded pdb=" O1G GTP D 501 " pdb="MG MG D 502 " model vdw 2.130 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.147 2.170 nonbonded pdb=" O ASN B 186 " pdb=" OG1 THR B 190 " model vdw 2.256 3.040 ... (remaining 156339 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' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.340 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.011 0.451 20836 Z= 0.631 Angle : 0.966 21.236 28364 Z= 0.535 Chirality : 0.062 0.592 3130 Planarity : 0.008 0.070 3668 Dihedral : 16.615 166.481 7862 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.74 % Allowed : 8.80 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.14), residues: 2544 helix: -1.84 (0.12), residues: 1120 sheet: -0.68 (0.26), residues: 384 loop : -2.97 (0.15), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 422 TYR 0.031 0.002 TYR D 432 PHE 0.025 0.003 PHE A 141 TRP 0.014 0.002 TRP A 21 HIS 0.012 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00984 (20834) covalent geometry : angle 0.96631 (28364) hydrogen bonds : bond 0.16469 ( 909) hydrogen bonds : angle 6.47251 ( 2640) Misc. bond : bond 0.44230 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 420 time to evaluate : 0.706 Fit side-chains REVERT: D 3 GLU cc_start: 0.7660 (mp0) cc_final: 0.7305 (mp0) REVERT: D 221 ARG cc_start: 0.8429 (mtt180) cc_final: 0.6327 (tpt170) REVERT: D 300 ASN cc_start: 0.8967 (m110) cc_final: 0.8763 (m110) REVERT: D 326 LYS cc_start: 0.7958 (tttt) cc_final: 0.7626 (tptt) REVERT: D 425 MET cc_start: 0.8224 (mmp) cc_final: 0.7936 (mmm) REVERT: A 31 GLN cc_start: 0.8160 (mt0) cc_final: 0.7262 (mm-40) REVERT: A 50 ASN cc_start: 0.8187 (t0) cc_final: 0.7447 (t0) REVERT: A 176 GLN cc_start: 0.7968 (mm110) cc_final: 0.7660 (mm-40) REVERT: A 197 HIS cc_start: 0.7638 (m90) cc_final: 0.7414 (m-70) REVERT: A 215 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6908 (tmm160) REVERT: A 249 ASN cc_start: 0.8316 (p0) cc_final: 0.7948 (p0) REVERT: A 398 MET cc_start: 0.8201 (mtm) cc_final: 0.7891 (mtp) REVERT: A 435 VAL cc_start: 0.8023 (t) cc_final: 0.7774 (m) REVERT: B 52 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7187 (m-10) REVERT: B 123 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7969 (tpp80) REVERT: B 176 GLN cc_start: 0.7980 (mm110) cc_final: 0.6803 (mt0) REVERT: B 214 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7292 (ttp-170) REVERT: B 219 ILE cc_start: 0.8135 (mm) cc_final: 0.7922 (mt) REVERT: B 392 ASP cc_start: 0.7407 (m-30) cc_final: 0.7050 (m-30) REVERT: C 141 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: C 149 PHE cc_start: 0.8131 (t80) cc_final: 0.7876 (t80) REVERT: C 176 GLN cc_start: 0.7403 (mm110) cc_final: 0.6853 (mt0) REVERT: C 178 SER cc_start: 0.8312 (m) cc_final: 0.7941 (p) REVERT: C 219 ILE cc_start: 0.8329 (mm) cc_final: 0.8100 (mt) REVERT: E 69 ASP cc_start: 0.8068 (t70) cc_final: 0.7830 (t0) REVERT: E 90 ASP cc_start: 0.7393 (t0) cc_final: 0.7090 (t0) REVERT: E 269 MET cc_start: 0.7783 (ptp) cc_final: 0.7573 (mtm) REVERT: E 302 MET cc_start: 0.8462 (mtt) cc_final: 0.8043 (mtm) REVERT: E 336 GLN cc_start: 0.7944 (tt0) cc_final: 0.7662 (mt0) REVERT: E 339 ASN cc_start: 0.8090 (p0) cc_final: 0.7431 (p0) REVERT: E 346 TRP cc_start: 0.8142 (p-90) cc_final: 0.7797 (p-90) REVERT: E 434 GLN cc_start: 0.8312 (tp40) cc_final: 0.8107 (tt0) REVERT: F 88 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7360 (ttp-170) REVERT: F 113 GLU cc_start: 0.6924 (mp0) cc_final: 0.6358 (mp0) REVERT: F 123 ARG cc_start: 0.8685 (ttm110) cc_final: 0.8016 (mtt180) REVERT: F 151 THR cc_start: 0.8793 (m) cc_final: 0.8556 (m) REVERT: F 166 MET cc_start: 0.7536 (ttt) cc_final: 0.7259 (ttt) REVERT: F 299 LYS cc_start: 0.8136 (pttt) cc_final: 0.7727 (pttt) REVERT: F 398 MET cc_start: 0.7782 (mtt) cc_final: 0.7574 (mtp) outliers start: 16 outliers final: 7 residues processed: 435 average time/residue: 0.1636 time to fit residues: 104.7420 Evaluate side-chains 331 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 322 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 88 HIS D 107 HIS D 128 GLN D 197 HIS D 258 ASN A 15 GLN A 88 HIS A 216 ASN A 226 ASN A 256 GLN A 301 GLN A 309 HIS A 372 GLN B 11 GLN B 50 ASN B 192 HIS B 283 HIS B 372 GLN C 197 HIS C 358 GLN C 372 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN E 139 HIS E 192 HIS ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN E 349 ASN E 406 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 91 ASN F 167 ASN ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 ASN F 436 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.119595 restraints weight = 25678.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122236 restraints weight = 15826.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124035 restraints weight = 11249.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125276 restraints weight = 8816.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126162 restraints weight = 7367.481| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20836 Z= 0.125 Angle : 0.569 10.457 28364 Z= 0.289 Chirality : 0.044 0.157 3130 Planarity : 0.005 0.043 3668 Dihedral : 11.436 167.646 3195 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2544 helix: -0.06 (0.15), residues: 1128 sheet: -0.08 (0.25), residues: 404 loop : -2.42 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 243 TYR 0.012 0.001 TYR A 103 PHE 0.013 0.001 PHE C 351 TRP 0.013 0.001 TRP A 21 HIS 0.009 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00271 (20834) covalent geometry : angle 0.56917 (28364) hydrogen bonds : bond 0.05074 ( 909) hydrogen bonds : angle 4.60401 ( 2640) Misc. bond : bond 0.00212 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 355 time to evaluate : 0.521 Fit side-chains REVERT: D 326 LYS cc_start: 0.7938 (tttt) cc_final: 0.7642 (tptt) REVERT: A 31 GLN cc_start: 0.8004 (mt0) cc_final: 0.7162 (mm-40) REVERT: A 52 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: A 176 GLN cc_start: 0.8140 (mm110) cc_final: 0.7801 (mm-40) REVERT: A 197 HIS cc_start: 0.7567 (m90) cc_final: 0.7351 (m-70) REVERT: A 249 ASN cc_start: 0.8383 (p0) cc_final: 0.8029 (p0) REVERT: A 269 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7747 (pt) REVERT: A 285 GLN cc_start: 0.7023 (pp30) cc_final: 0.5523 (mm-40) REVERT: A 391 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8451 (tt) REVERT: A 408 TYR cc_start: 0.7434 (m-80) cc_final: 0.7216 (m-80) REVERT: A 413 MET cc_start: 0.8272 (ttm) cc_final: 0.8043 (ttm) REVERT: B 52 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: B 123 ARG cc_start: 0.8370 (tpp-160) cc_final: 0.8077 (tpp80) REVERT: B 169 PHE cc_start: 0.8404 (m-80) cc_final: 0.8191 (m-80) REVERT: B 176 GLN cc_start: 0.7963 (mm110) cc_final: 0.6935 (mt0) REVERT: B 193 THR cc_start: 0.8216 (t) cc_final: 0.7771 (m) REVERT: B 214 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7306 (ttp-170) REVERT: B 219 ILE cc_start: 0.8157 (mm) cc_final: 0.7878 (mt) REVERT: B 221 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7150 (mmt180) REVERT: B 334 THR cc_start: 0.8486 (t) cc_final: 0.8276 (m) REVERT: B 432 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7170 (t80) REVERT: C 129 CYS cc_start: 0.6418 (m) cc_final: 0.6052 (m) REVERT: C 141 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: C 149 PHE cc_start: 0.8092 (t80) cc_final: 0.7862 (t80) REVERT: C 219 ILE cc_start: 0.8130 (mm) cc_final: 0.7885 (mt) REVERT: E 90 ASP cc_start: 0.7534 (t0) cc_final: 0.7195 (t0) REVERT: E 151 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7839 (m) REVERT: E 166 MET cc_start: 0.7657 (tpp) cc_final: 0.7332 (mtp) REVERT: E 302 MET cc_start: 0.8433 (mtt) cc_final: 0.8164 (mtm) REVERT: E 339 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7241 (p0) REVERT: E 346 TRP cc_start: 0.8122 (p-90) cc_final: 0.7797 (p-90) REVERT: E 434 GLN cc_start: 0.8283 (tp40) cc_final: 0.8037 (tt0) REVERT: F 60 LYS cc_start: 0.8443 (mttm) cc_final: 0.7353 (tttp) REVERT: F 88 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.7366 (ttp-170) REVERT: F 123 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8114 (mtt180) REVERT: F 151 THR cc_start: 0.8453 (m) cc_final: 0.8201 (m) REVERT: F 299 LYS cc_start: 0.8051 (pttt) cc_final: 0.7661 (pttt) REVERT: F 398 MET cc_start: 0.8081 (mtt) cc_final: 0.7814 (mtt) outliers start: 42 outliers final: 22 residues processed: 388 average time/residue: 0.1500 time to fit residues: 89.0507 Evaluate side-chains 354 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 324 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 78 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 226 ASN B 258 ASN B 283 HIS C 61 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 167 ASN E 266 HIS E 294 GLN ** E 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 HIS ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112857 restraints weight = 26272.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115392 restraints weight = 16246.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117104 restraints weight = 11598.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118288 restraints weight = 9090.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119038 restraints weight = 7652.653| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20836 Z= 0.263 Angle : 0.695 10.850 28364 Z= 0.353 Chirality : 0.050 0.206 3130 Planarity : 0.005 0.046 3668 Dihedral : 11.547 166.210 3195 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.80 % Allowed : 16.25 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2544 helix: 0.19 (0.15), residues: 1134 sheet: -0.28 (0.26), residues: 384 loop : -2.51 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 79 TYR 0.021 0.002 TYR F 432 PHE 0.025 0.002 PHE F 319 TRP 0.013 0.002 TRP A 21 HIS 0.010 0.002 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00632 (20834) covalent geometry : angle 0.69474 (28364) hydrogen bonds : bond 0.06888 ( 909) hydrogen bonds : angle 4.78519 ( 2640) Misc. bond : bond 0.00432 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 316 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: D 24 TYR cc_start: 0.8453 (m-10) cc_final: 0.7887 (m-10) REVERT: D 221 ARG cc_start: 0.8428 (mtt180) cc_final: 0.6223 (tpt170) REVERT: D 326 LYS cc_start: 0.8125 (tttt) cc_final: 0.7694 (tptt) REVERT: A 31 GLN cc_start: 0.8062 (mt0) cc_final: 0.7143 (mm-40) REVERT: A 50 ASN cc_start: 0.8179 (t0) cc_final: 0.7532 (t0) REVERT: A 52 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: A 249 ASN cc_start: 0.8309 (p0) cc_final: 0.7982 (p0) REVERT: A 269 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (pt) REVERT: A 285 GLN cc_start: 0.7142 (pp30) cc_final: 0.5653 (mm-40) REVERT: A 358 GLN cc_start: 0.7449 (pp30) cc_final: 0.7000 (pp30) REVERT: A 391 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 432 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6612 (t80) REVERT: B 52 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: B 123 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.8076 (tpp80) REVERT: B 176 GLN cc_start: 0.8210 (mm110) cc_final: 0.7326 (mt0) REVERT: B 193 THR cc_start: 0.8535 (t) cc_final: 0.8203 (m) REVERT: B 214 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7326 (ttp-170) REVERT: B 219 ILE cc_start: 0.8176 (mm) cc_final: 0.7877 (mt) REVERT: B 424 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (t0) REVERT: C 141 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7297 (m-10) REVERT: C 149 PHE cc_start: 0.8149 (t80) cc_final: 0.7777 (t80) REVERT: C 176 GLN cc_start: 0.7333 (mm110) cc_final: 0.6838 (mt0) REVERT: C 219 ILE cc_start: 0.8241 (mm) cc_final: 0.8003 (mt) REVERT: C 252 LEU cc_start: 0.8913 (mp) cc_final: 0.8637 (mp) REVERT: C 358 GLN cc_start: 0.7934 (tp40) cc_final: 0.7508 (mm-40) REVERT: E 151 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8102 (m) REVERT: E 166 MET cc_start: 0.7761 (tpp) cc_final: 0.7374 (mtp) REVERT: E 302 MET cc_start: 0.8584 (mtt) cc_final: 0.8232 (mtm) REVERT: E 338 LYS cc_start: 0.8325 (tppt) cc_final: 0.7811 (mptt) REVERT: E 346 TRP cc_start: 0.8082 (p-90) cc_final: 0.7751 (p-90) REVERT: E 434 GLN cc_start: 0.8362 (tp40) cc_final: 0.8066 (tt0) REVERT: F 88 ARG cc_start: 0.7647 (ttp-110) cc_final: 0.7306 (ttp-170) REVERT: F 123 ARG cc_start: 0.8640 (ttm110) cc_final: 0.8079 (mtt180) REVERT: F 299 LYS cc_start: 0.8091 (pttt) cc_final: 0.7775 (pttt) REVERT: F 323 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7918 (mtm) REVERT: F 398 MET cc_start: 0.8480 (mtt) cc_final: 0.8276 (mtt) outliers start: 82 outliers final: 57 residues processed: 374 average time/residue: 0.1534 time to fit residues: 88.8640 Evaluate side-chains 369 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 345 GLU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 75 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 ASN B 91 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126118 restraints weight = 25444.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128667 restraints weight = 15536.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130394 restraints weight = 10992.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131518 restraints weight = 8556.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132349 restraints weight = 7157.123| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20836 Z= 0.125 Angle : 0.552 11.032 28364 Z= 0.276 Chirality : 0.044 0.205 3130 Planarity : 0.004 0.039 3668 Dihedral : 11.039 169.285 3195 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.82 % Allowed : 18.15 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2544 helix: 0.77 (0.16), residues: 1124 sheet: -0.18 (0.26), residues: 392 loop : -2.20 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.016 0.001 TYR D 103 PHE 0.011 0.001 PHE E 319 TRP 0.011 0.001 TRP A 21 HIS 0.007 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00275 (20834) covalent geometry : angle 0.55169 (28364) hydrogen bonds : bond 0.04703 ( 909) hydrogen bonds : angle 4.32452 ( 2640) Misc. bond : bond 0.00396 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 335 time to evaluate : 0.764 Fit side-chains REVERT: D 221 ARG cc_start: 0.8453 (mtt180) cc_final: 0.6331 (tpt170) REVERT: D 326 LYS cc_start: 0.8087 (tttt) cc_final: 0.7743 (tptt) REVERT: A 26 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7431 (tt) REVERT: A 31 GLN cc_start: 0.8006 (mt0) cc_final: 0.7158 (mm-40) REVERT: A 50 ASN cc_start: 0.8145 (t0) cc_final: 0.7475 (t0) REVERT: A 52 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6988 (m-10) REVERT: A 249 ASN cc_start: 0.8353 (p0) cc_final: 0.8019 (p0) REVERT: A 269 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7761 (pt) REVERT: A 285 GLN cc_start: 0.7175 (pp30) cc_final: 0.5663 (mm-40) REVERT: A 391 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 392 ASP cc_start: 0.7189 (m-30) cc_final: 0.6243 (m-30) REVERT: A 432 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.6653 (t80) REVERT: B 52 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: B 123 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.7871 (tpp80) REVERT: B 176 GLN cc_start: 0.8111 (mm110) cc_final: 0.7259 (mt0) REVERT: B 193 THR cc_start: 0.8348 (t) cc_final: 0.8003 (m) REVERT: B 214 ARG cc_start: 0.7506 (ttp-170) cc_final: 0.7226 (ttp-170) REVERT: B 219 ILE cc_start: 0.8219 (mm) cc_final: 0.7947 (mt) REVERT: B 432 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7092 (t80) REVERT: C 141 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6743 (m-10) REVERT: C 149 PHE cc_start: 0.8175 (t80) cc_final: 0.7788 (t80) REVERT: C 176 GLN cc_start: 0.7275 (mm110) cc_final: 0.6660 (mt0) REVERT: C 178 SER cc_start: 0.8148 (m) cc_final: 0.7905 (p) REVERT: C 219 ILE cc_start: 0.8058 (mm) cc_final: 0.7808 (mt) REVERT: C 252 LEU cc_start: 0.8847 (mp) cc_final: 0.8635 (mp) REVERT: C 432 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7179 (t80) REVERT: E 151 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7777 (m) REVERT: E 302 MET cc_start: 0.8468 (mtt) cc_final: 0.8198 (mtm) REVERT: E 336 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: E 339 ASN cc_start: 0.7757 (p0) cc_final: 0.7347 (p0) REVERT: E 346 TRP cc_start: 0.7965 (p-90) cc_final: 0.7698 (p-90) REVERT: E 434 GLN cc_start: 0.8277 (tp40) cc_final: 0.7992 (tt0) REVERT: F 88 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7358 (ttp-170) REVERT: F 123 ARG cc_start: 0.8573 (ttm110) cc_final: 0.8099 (mtt180) REVERT: F 299 LYS cc_start: 0.7985 (pttt) cc_final: 0.7662 (pttt) REVERT: F 425 MET cc_start: 0.7800 (mmm) cc_final: 0.7283 (tpt) outliers start: 61 outliers final: 35 residues processed: 383 average time/residue: 0.1474 time to fit residues: 88.0664 Evaluate side-chains 369 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 323 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 HIS D 309 HIS B 50 ASN B 91 GLN B 283 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.113563 restraints weight = 26143.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116089 restraints weight = 16063.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117798 restraints weight = 11426.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.118977 restraints weight = 8948.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119765 restraints weight = 7498.806| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20836 Z= 0.230 Angle : 0.653 10.541 28364 Z= 0.330 Chirality : 0.049 0.224 3130 Planarity : 0.005 0.040 3668 Dihedral : 11.207 167.802 3194 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.07 % Allowed : 18.75 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2544 helix: 0.58 (0.16), residues: 1140 sheet: -0.33 (0.26), residues: 396 loop : -2.35 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.017 0.002 TYR D 103 PHE 0.019 0.002 PHE F 319 TRP 0.011 0.002 TRP A 21 HIS 0.011 0.001 HIS E 266 Details of bonding type rmsd covalent geometry : bond 0.00553 (20834) covalent geometry : angle 0.65256 (28364) hydrogen bonds : bond 0.06213 ( 909) hydrogen bonds : angle 4.55374 ( 2640) Misc. bond : bond 0.00479 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8519 (mtt180) cc_final: 0.6331 (tpt170) REVERT: D 326 LYS cc_start: 0.8186 (tttt) cc_final: 0.7770 (tptt) REVERT: A 26 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7605 (tt) REVERT: A 31 GLN cc_start: 0.8017 (mt0) cc_final: 0.7114 (mm-40) REVERT: A 50 ASN cc_start: 0.8152 (t0) cc_final: 0.7466 (t0) REVERT: A 52 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: A 154 MET cc_start: 0.8368 (mmm) cc_final: 0.8149 (mmm) REVERT: A 249 ASN cc_start: 0.8348 (p0) cc_final: 0.8033 (p0) REVERT: A 269 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7859 (pt) REVERT: A 285 GLN cc_start: 0.7206 (pp30) cc_final: 0.5685 (mm-40) REVERT: A 358 GLN cc_start: 0.7304 (pp30) cc_final: 0.6846 (pp30) REVERT: A 391 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 392 ASP cc_start: 0.7232 (m-30) cc_final: 0.6279 (m-30) REVERT: A 432 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 52 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: B 117 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7259 (tp) REVERT: B 123 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.7940 (tpp80) REVERT: B 176 GLN cc_start: 0.8150 (mm110) cc_final: 0.7307 (mt0) REVERT: B 193 THR cc_start: 0.8526 (t) cc_final: 0.8226 (m) REVERT: B 214 ARG cc_start: 0.7613 (ttp-170) cc_final: 0.7292 (ttp-170) REVERT: B 219 ILE cc_start: 0.8203 (mm) cc_final: 0.7908 (mt) REVERT: B 221 ARG cc_start: 0.8114 (mtt180) cc_final: 0.7327 (mmt180) REVERT: B 424 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7933 (t0) REVERT: C 141 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7097 (m-10) REVERT: C 149 PHE cc_start: 0.8271 (t80) cc_final: 0.7853 (t80) REVERT: C 219 ILE cc_start: 0.7996 (mm) cc_final: 0.7754 (mt) REVERT: C 252 LEU cc_start: 0.8813 (mp) cc_final: 0.8558 (mp) REVERT: C 432 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7165 (t80) REVERT: E 90 ASP cc_start: 0.7497 (t0) cc_final: 0.7235 (t0) REVERT: E 149 MET cc_start: 0.8492 (tpp) cc_final: 0.8158 (tpt) REVERT: E 151 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7901 (m) REVERT: E 302 MET cc_start: 0.8511 (mtt) cc_final: 0.8219 (mtm) REVERT: E 338 LYS cc_start: 0.8447 (tppt) cc_final: 0.8181 (ttmm) REVERT: E 346 TRP cc_start: 0.7980 (p-90) cc_final: 0.7697 (p-90) REVERT: E 434 GLN cc_start: 0.8382 (tp40) cc_final: 0.8050 (tt0) REVERT: F 88 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.7344 (ttp-170) REVERT: F 123 ARG cc_start: 0.8629 (ttm110) cc_final: 0.8020 (mtt180) REVERT: F 248 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.6920 (tt) REVERT: F 299 LYS cc_start: 0.8057 (pttt) cc_final: 0.7721 (pttt) REVERT: F 337 ASN cc_start: 0.6560 (t160) cc_final: 0.6211 (p0) outliers start: 88 outliers final: 61 residues processed: 382 average time/residue: 0.1454 time to fit residues: 85.2637 Evaluate side-chains 384 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 311 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 82 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B 197 HIS B 283 HIS C 139 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114444 restraints weight = 26028.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116905 restraints weight = 16193.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118638 restraints weight = 11599.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119701 restraints weight = 9144.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120546 restraints weight = 7751.637| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20836 Z= 0.204 Angle : 0.628 10.658 28364 Z= 0.316 Chirality : 0.048 0.234 3130 Planarity : 0.004 0.040 3668 Dihedral : 11.168 167.914 3194 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.35 % Allowed : 18.98 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2544 helix: 0.65 (0.16), residues: 1136 sheet: -0.34 (0.26), residues: 396 loop : -2.29 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.013 0.001 TYR D 103 PHE 0.017 0.002 PHE E 135 TRP 0.011 0.002 TRP A 21 HIS 0.009 0.001 HIS E 266 Details of bonding type rmsd covalent geometry : bond 0.00488 (20834) covalent geometry : angle 0.62796 (28364) hydrogen bonds : bond 0.05856 ( 909) hydrogen bonds : angle 4.50696 ( 2640) Misc. bond : bond 0.00421 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 315 time to evaluate : 0.689 Fit side-chains REVERT: D 24 TYR cc_start: 0.8400 (m-10) cc_final: 0.7824 (m-10) REVERT: D 221 ARG cc_start: 0.8579 (mtt180) cc_final: 0.6357 (tpt170) REVERT: D 326 LYS cc_start: 0.8179 (tttt) cc_final: 0.7741 (tptt) REVERT: A 26 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 31 GLN cc_start: 0.7967 (mt0) cc_final: 0.7051 (mm-40) REVERT: A 50 ASN cc_start: 0.8156 (t0) cc_final: 0.7474 (t0) REVERT: A 52 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6992 (m-10) REVERT: A 249 ASN cc_start: 0.8380 (p0) cc_final: 0.8031 (p0) REVERT: A 269 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7751 (pt) REVERT: A 285 GLN cc_start: 0.7202 (pp30) cc_final: 0.5677 (mm-40) REVERT: A 391 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 392 ASP cc_start: 0.7278 (m-30) cc_final: 0.6335 (m-30) REVERT: A 414 GLU cc_start: 0.7102 (tt0) cc_final: 0.6782 (mt-10) REVERT: A 432 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6654 (t80) REVERT: B 52 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: B 117 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7274 (tp) REVERT: B 123 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.7854 (tpp80) REVERT: B 176 GLN cc_start: 0.8157 (mm110) cc_final: 0.7314 (mt0) REVERT: B 193 THR cc_start: 0.8502 (t) cc_final: 0.8237 (m) REVERT: B 214 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7296 (ttp-170) REVERT: B 219 ILE cc_start: 0.8171 (mm) cc_final: 0.7878 (mt) REVERT: B 221 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7291 (mmt180) REVERT: B 254 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: B 424 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7876 (t0) REVERT: C 125 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7296 (tt) REVERT: C 141 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: C 149 PHE cc_start: 0.8261 (t80) cc_final: 0.7838 (t80) REVERT: C 178 SER cc_start: 0.8194 (m) cc_final: 0.7915 (p) REVERT: C 219 ILE cc_start: 0.7938 (mm) cc_final: 0.7708 (mt) REVERT: C 252 LEU cc_start: 0.8775 (mp) cc_final: 0.8509 (mp) REVERT: C 358 GLN cc_start: 0.8014 (tp40) cc_final: 0.7727 (tp-100) REVERT: C 432 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7163 (t80) REVERT: E 149 MET cc_start: 0.8469 (tpp) cc_final: 0.8144 (tpt) REVERT: E 151 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7885 (m) REVERT: E 302 MET cc_start: 0.8530 (mtt) cc_final: 0.8247 (mtm) REVERT: E 338 LYS cc_start: 0.8520 (tppt) cc_final: 0.8235 (ttmm) REVERT: E 346 TRP cc_start: 0.8002 (p-90) cc_final: 0.7721 (p-90) REVERT: E 434 GLN cc_start: 0.8403 (tp40) cc_final: 0.8027 (tt0) REVERT: F 55 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7491 (mm-30) REVERT: F 88 ARG cc_start: 0.7652 (ttp-110) cc_final: 0.7318 (ttp-170) REVERT: F 248 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6861 (tt) REVERT: F 299 LYS cc_start: 0.8088 (pttt) cc_final: 0.7761 (pttt) outliers start: 94 outliers final: 71 residues processed: 387 average time/residue: 0.1505 time to fit residues: 89.3395 Evaluate side-chains 394 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 309 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN B 283 HIS ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.123045 restraints weight = 25567.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125544 restraints weight = 15891.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127186 restraints weight = 11406.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128362 restraints weight = 8995.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129113 restraints weight = 7597.626| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20836 Z= 0.126 Angle : 0.556 10.816 28364 Z= 0.278 Chirality : 0.045 0.219 3130 Planarity : 0.004 0.039 3668 Dihedral : 10.879 169.918 3194 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.61 % Allowed : 20.28 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2544 helix: 0.94 (0.16), residues: 1138 sheet: -0.19 (0.26), residues: 392 loop : -2.12 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.015 0.001 TYR D 103 PHE 0.013 0.001 PHE E 377 TRP 0.011 0.001 TRP A 21 HIS 0.005 0.001 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00286 (20834) covalent geometry : angle 0.55631 (28364) hydrogen bonds : bond 0.04683 ( 909) hydrogen bonds : angle 4.25001 ( 2640) Misc. bond : bond 0.00310 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 325 time to evaluate : 0.752 Fit side-chains REVERT: D 221 ARG cc_start: 0.8469 (mtt180) cc_final: 0.6398 (tpt170) REVERT: D 326 LYS cc_start: 0.8089 (tttt) cc_final: 0.7772 (tptt) REVERT: A 26 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7498 (tt) REVERT: A 31 GLN cc_start: 0.7938 (mt0) cc_final: 0.7081 (mm-40) REVERT: A 50 ASN cc_start: 0.8219 (t0) cc_final: 0.7541 (t0) REVERT: A 52 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7011 (m-10) REVERT: A 249 ASN cc_start: 0.8295 (p0) cc_final: 0.7985 (p0) REVERT: A 260 VAL cc_start: 0.7826 (t) cc_final: 0.7581 (p) REVERT: A 269 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7647 (pt) REVERT: A 285 GLN cc_start: 0.7210 (pp30) cc_final: 0.5684 (mm-40) REVERT: A 391 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8444 (tt) REVERT: A 392 ASP cc_start: 0.7144 (m-30) cc_final: 0.6247 (m-30) REVERT: A 414 GLU cc_start: 0.7026 (tt0) cc_final: 0.6780 (mt-10) REVERT: A 432 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 52 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7358 (m-10) REVERT: B 117 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7254 (tp) REVERT: B 123 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7852 (tpp80) REVERT: B 176 GLN cc_start: 0.8152 (mm110) cc_final: 0.7368 (mt0) REVERT: B 193 THR cc_start: 0.8436 (t) cc_final: 0.8171 (m) REVERT: B 214 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.7201 (ttp-170) REVERT: B 219 ILE cc_start: 0.8001 (mm) cc_final: 0.7712 (mt) REVERT: B 221 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7334 (mmt180) REVERT: B 254 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7680 (mm-30) REVERT: B 424 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7768 (t0) REVERT: B 432 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7190 (t80) REVERT: C 141 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7123 (m-10) REVERT: C 149 PHE cc_start: 0.8028 (t80) cc_final: 0.7665 (t80) REVERT: C 178 SER cc_start: 0.8153 (m) cc_final: 0.7881 (p) REVERT: C 252 LEU cc_start: 0.8755 (mp) cc_final: 0.8469 (mp) REVERT: C 432 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7201 (t80) REVERT: E 151 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7760 (m) REVERT: E 302 MET cc_start: 0.8454 (mtt) cc_final: 0.8204 (mtm) REVERT: E 338 LYS cc_start: 0.8478 (tppt) cc_final: 0.8251 (ttmm) REVERT: E 339 ASN cc_start: 0.7741 (p0) cc_final: 0.7353 (p0) REVERT: E 346 TRP cc_start: 0.7956 (p-90) cc_final: 0.7685 (p-90) REVERT: E 434 GLN cc_start: 0.8342 (tp40) cc_final: 0.7985 (tt0) REVERT: F 88 ARG cc_start: 0.7635 (ttp-110) cc_final: 0.7342 (ttp-170) REVERT: F 113 GLU cc_start: 0.7005 (mp0) cc_final: 0.6362 (mp0) REVERT: F 123 ARG cc_start: 0.8433 (mtm-85) cc_final: 0.7985 (mtt180) REVERT: F 151 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8405 (m) REVERT: F 248 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6852 (tt) REVERT: F 299 LYS cc_start: 0.8013 (pttt) cc_final: 0.7674 (pttt) REVERT: F 337 ASN cc_start: 0.6137 (t160) cc_final: 0.5834 (p0) outliers start: 78 outliers final: 51 residues processed: 389 average time/residue: 0.1478 time to fit residues: 88.9863 Evaluate side-chains 384 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 318 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 PHE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 181 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 178 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 ASN B 91 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 385 GLN F 433 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.145857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126759 restraints weight = 25461.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129332 restraints weight = 15671.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131033 restraints weight = 11137.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132241 restraints weight = 8736.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133013 restraints weight = 7330.958| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20836 Z= 0.100 Angle : 0.528 11.051 28364 Z= 0.261 Chirality : 0.043 0.217 3130 Planarity : 0.004 0.038 3668 Dihedral : 10.491 171.892 3194 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 21.53 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2544 helix: 1.34 (0.16), residues: 1128 sheet: -0.15 (0.25), residues: 434 loop : -1.87 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 339 TYR 0.012 0.001 TYR A 103 PHE 0.012 0.001 PHE E 377 TRP 0.010 0.001 TRP E 103 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00208 (20834) covalent geometry : angle 0.52820 (28364) hydrogen bonds : bond 0.03724 ( 909) hydrogen bonds : angle 4.00013 ( 2640) Misc. bond : bond 0.00237 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 350 time to evaluate : 0.766 Fit side-chains REVERT: D 221 ARG cc_start: 0.8508 (mtt180) cc_final: 0.6426 (tpt170) REVERT: D 326 LYS cc_start: 0.8027 (tttt) cc_final: 0.7746 (tptt) REVERT: D 432 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.6329 (t80) REVERT: A 31 GLN cc_start: 0.7903 (mt0) cc_final: 0.7100 (mm-40) REVERT: A 50 ASN cc_start: 0.8193 (t0) cc_final: 0.7492 (t0) REVERT: A 176 GLN cc_start: 0.8094 (mm110) cc_final: 0.7822 (mm-40) REVERT: A 249 ASN cc_start: 0.8248 (p0) cc_final: 0.7954 (p0) REVERT: A 285 GLN cc_start: 0.7087 (pp30) cc_final: 0.5573 (mm-40) REVERT: A 391 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 392 ASP cc_start: 0.7070 (m-30) cc_final: 0.6203 (m-30) REVERT: A 432 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6903 (t80) REVERT: B 26 LEU cc_start: 0.8796 (tp) cc_final: 0.8515 (mm) REVERT: B 52 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: B 117 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7165 (tp) REVERT: B 123 ARG cc_start: 0.8176 (tpp-160) cc_final: 0.7790 (tpp80) REVERT: B 176 GLN cc_start: 0.8146 (mm110) cc_final: 0.7368 (mt0) REVERT: B 193 THR cc_start: 0.8317 (t) cc_final: 0.8053 (m) REVERT: B 214 ARG cc_start: 0.7404 (ttp-170) cc_final: 0.7100 (ttp-170) REVERT: B 219 ILE cc_start: 0.7938 (mm) cc_final: 0.7682 (mt) REVERT: B 221 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7320 (mmt180) REVERT: B 254 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: B 424 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7600 (t0) REVERT: B 432 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7116 (t80) REVERT: C 141 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: C 149 PHE cc_start: 0.7892 (t80) cc_final: 0.7603 (t80) REVERT: C 176 GLN cc_start: 0.7210 (mm110) cc_final: 0.6646 (mt0) REVERT: C 178 SER cc_start: 0.8130 (m) cc_final: 0.7920 (p) REVERT: C 252 LEU cc_start: 0.8708 (mp) cc_final: 0.8461 (mp) REVERT: C 432 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7231 (t80) REVERT: E 31 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7602 (t0) REVERT: E 302 MET cc_start: 0.8375 (mtt) cc_final: 0.8136 (mtm) REVERT: E 338 LYS cc_start: 0.8409 (tppt) cc_final: 0.8203 (ttmm) REVERT: E 339 ASN cc_start: 0.7370 (p0) cc_final: 0.6958 (p0) REVERT: E 346 TRP cc_start: 0.7904 (p-90) cc_final: 0.7627 (p-90) REVERT: E 434 GLN cc_start: 0.8196 (tp40) cc_final: 0.7954 (tt0) REVERT: F 88 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7310 (ttp-170) REVERT: F 113 GLU cc_start: 0.6887 (mp0) cc_final: 0.6320 (mp0) REVERT: F 123 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8083 (mtt180) REVERT: F 151 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8083 (m) REVERT: F 197 ASN cc_start: 0.7513 (m-40) cc_final: 0.7309 (m-40) REVERT: F 248 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6825 (tt) REVERT: F 299 LYS cc_start: 0.8038 (pttt) cc_final: 0.7638 (pttt) REVERT: F 325 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6209 (mmm) outliers start: 57 outliers final: 32 residues processed: 393 average time/residue: 0.1528 time to fit residues: 91.8973 Evaluate side-chains 376 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 330 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 190 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 0.5980 chunk 250 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN B 91 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.126300 restraints weight = 25470.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128842 restraints weight = 15736.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130545 restraints weight = 11228.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131757 restraints weight = 8853.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132519 restraints weight = 7409.681| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 20836 Z= 0.104 Angle : 0.532 11.003 28364 Z= 0.264 Chirality : 0.044 0.194 3130 Planarity : 0.004 0.039 3668 Dihedral : 10.401 171.599 3194 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.50 % Allowed : 22.50 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2544 helix: 1.47 (0.16), residues: 1124 sheet: -0.07 (0.25), residues: 434 loop : -1.79 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.011 0.001 TYR D 103 PHE 0.023 0.001 PHE F 272 TRP 0.010 0.001 TRP A 21 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00232 (20834) covalent geometry : angle 0.53184 (28364) hydrogen bonds : bond 0.03896 ( 909) hydrogen bonds : angle 3.96688 ( 2640) Misc. bond : bond 0.00264 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 333 time to evaluate : 0.787 Fit side-chains REVERT: D 76 ASP cc_start: 0.7557 (m-30) cc_final: 0.7248 (m-30) REVERT: D 221 ARG cc_start: 0.8457 (mtt180) cc_final: 0.6387 (tpt170) REVERT: D 326 LYS cc_start: 0.8051 (tttt) cc_final: 0.7740 (tptt) REVERT: D 432 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.6353 (t80) REVERT: A 50 ASN cc_start: 0.8229 (t0) cc_final: 0.7525 (t0) REVERT: A 176 GLN cc_start: 0.8055 (mm110) cc_final: 0.7772 (mm-40) REVERT: A 249 ASN cc_start: 0.8236 (p0) cc_final: 0.7901 (p0) REVERT: A 285 GLN cc_start: 0.7118 (pp30) cc_final: 0.5541 (mm-40) REVERT: A 358 GLN cc_start: 0.7006 (pp30) cc_final: 0.6750 (pp30) REVERT: A 391 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 392 ASP cc_start: 0.7148 (m-30) cc_final: 0.6271 (m-30) REVERT: A 432 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6734 (t80) REVERT: B 26 LEU cc_start: 0.8782 (tp) cc_final: 0.8517 (mm) REVERT: B 52 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7330 (m-10) REVERT: B 117 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7173 (tp) REVERT: B 123 ARG cc_start: 0.8259 (tpp-160) cc_final: 0.7836 (tpp80) REVERT: B 176 GLN cc_start: 0.8189 (mm110) cc_final: 0.7394 (mt0) REVERT: B 193 THR cc_start: 0.8399 (t) cc_final: 0.8144 (m) REVERT: B 214 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7133 (ttp-170) REVERT: B 219 ILE cc_start: 0.7913 (mm) cc_final: 0.7667 (mt) REVERT: B 221 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7292 (mmt180) REVERT: B 254 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: B 424 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7528 (t0) REVERT: B 432 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7081 (t80) REVERT: C 141 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6533 (m-10) REVERT: C 149 PHE cc_start: 0.7910 (t80) cc_final: 0.7666 (t80) REVERT: C 176 GLN cc_start: 0.7278 (mm110) cc_final: 0.6714 (mt0) REVERT: C 178 SER cc_start: 0.8286 (m) cc_final: 0.8053 (p) REVERT: C 252 LEU cc_start: 0.8718 (mp) cc_final: 0.8486 (mp) REVERT: C 293 ASN cc_start: 0.8592 (t0) cc_final: 0.8332 (t0) REVERT: C 432 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7185 (t80) REVERT: E 31 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7658 (t0) REVERT: E 302 MET cc_start: 0.8406 (mtt) cc_final: 0.8156 (mtm) REVERT: E 338 LYS cc_start: 0.8389 (tppt) cc_final: 0.8169 (ttmm) REVERT: E 339 ASN cc_start: 0.7494 (p0) cc_final: 0.7054 (p0) REVERT: E 346 TRP cc_start: 0.7933 (p-90) cc_final: 0.7635 (p-90) REVERT: E 434 GLN cc_start: 0.8193 (tp40) cc_final: 0.7962 (tt0) REVERT: F 88 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7306 (ttp-170) REVERT: F 113 GLU cc_start: 0.6964 (mp0) cc_final: 0.6367 (mp0) REVERT: F 123 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8062 (mtt180) REVERT: F 151 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8137 (m) REVERT: F 248 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6759 (tt) REVERT: F 299 LYS cc_start: 0.8091 (pttt) cc_final: 0.7677 (pttt) REVERT: F 325 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6180 (mmm) REVERT: F 329 ASP cc_start: 0.7780 (m-30) cc_final: 0.7569 (m-30) outliers start: 54 outliers final: 36 residues processed: 375 average time/residue: 0.1437 time to fit residues: 82.6044 Evaluate side-chains 373 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 432 TYR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 0.5980 chunk 242 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN F 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119587 restraints weight = 26044.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.122035 restraints weight = 16325.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123692 restraints weight = 11769.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124794 restraints weight = 9318.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125538 restraints weight = 7914.223| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20836 Z= 0.198 Angle : 0.624 10.172 28364 Z= 0.314 Chirality : 0.047 0.202 3130 Planarity : 0.004 0.040 3668 Dihedral : 10.824 169.874 3194 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.96 % Allowed : 22.41 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2544 helix: 1.15 (0.16), residues: 1128 sheet: 0.26 (0.27), residues: 364 loop : -1.97 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 339 TYR 0.012 0.001 TYR B 319 PHE 0.027 0.002 PHE F 272 TRP 0.020 0.002 TRP E 103 HIS 0.011 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00474 (20834) covalent geometry : angle 0.62448 (28364) hydrogen bonds : bond 0.05576 ( 909) hydrogen bonds : angle 4.31728 ( 2640) Misc. bond : bond 0.00407 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 325 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 221 ARG cc_start: 0.8514 (mtt180) cc_final: 0.6332 (tpt170) REVERT: D 326 LYS cc_start: 0.8138 (tttt) cc_final: 0.7763 (tptt) REVERT: A 50 ASN cc_start: 0.8250 (t0) cc_final: 0.7504 (t0) REVERT: A 176 GLN cc_start: 0.8119 (mm110) cc_final: 0.7862 (mm-40) REVERT: A 249 ASN cc_start: 0.8232 (p0) cc_final: 0.7924 (p0) REVERT: A 269 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7603 (pt) REVERT: A 285 GLN cc_start: 0.7122 (pp30) cc_final: 0.5501 (mm-40) REVERT: A 391 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8447 (tt) REVERT: A 392 ASP cc_start: 0.7298 (m-30) cc_final: 0.6399 (m-30) REVERT: A 414 GLU cc_start: 0.7041 (tt0) cc_final: 0.6764 (mt-10) REVERT: A 432 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.6703 (t80) REVERT: B 52 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: B 117 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 123 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.7938 (tpp80) REVERT: B 176 GLN cc_start: 0.8188 (mm110) cc_final: 0.7351 (mt0) REVERT: B 193 THR cc_start: 0.8563 (t) cc_final: 0.8300 (m) REVERT: B 214 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.7134 (ttp-170) REVERT: B 219 ILE cc_start: 0.8006 (mm) cc_final: 0.7720 (mt) REVERT: B 221 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7302 (mmt180) REVERT: B 254 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: B 424 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7765 (t0) REVERT: C 141 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7009 (m-10) REVERT: C 149 PHE cc_start: 0.8129 (t80) cc_final: 0.7769 (t80) REVERT: C 176 GLN cc_start: 0.7320 (mm110) cc_final: 0.6744 (mt0) REVERT: C 178 SER cc_start: 0.8278 (m) cc_final: 0.8043 (p) REVERT: C 252 LEU cc_start: 0.8766 (mp) cc_final: 0.8508 (mp) REVERT: C 432 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7223 (t80) REVERT: E 31 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7769 (t0) REVERT: E 302 MET cc_start: 0.8419 (mtt) cc_final: 0.8121 (mtm) REVERT: E 346 TRP cc_start: 0.7979 (p-90) cc_final: 0.7688 (p-90) REVERT: E 434 GLN cc_start: 0.8313 (tp40) cc_final: 0.7996 (tt0) REVERT: F 88 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7327 (ttp-170) REVERT: F 113 GLU cc_start: 0.7100 (mp0) cc_final: 0.6450 (mp0) REVERT: F 123 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8001 (mtt180) REVERT: F 248 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6849 (tt) REVERT: F 299 LYS cc_start: 0.8186 (pttt) cc_final: 0.7778 (pttt) REVERT: F 329 ASP cc_start: 0.7916 (m-30) cc_final: 0.7712 (m-30) REVERT: F 337 ASN cc_start: 0.6453 (t0) cc_final: 0.6070 (p0) outliers start: 64 outliers final: 47 residues processed: 375 average time/residue: 0.1581 time to fit residues: 90.8048 Evaluate side-chains 377 residues out of total 2182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 319 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 52 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 192 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 129 CYS Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 384 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 94 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 193 optimal weight: 1.9990 chunk 218 optimal weight: 0.2980 chunk 124 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128455 restraints weight = 25397.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131007 restraints weight = 15511.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132708 restraints weight = 10951.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133833 restraints weight = 8552.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134672 restraints weight = 7161.326| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20836 Z= 0.111 Angle : 0.550 10.392 28364 Z= 0.274 Chirality : 0.044 0.189 3130 Planarity : 0.004 0.038 3668 Dihedral : 10.533 173.540 3194 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.50 % Allowed : 22.64 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2544 helix: 1.33 (0.16), residues: 1140 sheet: -0.07 (0.25), residues: 424 loop : -1.87 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.013 0.001 TYR D 103 PHE 0.024 0.001 PHE F 272 TRP 0.020 0.001 TRP E 103 HIS 0.006 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00245 (20834) covalent geometry : angle 0.55046 (28364) hydrogen bonds : bond 0.04118 ( 909) hydrogen bonds : angle 4.05631 ( 2640) Misc. bond : bond 0.00248 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.38 seconds wall clock time: 56 minutes 35.88 seconds (3395.88 seconds total)