Starting phenix.real_space_refine on Sat Jun 21 03:33:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049.map" model { file = "/net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eea_28049/06_2025/8eea_28049_neut.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.072 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 112 5.16 5 C 15408 2.51 5 N 4363 2.21 5 O 4585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24480 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3032 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3573 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 425} Chain breaks: 2 Chain: "D" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3664 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 436} Chain breaks: 1 Chain: "E" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3664 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 436} Chain breaks: 1 Chain: "F" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3573 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 425} Chain breaks: 2 Chain: "G" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "H" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1920 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.26, per 1000 atoms: 0.58 Number of scatterers: 24480 At special positions: 0 Unit cell: (202.72, 113.12, 132.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 12 15.00 O 4585 8.00 N 4363 7.00 C 15408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 3.1 seconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5750 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 28 sheets defined 50.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.665A pdb=" N LEU A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 54 through 60 removed outlier: 3.620A pdb=" N SER A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 60 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.553A pdb=" N LEU A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.650A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.534A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 removed outlier: 3.770A pdb=" N PHE A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 251 removed outlier: 4.279A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.618A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.642A pdb=" N GLN A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.619A pdb=" N SER A 358 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.659A pdb=" N LEU B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 54 through 60 removed outlier: 3.598A pdb=" N SER B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 59 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 60 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.557A pdb=" N LEU B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 66 " --> pdb=" O LYS B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.843A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.512A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 180 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 183 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 217 removed outlier: 3.560A pdb=" N PHE B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 251 removed outlier: 3.649A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.612A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 306 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.618A pdb=" N GLN B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.581A pdb=" N SER B 358 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 35 through 47 Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.643A pdb=" N ILE C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.526A pdb=" N LEU C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 66 " --> pdb=" O LYS C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.800A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 192 through 217 removed outlier: 3.607A pdb=" N GLN C 214 " --> pdb=" O HIS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 247 removed outlier: 3.633A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 302 Processing helix chain 'C' and resid 303 through 307 removed outlier: 6.810A pdb=" N ASN C 307 " --> pdb=" O HIS C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.624A pdb=" N LEU C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 360 No H-bonds generated for 'chain 'C' and resid 359 through 360' Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 389 through 397 Processing helix chain 'C' and resid 408 through 421 Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'D' and resid 34 through 47 Processing helix chain 'D' and resid 47 through 53 removed outlier: 3.822A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 removed outlier: 4.271A pdb=" N VAL D 60 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 66 removed outlier: 3.650A pdb=" N LEU D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 66 " --> pdb=" O LYS D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 66' Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.713A pdb=" N LEU D 72 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 137 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 181 through 184 Processing helix chain 'D' and resid 192 through 217 removed outlier: 3.715A pdb=" N PHE D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 251 removed outlier: 5.288A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 281 through 302 removed outlier: 3.796A pdb=" N ILE D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 353 through 358 Processing helix chain 'D' and resid 359 through 360 No H-bonds generated for 'chain 'D' and resid 359 through 360' Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 389 through 397 Processing helix chain 'D' and resid 408 through 421 removed outlier: 3.655A pdb=" N GLN D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 444 through 461 Processing helix chain 'E' and resid 34 through 47 Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.822A pdb=" N ILE E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 4.275A pdb=" N VAL E 60 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.629A pdb=" N LEU E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 68 through 72 removed outlier: 3.686A pdb=" N LEU E 72 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 137 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 181 through 184 Processing helix chain 'E' and resid 192 through 217 removed outlier: 3.674A pdb=" N PHE E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 251 removed outlier: 5.419A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLN E 248 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 302 removed outlier: 3.805A pdb=" N ILE E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 333 through 342 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 359 through 360 No H-bonds generated for 'chain 'E' and resid 359 through 360' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'E' and resid 408 through 420 Processing helix chain 'E' and resid 426 through 441 Processing helix chain 'E' and resid 444 through 461 Processing helix chain 'F' and resid 35 through 47 Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.642A pdb=" N ILE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 59 removed outlier: 4.314A pdb=" N TYR F 59 " --> pdb=" O ASP F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.524A pdb=" N LEU F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 66 " --> pdb=" O LYS F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 66' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 118 through 136 removed outlier: 3.811A pdb=" N ALA F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU F 124 " --> pdb=" O MET F 120 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 181 Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 192 through 217 removed outlier: 3.595A pdb=" N GLN F 214 " --> pdb=" O HIS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 247 removed outlier: 3.668A pdb=" N LEU F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 281 through 302 Processing helix chain 'F' and resid 303 through 307 removed outlier: 6.790A pdb=" N ASN F 307 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 313 Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 334 through 342 Processing helix chain 'F' and resid 353 through 358 removed outlier: 3.655A pdb=" N LEU F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 360 No H-bonds generated for 'chain 'F' and resid 359 through 360' Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 408 through 421 Processing helix chain 'F' and resid 426 through 441 Processing helix chain 'F' and resid 444 through 457 Processing helix chain 'G' and resid 11 through 18 Processing helix chain 'G' and resid 24 through 35 Processing helix chain 'G' and resid 38 through 50 removed outlier: 3.933A pdb=" N VAL G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'G' and resid 85 through 87 No H-bonds generated for 'chain 'G' and resid 85 through 87' Processing helix chain 'G' and resid 111 through 114 removed outlier: 3.573A pdb=" N HIS G 114 " --> pdb=" O PHE G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 115 through 121 removed outlier: 3.657A pdb=" N ASP G 120 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL G 121 " --> pdb=" O GLY G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 172 through 197 Processing helix chain 'G' and resid 203 through 209 removed outlier: 4.046A pdb=" N ASP G 207 " --> pdb=" O LEU G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 227 Processing helix chain 'G' and resid 227 through 238 removed outlier: 3.545A pdb=" N ALA G 231 " --> pdb=" O PHE G 227 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 18 Processing helix chain 'H' and resid 24 through 35 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.974A pdb=" N VAL H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 111 through 114 removed outlier: 3.557A pdb=" N HIS H 114 " --> pdb=" O PHE H 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 115 through 121 removed outlier: 3.653A pdb=" N ASP H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 172 through 197 Processing helix chain 'H' and resid 203 through 209 removed outlier: 4.029A pdb=" N ASP H 207 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 227 Processing helix chain 'H' and resid 227 through 238 removed outlier: 4.008A pdb=" N GLU H 232 " --> pdb=" O GLN H 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.727A pdb=" N GLN A 16 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 9 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP A 18 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER A 7 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR A 20 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS A 5 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 6.490A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR A 26 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR A 351 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU A 28 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 5.553A pdb=" N ASP A 254 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 268 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 20 removed outlier: 6.755A pdb=" N LYS B 15 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 94 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 6 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 92 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 8 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B 90 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 152 removed outlier: 6.489A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 26 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR B 351 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 28 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'B' and resid 256 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 20 removed outlier: 6.725A pdb=" N THR C 94 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 6 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 92 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU C 8 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS C 90 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 148 through 152 removed outlier: 5.995A pdb=" N LEU C 148 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU C 318 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 150 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR C 26 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR C 351 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU C 28 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB3, first strand: chain 'C' and resid 253 through 258 removed outlier: 5.611A pdb=" N ASP C 254 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 268 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 20 removed outlier: 6.721A pdb=" N THR D 94 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU D 6 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR D 92 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU D 8 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS D 90 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 148 through 152 removed outlier: 6.525A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 26 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG D 366 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 27 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 368 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 29 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N GLN D 370 " --> pdb=" O VAL D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 73 through 75 removed outlier: 4.309A pdb=" N ARG D 73 " --> pdb=" O SER D 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 75 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU D 84 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 253 through 258 removed outlier: 5.616A pdb=" N ASP D 254 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER D 268 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 16 through 20 removed outlier: 6.736A pdb=" N THR E 94 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU E 6 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 8 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS E 90 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 148 through 152 removed outlier: 6.571A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR E 26 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ARG E 366 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE E 27 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU E 368 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL E 29 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLN E 370 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 73 through 74 removed outlier: 4.340A pdb=" N ARG E 73 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 253 through 258 removed outlier: 5.581A pdb=" N ASP E 254 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER E 268 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.765A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 148 through 152 removed outlier: 5.985A pdb=" N LEU F 148 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU F 318 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU F 150 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR F 26 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N THR F 351 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU F 28 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'F' and resid 253 through 258 removed outlier: 5.592A pdb=" N ASP F 254 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER F 268 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 68 through 72 Processing sheet with id=AC8, first strand: chain 'G' and resid 139 through 141 Processing sheet with id=AC9, first strand: chain 'H' and resid 68 through 72 Processing sheet with id=AD1, first strand: chain 'H' and resid 139 through 141 1107 hydrogen bonds defined for protein. 3084 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: 8.00 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8219 1.34 - 1.46: 4224 1.46 - 1.58: 12328 1.58 - 1.69: 20 1.69 - 1.81: 192 Bond restraints: 24983 Sorted by residual: bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 24978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 33101 1.37 - 2.75: 559 2.75 - 4.12: 131 4.12 - 5.50: 16 5.50 - 6.87: 16 Bond angle restraints: 33823 Sorted by residual: angle pdb=" N VAL D 60 " pdb=" CA VAL D 60 " pdb=" C VAL D 60 " ideal model delta sigma weight residual 112.29 107.70 4.59 9.40e-01 1.13e+00 2.38e+01 angle pdb=" N PHE F 11 " pdb=" CA PHE F 11 " pdb=" C PHE F 11 " ideal model delta sigma weight residual 109.86 104.85 5.01 1.55e+00 4.16e-01 1.04e+01 angle pdb=" N ASN B 307 " pdb=" CA ASN B 307 " pdb=" C ASN B 307 " ideal model delta sigma weight residual 114.75 110.72 4.03 1.26e+00 6.30e-01 1.03e+01 angle pdb=" C3' ATP B 501 " pdb=" C4' ATP B 501 " pdb=" O4' ATP B 501 " ideal model delta sigma weight residual 105.22 101.49 3.73 1.30e+00 5.94e-01 8.28e+00 angle pdb=" C3' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O4' ATP A 501 " ideal model delta sigma weight residual 105.22 101.54 3.68 1.30e+00 5.94e-01 8.04e+00 ... (remaining 33818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 13541 17.63 - 35.27: 1298 35.27 - 52.90: 288 52.90 - 70.53: 80 70.53 - 88.17: 28 Dihedral angle restraints: 15235 sinusoidal: 6401 harmonic: 8834 Sorted by residual: dihedral pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ARG B 12 " pdb=" CA ARG B 12 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA THR D 246 " pdb=" C THR D 246 " pdb=" N GLN D 247 " pdb=" CA GLN D 247 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR E 246 " pdb=" C THR E 246 " pdb=" N GLN E 247 " pdb=" CA GLN E 247 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 15232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3307 0.059 - 0.118: 352 0.118 - 0.178: 35 0.178 - 0.237: 1 0.237 - 0.296: 11 Chirality restraints: 3706 Sorted by residual: chirality pdb=" C2' ATP C 501 " pdb=" C1' ATP C 501 " pdb=" C3' ATP C 501 " pdb=" O2' ATP C 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP F 501 " pdb=" C1' ATP F 501 " pdb=" C3' ATP F 501 " pdb=" O2' ATP F 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C3' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O3' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3703 not shown) Planarity restraints: 4369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 269 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 270 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 296 " -0.015 2.00e-02 2.50e+03 1.59e-02 4.41e+00 pdb=" CG PHE A 296 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 296 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 296 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 296 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 296 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 296 " 0.014 2.00e-02 2.50e+03 1.52e-02 4.02e+00 pdb=" CG PHE B 296 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 296 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 296 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 296 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 296 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 296 " 0.004 2.00e-02 2.50e+03 ... (remaining 4366 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 125 2.57 - 3.15: 18495 3.15 - 3.73: 35037 3.73 - 4.32: 52606 4.32 - 4.90: 89475 Nonbonded interactions: 195738 Sorted by model distance: nonbonded pdb=" OG1 THR G 211 " pdb=" OD1 ASP G 213 " model vdw 1.983 3.040 nonbonded pdb=" OG1 THR H 211 " pdb=" OD1 ASP H 213 " model vdw 1.994 3.040 nonbonded pdb=" O ALA E 309 " pdb=" OG1 THR E 313 " model vdw 2.046 3.040 nonbonded pdb=" OE1 GLU A 224 " pdb=" NE2 GLN E 78 " model vdw 2.071 3.120 nonbonded pdb=" O ALA D 309 " pdb=" OG1 THR D 313 " model vdw 2.106 3.040 ... (remaining 195733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 219 or resid 224 through 382 or resid 501)) selection = (chain 'B' and (resid 1 through 163 or resid 171 through 382 or resid 501)) } ncs_group { reference = (chain 'C' and resid 1 through 460) selection = (chain 'D' and (resid 1 through 160 or resid 171 through 218 or resid 224 throug \ h 460)) selection = (chain 'E' and (resid 1 through 160 or resid 171 through 218 or resid 224 throug \ h 460)) selection = (chain 'F' and resid 1 through 460) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.010 Extract box with map and model: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 52.610 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.110 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 : 0.003 0.032 24983 Z= 0.134 Angle : 0.518 6.872 33823 Z= 0.283 Chirality : 0.042 0.296 3706 Planarity : 0.004 0.054 4369 Dihedral : 15.178 88.165 9485 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2979 helix: 1.77 (0.15), residues: 1164 sheet: -0.52 (0.21), residues: 544 loop : -0.38 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 199 HIS 0.007 0.001 HIS A 352 PHE 0.036 0.001 PHE A 296 TYR 0.026 0.001 TYR A 272 ARG 0.005 0.000 ARG F 12 Details of bonding type rmsd hydrogen bonds : bond 0.17762 ( 1107) hydrogen bonds : angle 6.03947 ( 3084) covalent geometry : bond 0.00294 (24983) covalent geometry : angle 0.51750 (33823) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 2.926 Fit side-chains REVERT: A 5 LYS cc_start: 0.8874 (tptm) cc_final: 0.8596 (tptp) REVERT: A 15 LYS cc_start: 0.9009 (tttt) cc_final: 0.8772 (tttp) REVERT: A 90 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8674 (mtpt) REVERT: A 118 ASP cc_start: 0.8737 (p0) cc_final: 0.8455 (p0) REVERT: A 363 GLU cc_start: 0.8231 (mp0) cc_final: 0.7982 (mp0) REVERT: A 372 GLU cc_start: 0.7457 (pm20) cc_final: 0.7231 (pm20) REVERT: A 373 ASN cc_start: 0.8126 (m-40) cc_final: 0.7599 (m-40) REVERT: B 1 MET cc_start: 0.7635 (ttt) cc_final: 0.7106 (ttt) REVERT: B 85 MET cc_start: 0.8856 (ttm) cc_final: 0.8316 (ttm) REVERT: B 134 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7768 (mtp180) REVERT: B 248 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 18 ASP cc_start: 0.7572 (p0) cc_final: 0.7324 (p0) REVERT: C 84 GLU cc_start: 0.7411 (tt0) cc_final: 0.7211 (tt0) REVERT: C 110 ARG cc_start: 0.6922 (ttm-80) cc_final: 0.6649 (ttt-90) REVERT: C 126 ARG cc_start: 0.6879 (mmp80) cc_final: 0.6160 (mtm180) REVERT: C 210 HIS cc_start: 0.7153 (m-70) cc_final: 0.6332 (t70) REVERT: C 396 SER cc_start: 0.7742 (t) cc_final: 0.7468 (m) REVERT: D 41 ASP cc_start: 0.7669 (m-30) cc_final: 0.7391 (m-30) REVERT: D 101 LYS cc_start: 0.7532 (tptp) cc_final: 0.7324 (tptp) REVERT: D 126 ARG cc_start: 0.7390 (mmp80) cc_final: 0.6663 (mtm-85) REVERT: D 143 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7344 (mm-40) REVERT: D 171 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7598 (ptm-80) REVERT: D 267 MET cc_start: 0.8900 (mtp) cc_final: 0.8449 (mtt) REVERT: D 372 GLU cc_start: 0.7401 (pm20) cc_final: 0.6900 (pm20) REVERT: D 380 MET cc_start: 0.8487 (mtt) cc_final: 0.8157 (mtm) REVERT: D 407 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7772 (mtmm) REVERT: D 443 LYS cc_start: 0.7779 (mttt) cc_final: 0.7442 (mtpm) REVERT: D 451 GLN cc_start: 0.6890 (mm110) cc_final: 0.6512 (mm-40) REVERT: E 41 ASP cc_start: 0.7567 (m-30) cc_final: 0.7281 (m-30) REVERT: E 77 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7101 (mtm-85) REVERT: E 126 ARG cc_start: 0.7389 (mmp80) cc_final: 0.6536 (mtm-85) REVERT: E 372 GLU cc_start: 0.7391 (pm20) cc_final: 0.6833 (pm20) REVERT: E 380 MET cc_start: 0.8544 (mtt) cc_final: 0.8239 (mtm) REVERT: E 443 LYS cc_start: 0.7864 (mttt) cc_final: 0.7532 (mtpm) REVERT: E 451 GLN cc_start: 0.6914 (mm110) cc_final: 0.6477 (mm-40) REVERT: F 18 ASP cc_start: 0.7427 (p0) cc_final: 0.7195 (p0) REVERT: F 84 GLU cc_start: 0.7402 (tt0) cc_final: 0.7155 (tt0) REVERT: F 110 ARG cc_start: 0.7000 (ttm-80) cc_final: 0.6784 (ttt-90) REVERT: F 126 ARG cc_start: 0.6671 (mmp80) cc_final: 0.5865 (mtt180) REVERT: F 210 HIS cc_start: 0.7469 (m-70) cc_final: 0.6816 (t70) REVERT: F 267 MET cc_start: 0.8778 (mtt) cc_final: 0.8420 (mtp) REVERT: F 373 ASN cc_start: 0.7567 (m110) cc_final: 0.7292 (m-40) REVERT: F 396 SER cc_start: 0.7664 (t) cc_final: 0.7363 (m) REVERT: F 443 LYS cc_start: 0.7939 (pttt) cc_final: 0.7734 (ptpp) REVERT: F 451 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7549 (mm-40) REVERT: G 205 GLN cc_start: 0.7569 (mt0) cc_final: 0.7325 (mt0) REVERT: H 190 PHE cc_start: 0.7449 (t80) cc_final: 0.7194 (t80) REVERT: H 191 ASP cc_start: 0.7003 (m-30) cc_final: 0.6713 (m-30) REVERT: H 236 GLN cc_start: 0.6781 (tt0) cc_final: 0.6552 (mt0) outliers start: 0 outliers final: 1 residues processed: 433 average time/residue: 1.7832 time to fit residues: 861.6336 Evaluate side-chains 337 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 233 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 270 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS C 174 ASN D 214 GLN E 214 GLN G 50 GLN G 201 GLN G 202 GLN G 236 GLN H 50 GLN H 202 GLN ** H 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124250 restraints weight = 24520.320| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.10 r_work: 0.3309 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24983 Z= 0.177 Angle : 0.583 7.308 33823 Z= 0.317 Chirality : 0.043 0.193 3706 Planarity : 0.005 0.059 4369 Dihedral : 7.824 84.811 3404 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.40 % Allowed : 7.80 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2979 helix: 1.67 (0.15), residues: 1211 sheet: -0.51 (0.21), residues: 549 loop : -0.41 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 199 HIS 0.008 0.001 HIS A 352 PHE 0.033 0.002 PHE A 296 TYR 0.024 0.002 TYR A 272 ARG 0.007 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.06702 ( 1107) hydrogen bonds : angle 4.84694 ( 3084) covalent geometry : bond 0.00410 (24983) covalent geometry : angle 0.58287 (33823) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 348 time to evaluate : 2.735 Fit side-chains REVERT: A 118 ASP cc_start: 0.8661 (p0) cc_final: 0.8441 (p0) REVERT: A 372 GLU cc_start: 0.7855 (pm20) cc_final: 0.7627 (pm20) REVERT: B 85 MET cc_start: 0.8869 (ttm) cc_final: 0.8328 (ttm) REVERT: B 134 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8006 (mtp180) REVERT: B 248 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8103 (tm-30) REVERT: C 18 ASP cc_start: 0.8028 (p0) cc_final: 0.7742 (p0) REVERT: C 110 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6928 (ttt-90) REVERT: C 120 MET cc_start: 0.8608 (tpp) cc_final: 0.8252 (tpt) REVERT: C 126 ARG cc_start: 0.7323 (mmp80) cc_final: 0.6428 (mtm180) REVERT: C 210 HIS cc_start: 0.7976 (m-70) cc_final: 0.7045 (t70) REVERT: C 262 ASN cc_start: 0.7757 (m110) cc_final: 0.7294 (m110) REVERT: C 293 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: C 396 SER cc_start: 0.7970 (t) cc_final: 0.7723 (m) REVERT: C 407 LYS cc_start: 0.7983 (mttt) cc_final: 0.7496 (ttmt) REVERT: C 443 LYS cc_start: 0.7916 (pttt) cc_final: 0.6063 (tptt) REVERT: D 126 ARG cc_start: 0.7778 (mmp80) cc_final: 0.7107 (mtm-85) REVERT: D 143 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7326 (mm-40) REVERT: D 171 ARG cc_start: 0.8339 (ptm160) cc_final: 0.8091 (ptm-80) REVERT: D 230 ARG cc_start: 0.7016 (mtm110) cc_final: 0.6743 (mtm110) REVERT: D 296 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.7711 (p90) REVERT: D 324 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7425 (ttp) REVERT: D 372 GLU cc_start: 0.7586 (pm20) cc_final: 0.7335 (pm20) REVERT: D 380 MET cc_start: 0.8627 (mtt) cc_final: 0.8243 (mtm) REVERT: D 407 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7834 (mtmm) REVERT: D 443 LYS cc_start: 0.7830 (mttt) cc_final: 0.7514 (mtpm) REVERT: D 451 GLN cc_start: 0.7052 (mm110) cc_final: 0.6641 (mm-40) REVERT: E 126 ARG cc_start: 0.7831 (mmp80) cc_final: 0.7064 (mtm-85) REVERT: E 372 GLU cc_start: 0.7557 (pm20) cc_final: 0.7350 (pm20) REVERT: E 443 LYS cc_start: 0.7823 (mttt) cc_final: 0.7457 (mtpm) REVERT: E 451 GLN cc_start: 0.7055 (mm110) cc_final: 0.6621 (mm-40) REVERT: F 18 ASP cc_start: 0.7992 (p0) cc_final: 0.7757 (p0) REVERT: F 83 MET cc_start: 0.7991 (mmp) cc_final: 0.7694 (mmt) REVERT: F 84 GLU cc_start: 0.7450 (tt0) cc_final: 0.7230 (tt0) REVERT: F 110 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.7022 (ttt-90) REVERT: F 126 ARG cc_start: 0.7144 (mmp80) cc_final: 0.6329 (mtt180) REVERT: F 136 ARG cc_start: 0.7320 (mtt180) cc_final: 0.7101 (mtt-85) REVERT: F 210 HIS cc_start: 0.7858 (m-70) cc_final: 0.6874 (t70) REVERT: F 262 ASN cc_start: 0.7534 (m110) cc_final: 0.7272 (m110) REVERT: F 369 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: F 396 SER cc_start: 0.7899 (t) cc_final: 0.7640 (m) REVERT: F 442 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7176 (mm-30) REVERT: G 205 GLN cc_start: 0.6749 (mt0) cc_final: 0.6492 (mt0) REVERT: H 71 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7771 (tp30) REVERT: H 190 PHE cc_start: 0.7473 (t80) cc_final: 0.7143 (t80) REVERT: H 191 ASP cc_start: 0.6913 (m-30) cc_final: 0.6585 (m-30) REVERT: H 236 GLN cc_start: 0.6703 (tt0) cc_final: 0.6477 (mt0) outliers start: 37 outliers final: 12 residues processed: 360 average time/residue: 1.7494 time to fit residues: 702.6656 Evaluate side-chains 336 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 318 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 174 ASN C 413 GLN D 430 GLN E 430 GLN F 174 ASN F 370 GLN G 236 GLN H 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.185618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126371 restraints weight = 24493.077| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.23 r_work: 0.3329 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24983 Z= 0.123 Angle : 0.497 7.267 33823 Z= 0.274 Chirality : 0.041 0.149 3706 Planarity : 0.004 0.053 4369 Dihedral : 7.277 89.701 3402 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.44 % Allowed : 10.11 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2979 helix: 1.94 (0.15), residues: 1203 sheet: -0.28 (0.21), residues: 562 loop : -0.44 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 199 HIS 0.006 0.001 HIS A 352 PHE 0.020 0.001 PHE D 296 TYR 0.015 0.001 TYR A 272 ARG 0.004 0.000 ARG E 208 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 1107) hydrogen bonds : angle 4.52649 ( 3084) covalent geometry : bond 0.00266 (24983) covalent geometry : angle 0.49671 (33823) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 2.543 Fit side-chains REVERT: A 118 ASP cc_start: 0.8546 (p0) cc_final: 0.8341 (p0) REVERT: A 236 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: A 372 GLU cc_start: 0.7848 (pm20) cc_final: 0.7461 (mp0) REVERT: B 85 MET cc_start: 0.8832 (ttm) cc_final: 0.8303 (ttm) REVERT: B 134 ARG cc_start: 0.8335 (mtp180) cc_final: 0.8014 (mtp180) REVERT: B 248 GLN cc_start: 0.8327 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 18 ASP cc_start: 0.8030 (p0) cc_final: 0.7731 (p0) REVERT: C 110 ARG cc_start: 0.7168 (ttm-80) cc_final: 0.6887 (ttt-90) REVERT: C 126 ARG cc_start: 0.7248 (mmp80) cc_final: 0.6344 (mtm180) REVERT: C 210 HIS cc_start: 0.7850 (m-70) cc_final: 0.6947 (t70) REVERT: C 293 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: C 396 SER cc_start: 0.7917 (t) cc_final: 0.7670 (m) REVERT: C 443 LYS cc_start: 0.7810 (pttt) cc_final: 0.5916 (tptt) REVERT: D 126 ARG cc_start: 0.7828 (mmp80) cc_final: 0.7157 (mtm-85) REVERT: D 130 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6855 (tp40) REVERT: D 171 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8072 (ptm-80) REVERT: D 296 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7666 (p90) REVERT: D 372 GLU cc_start: 0.7674 (pm20) cc_final: 0.7178 (pm20) REVERT: D 380 MET cc_start: 0.8519 (mtt) cc_final: 0.8138 (mtm) REVERT: D 407 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7814 (mtmm) REVERT: D 443 LYS cc_start: 0.7849 (mttt) cc_final: 0.7488 (mtpm) REVERT: D 451 GLN cc_start: 0.6865 (mm110) cc_final: 0.6477 (mm-40) REVERT: E 126 ARG cc_start: 0.7804 (mmp80) cc_final: 0.6992 (mtm-85) REVERT: E 333 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7330 (mt0) REVERT: E 372 GLU cc_start: 0.7584 (pm20) cc_final: 0.7063 (pm20) REVERT: E 443 LYS cc_start: 0.7859 (mttt) cc_final: 0.7487 (mtpm) REVERT: E 451 GLN cc_start: 0.6960 (mm110) cc_final: 0.6506 (mm-40) REVERT: F 18 ASP cc_start: 0.7932 (p0) cc_final: 0.7699 (p0) REVERT: F 83 MET cc_start: 0.7819 (mmp) cc_final: 0.7575 (mmt) REVERT: F 84 GLU cc_start: 0.7418 (tt0) cc_final: 0.7189 (tt0) REVERT: F 110 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6937 (ttt-90) REVERT: F 120 MET cc_start: 0.8494 (tpp) cc_final: 0.8203 (tpt) REVERT: F 210 HIS cc_start: 0.7728 (m-70) cc_final: 0.6775 (t70) REVERT: F 262 ASN cc_start: 0.7467 (m110) cc_final: 0.7202 (m110) REVERT: F 369 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: F 396 SER cc_start: 0.7924 (t) cc_final: 0.7664 (m) REVERT: F 442 GLU cc_start: 0.7511 (tt0) cc_final: 0.7224 (mm-30) REVERT: G 205 GLN cc_start: 0.6669 (mt0) cc_final: 0.6410 (mt0) REVERT: H 1 MET cc_start: 0.8293 (mtt) cc_final: 0.8080 (mtt) REVERT: H 71 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: H 191 ASP cc_start: 0.6655 (m-30) cc_final: 0.6311 (m-30) REVERT: H 236 GLN cc_start: 0.6679 (tt0) cc_final: 0.6459 (mt0) outliers start: 38 outliers final: 10 residues processed: 353 average time/residue: 2.0818 time to fit residues: 826.8098 Evaluate side-chains 339 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 144 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 253 HIS B 253 HIS C 143 GLN C 174 ASN C 413 GLN F 174 ASN G 236 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.181560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122787 restraints weight = 24658.105| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.97 r_work: 0.3275 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 24983 Z= 0.263 Angle : 0.677 7.837 33823 Z= 0.364 Chirality : 0.048 0.246 3706 Planarity : 0.006 0.061 4369 Dihedral : 7.390 77.125 3402 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.05 % Allowed : 11.17 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 2979 helix: 1.48 (0.15), residues: 1208 sheet: -0.33 (0.21), residues: 531 loop : -0.67 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 199 HIS 0.014 0.002 HIS A 352 PHE 0.030 0.002 PHE A 296 TYR 0.020 0.002 TYR B 193 ARG 0.010 0.001 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.07654 ( 1107) hydrogen bonds : angle 4.73103 ( 3084) covalent geometry : bond 0.00645 (24983) covalent geometry : angle 0.67684 (33823) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 2.799 Fit side-chains REVERT: A 134 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: B 85 MET cc_start: 0.8807 (ttm) cc_final: 0.8312 (ttm) REVERT: B 134 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8133 (mtp180) REVERT: B 248 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 18 ASP cc_start: 0.8068 (p0) cc_final: 0.7782 (p0) REVERT: C 110 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7148 (ttt-90) REVERT: C 126 ARG cc_start: 0.7401 (mmp80) cc_final: 0.6493 (mtm180) REVERT: C 210 HIS cc_start: 0.8017 (m-70) cc_final: 0.7053 (t70) REVERT: C 396 SER cc_start: 0.7940 (t) cc_final: 0.7668 (m) REVERT: C 456 ARG cc_start: 0.6916 (ttm110) cc_final: 0.6407 (mtt180) REVERT: D 126 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7313 (mtm-85) REVERT: D 197 GLU cc_start: 0.8357 (tt0) cc_final: 0.8027 (tt0) REVERT: D 230 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6891 (mtm110) REVERT: D 296 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7775 (p90) REVERT: D 372 GLU cc_start: 0.7564 (pm20) cc_final: 0.7355 (pm20) REVERT: D 407 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7852 (mtmm) REVERT: D 443 LYS cc_start: 0.7888 (mttt) cc_final: 0.7506 (mtpm) REVERT: D 451 GLN cc_start: 0.7355 (mm110) cc_final: 0.6983 (mm-40) REVERT: E 126 ARG cc_start: 0.7936 (mmp80) cc_final: 0.7253 (mtm-85) REVERT: E 296 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8188 (p90) REVERT: E 372 GLU cc_start: 0.7565 (pm20) cc_final: 0.7364 (pm20) REVERT: E 443 LYS cc_start: 0.7911 (mttt) cc_final: 0.7515 (mtpm) REVERT: E 451 GLN cc_start: 0.7135 (mm110) cc_final: 0.6677 (mm-40) REVERT: F 83 MET cc_start: 0.7971 (mmp) cc_final: 0.7581 (mmt) REVERT: F 84 GLU cc_start: 0.7500 (tt0) cc_final: 0.7272 (tt0) REVERT: F 110 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7067 (ttt-90) REVERT: F 120 MET cc_start: 0.8601 (tpp) cc_final: 0.8288 (tpt) REVERT: F 126 ARG cc_start: 0.7260 (mmp80) cc_final: 0.6372 (mtt180) REVERT: F 210 HIS cc_start: 0.7843 (m-70) cc_final: 0.6801 (t70) REVERT: F 262 ASN cc_start: 0.7542 (m110) cc_final: 0.7283 (m110) REVERT: F 370 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: F 396 SER cc_start: 0.7981 (t) cc_final: 0.7722 (m) REVERT: F 442 GLU cc_start: 0.7518 (tt0) cc_final: 0.7260 (mm-30) REVERT: G 193 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6551 (p-80) REVERT: G 205 GLN cc_start: 0.6801 (mt0) cc_final: 0.6583 (mt0) REVERT: G 206 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7590 (mt) REVERT: H 1 MET cc_start: 0.8279 (mtt) cc_final: 0.8074 (mtt) REVERT: H 71 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: H 236 GLN cc_start: 0.6745 (tt0) cc_final: 0.6531 (mt0) outliers start: 54 outliers final: 21 residues processed: 365 average time/residue: 1.7475 time to fit residues: 716.8770 Evaluate side-chains 353 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 370 GLN Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 243 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 247 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 0.0570 chunk 165 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 143 GLN C 174 ASN C 413 GLN E 32 ASN F 174 ASN G 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.181617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117936 restraints weight = 24193.024| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.83 r_work: 0.3216 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24983 Z= 0.152 Angle : 0.541 7.532 33823 Z= 0.297 Chirality : 0.042 0.161 3706 Planarity : 0.005 0.057 4369 Dihedral : 7.036 76.772 3402 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.70 % Allowed : 12.50 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 2979 helix: 1.72 (0.15), residues: 1207 sheet: -0.31 (0.21), residues: 541 loop : -0.58 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 199 HIS 0.008 0.001 HIS B 116 PHE 0.024 0.002 PHE A 296 TYR 0.013 0.001 TYR B 193 ARG 0.005 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.05843 ( 1107) hydrogen bonds : angle 4.52381 ( 3084) covalent geometry : bond 0.00347 (24983) covalent geometry : angle 0.54075 (33823) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 325 time to evaluate : 4.870 Fit side-chains REVERT: B 85 MET cc_start: 0.8780 (ttm) cc_final: 0.8305 (ttm) REVERT: B 134 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7928 (mtp180) REVERT: B 248 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 18 ASP cc_start: 0.7970 (p0) cc_final: 0.7659 (p0) REVERT: C 110 ARG cc_start: 0.7169 (ttm-80) cc_final: 0.6908 (ttt-90) REVERT: C 126 ARG cc_start: 0.7137 (mmp80) cc_final: 0.6181 (mtm180) REVERT: C 149 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8195 (mmt) REVERT: C 210 HIS cc_start: 0.7785 (m-70) cc_final: 0.6841 (t70) REVERT: C 293 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: C 396 SER cc_start: 0.7857 (t) cc_final: 0.7610 (m) REVERT: D 126 ARG cc_start: 0.7748 (mmp80) cc_final: 0.7039 (mtm-85) REVERT: D 130 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6630 (mm110) REVERT: D 230 ARG cc_start: 0.6826 (mtm110) cc_final: 0.6563 (mtm110) REVERT: D 296 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7675 (p90) REVERT: D 372 GLU cc_start: 0.7547 (pm20) cc_final: 0.7170 (pm20) REVERT: D 407 LYS cc_start: 0.8047 (mtmm) cc_final: 0.7826 (mtmm) REVERT: D 443 LYS cc_start: 0.7835 (mttt) cc_final: 0.7452 (mtpm) REVERT: D 451 GLN cc_start: 0.7104 (mm110) cc_final: 0.6725 (mm-40) REVERT: E 126 ARG cc_start: 0.7684 (mmp80) cc_final: 0.6861 (mtm-85) REVERT: E 372 GLU cc_start: 0.7546 (pm20) cc_final: 0.7312 (pm20) REVERT: E 443 LYS cc_start: 0.7813 (mttt) cc_final: 0.7427 (mtpm) REVERT: E 451 GLN cc_start: 0.6835 (mm110) cc_final: 0.6375 (mm-40) REVERT: F 1 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (ttt) REVERT: F 83 MET cc_start: 0.7835 (mmp) cc_final: 0.7491 (mmt) REVERT: F 84 GLU cc_start: 0.7360 (tt0) cc_final: 0.7124 (tt0) REVERT: F 110 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.6840 (ttt-90) REVERT: F 126 ARG cc_start: 0.7012 (mmp80) cc_final: 0.6121 (mtt180) REVERT: F 210 HIS cc_start: 0.7668 (m-70) cc_final: 0.6668 (t70) REVERT: F 262 ASN cc_start: 0.7431 (m110) cc_final: 0.7187 (m110) REVERT: F 267 MET cc_start: 0.8670 (mtt) cc_final: 0.8238 (mtp) REVERT: F 369 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7606 (pp20) REVERT: F 396 SER cc_start: 0.7844 (t) cc_final: 0.7604 (m) REVERT: F 442 GLU cc_start: 0.7486 (tt0) cc_final: 0.7262 (mm-30) REVERT: G 205 GLN cc_start: 0.6590 (mt0) cc_final: 0.6365 (mt0) REVERT: G 206 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7453 (mt) REVERT: H 1 MET cc_start: 0.8221 (mtt) cc_final: 0.8013 (mtt) REVERT: H 71 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7640 (tp30) REVERT: H 236 GLN cc_start: 0.6689 (tt0) cc_final: 0.6482 (mt0) outliers start: 45 outliers final: 20 residues processed: 347 average time/residue: 2.2393 time to fit residues: 871.6887 Evaluate side-chains 345 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 317 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 236 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 204 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 174 ASN C 413 GLN F 174 ASN G 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.185439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.127294 restraints weight = 24603.302| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.10 r_work: 0.3323 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24983 Z= 0.117 Angle : 0.490 7.905 33823 Z= 0.270 Chirality : 0.040 0.148 3706 Planarity : 0.004 0.055 4369 Dihedral : 6.755 79.189 3402 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 13.22 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2979 helix: 1.97 (0.15), residues: 1207 sheet: -0.18 (0.21), residues: 546 loop : -0.51 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 199 HIS 0.006 0.001 HIS B 116 PHE 0.019 0.001 PHE D 296 TYR 0.010 0.001 TYR F 272 ARG 0.004 0.000 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 1107) hydrogen bonds : angle 4.34962 ( 3084) covalent geometry : bond 0.00252 (24983) covalent geometry : angle 0.49014 (33823) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 2.807 Fit side-chains REVERT: A 118 ASP cc_start: 0.8514 (p0) cc_final: 0.8310 (p0) REVERT: A 203 LEU cc_start: 0.3460 (OUTLIER) cc_final: 0.2840 (mt) REVERT: B 85 MET cc_start: 0.8806 (ttm) cc_final: 0.8308 (ttm) REVERT: B 134 ARG cc_start: 0.8387 (mtp180) cc_final: 0.8143 (mtp180) REVERT: B 248 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 18 ASP cc_start: 0.8088 (p0) cc_final: 0.7784 (p0) REVERT: C 110 ARG cc_start: 0.7229 (ttm-80) cc_final: 0.6949 (ttt-90) REVERT: C 126 ARG cc_start: 0.7345 (mmp80) cc_final: 0.6425 (mtm180) REVERT: C 149 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8190 (mmt) REVERT: C 210 HIS cc_start: 0.7918 (m-70) cc_final: 0.6998 (t70) REVERT: C 214 GLN cc_start: 0.7113 (mm-40) cc_final: 0.6834 (tp40) REVERT: C 293 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: C 396 SER cc_start: 0.7905 (t) cc_final: 0.7682 (m) REVERT: D 126 ARG cc_start: 0.7954 (mmp80) cc_final: 0.7317 (mtm-85) REVERT: D 130 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6766 (mm110) REVERT: D 296 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7724 (p90) REVERT: D 372 GLU cc_start: 0.7595 (pm20) cc_final: 0.7375 (pm20) REVERT: D 407 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7890 (mtmm) REVERT: D 443 LYS cc_start: 0.7898 (mttt) cc_final: 0.7476 (mtpm) REVERT: D 451 GLN cc_start: 0.7231 (mm110) cc_final: 0.6884 (mm-40) REVERT: E 126 ARG cc_start: 0.7906 (mmp80) cc_final: 0.7172 (mtm-85) REVERT: E 130 GLN cc_start: 0.7614 (pt0) cc_final: 0.7085 (tp40) REVERT: E 333 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: E 372 GLU cc_start: 0.7655 (pm20) cc_final: 0.7134 (pm20) REVERT: E 443 LYS cc_start: 0.7865 (mttt) cc_final: 0.7457 (mtpm) REVERT: E 451 GLN cc_start: 0.7069 (mm110) cc_final: 0.6635 (mm-40) REVERT: F 83 MET cc_start: 0.7860 (mmp) cc_final: 0.7581 (mmt) REVERT: F 110 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6870 (ttt-90) REVERT: F 210 HIS cc_start: 0.7768 (m-70) cc_final: 0.6836 (t70) REVERT: F 262 ASN cc_start: 0.7467 (m110) cc_final: 0.7265 (m110) REVERT: F 267 MET cc_start: 0.8791 (mtt) cc_final: 0.8408 (mtp) REVERT: F 369 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: F 396 SER cc_start: 0.7959 (t) cc_final: 0.7723 (m) REVERT: F 442 GLU cc_start: 0.7476 (tt0) cc_final: 0.7253 (mm-30) REVERT: G 205 GLN cc_start: 0.6700 (mt0) cc_final: 0.6466 (mt0) REVERT: H 1 MET cc_start: 0.8274 (mtt) cc_final: 0.8051 (mtt) REVERT: H 9 LEU cc_start: 0.7538 (mm) cc_final: 0.7273 (mm) REVERT: H 71 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: H 236 GLN cc_start: 0.6783 (tt0) cc_final: 0.6535 (mt0) outliers start: 40 outliers final: 19 residues processed: 360 average time/residue: 2.0269 time to fit residues: 839.2607 Evaluate side-chains 353 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 7.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 250 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 179 optimal weight: 0.0770 chunk 247 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 289 optimal weight: 0.0870 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN C 143 GLN C 174 ASN C 413 GLN F 174 ASN F 214 GLN G 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116314 restraints weight = 24153.933| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.82 r_work: 0.3215 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24983 Z= 0.213 Angle : 0.609 7.469 33823 Z= 0.329 Chirality : 0.045 0.206 3706 Planarity : 0.005 0.059 4369 Dihedral : 6.996 76.335 3402 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.01 % Allowed : 13.52 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 2979 helix: 1.70 (0.15), residues: 1207 sheet: -0.34 (0.21), residues: 543 loop : -0.62 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 199 HIS 0.009 0.001 HIS A 352 PHE 0.022 0.002 PHE E 296 TYR 0.017 0.002 TYR B 193 ARG 0.008 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.06627 ( 1107) hydrogen bonds : angle 4.51745 ( 3084) covalent geometry : bond 0.00516 (24983) covalent geometry : angle 0.60932 (33823) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 330 time to evaluate : 2.776 Fit side-chains REVERT: A 203 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2622 (mt) REVERT: B 85 MET cc_start: 0.8770 (ttm) cc_final: 0.8299 (ttm) REVERT: B 134 ARG cc_start: 0.8309 (mtp180) cc_final: 0.8100 (mtp180) REVERT: B 248 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 18 ASP cc_start: 0.7967 (p0) cc_final: 0.7655 (p0) REVERT: C 110 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.7038 (ttt-90) REVERT: C 126 ARG cc_start: 0.7164 (mmp80) cc_final: 0.6214 (mtm180) REVERT: C 149 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8233 (mmt) REVERT: C 210 HIS cc_start: 0.7817 (m-70) cc_final: 0.6851 (t70) REVERT: C 293 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: C 396 SER cc_start: 0.7899 (t) cc_final: 0.7631 (m) REVERT: C 411 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7569 (t0) REVERT: C 456 ARG cc_start: 0.6697 (ttm110) cc_final: 0.6170 (mtt180) REVERT: D 126 ARG cc_start: 0.7763 (mmp80) cc_final: 0.7070 (mtm-85) REVERT: D 130 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6659 (mm110) REVERT: D 230 ARG cc_start: 0.6877 (mtm110) cc_final: 0.6606 (mtm110) REVERT: D 296 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7719 (p90) REVERT: D 372 GLU cc_start: 0.7519 (pm20) cc_final: 0.7314 (pm20) REVERT: D 407 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7774 (mtmm) REVERT: D 443 LYS cc_start: 0.7879 (mttt) cc_final: 0.7465 (mtpm) REVERT: D 451 GLN cc_start: 0.7133 (mm110) cc_final: 0.6763 (mm-40) REVERT: E 126 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7055 (mtm-85) REVERT: E 130 GLN cc_start: 0.7443 (pt0) cc_final: 0.6789 (tp40) REVERT: E 214 GLN cc_start: 0.4232 (OUTLIER) cc_final: 0.3661 (mm-40) REVERT: E 372 GLU cc_start: 0.7475 (pm20) cc_final: 0.7273 (pm20) REVERT: E 443 LYS cc_start: 0.7820 (mttt) cc_final: 0.7425 (mtpm) REVERT: E 451 GLN cc_start: 0.6901 (mm110) cc_final: 0.6439 (mm-40) REVERT: F 83 MET cc_start: 0.7858 (mmp) cc_final: 0.7477 (mmt) REVERT: F 110 ARG cc_start: 0.7351 (ttm-80) cc_final: 0.6889 (ttt-90) REVERT: F 126 ARG cc_start: 0.7043 (mmp80) cc_final: 0.6104 (mtt180) REVERT: F 210 HIS cc_start: 0.7600 (m-70) cc_final: 0.6595 (t70) REVERT: F 262 ASN cc_start: 0.7412 (m110) cc_final: 0.7207 (m110) REVERT: F 267 MET cc_start: 0.8750 (mtt) cc_final: 0.8362 (mtp) REVERT: F 369 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: F 396 SER cc_start: 0.7842 (t) cc_final: 0.7585 (m) REVERT: F 442 GLU cc_start: 0.7508 (tt0) cc_final: 0.7296 (mm-30) REVERT: G 205 GLN cc_start: 0.6695 (mt0) cc_final: 0.6482 (mt0) REVERT: G 206 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7510 (mt) REVERT: H 1 MET cc_start: 0.8232 (mtt) cc_final: 0.8019 (mtt) REVERT: H 9 LEU cc_start: 0.7535 (mm) cc_final: 0.7248 (mm) REVERT: H 71 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: H 236 GLN cc_start: 0.6648 (tt0) cc_final: 0.6374 (mt0) outliers start: 53 outliers final: 22 residues processed: 361 average time/residue: 1.6891 time to fit residues: 684.6893 Evaluate side-chains 361 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain G residue 206 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 100 optimal weight: 0.6980 chunk 281 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 229 GLN B 240 GLN C 413 GLN F 174 ASN F 214 GLN G 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119514 restraints weight = 24088.675| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.00 r_work: 0.3226 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24983 Z= 0.123 Angle : 0.503 7.782 33823 Z= 0.276 Chirality : 0.040 0.144 3706 Planarity : 0.004 0.056 4369 Dihedral : 6.779 78.136 3402 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 14.51 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2979 helix: 1.93 (0.15), residues: 1207 sheet: -0.17 (0.21), residues: 546 loop : -0.55 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 199 HIS 0.006 0.001 HIS B 116 PHE 0.020 0.001 PHE D 296 TYR 0.010 0.001 TYR B 193 ARG 0.006 0.000 ARG F 456 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 1107) hydrogen bonds : angle 4.35429 ( 3084) covalent geometry : bond 0.00271 (24983) covalent geometry : angle 0.50280 (33823) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 340 time to evaluate : 2.627 Fit side-chains REVERT: A 203 LEU cc_start: 0.3220 (OUTLIER) cc_final: 0.2617 (mt) REVERT: A 248 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 334 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8437 (tp) REVERT: B 85 MET cc_start: 0.8777 (ttm) cc_final: 0.8302 (ttm) REVERT: B 134 ARG cc_start: 0.8355 (mtp180) cc_final: 0.8019 (mtp180) REVERT: B 248 GLN cc_start: 0.8279 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 1 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7940 (ttt) REVERT: C 18 ASP cc_start: 0.7951 (p0) cc_final: 0.7641 (p0) REVERT: C 110 ARG cc_start: 0.7208 (ttm-80) cc_final: 0.6926 (ttt-90) REVERT: C 126 ARG cc_start: 0.7163 (mmp80) cc_final: 0.6197 (mtm180) REVERT: C 210 HIS cc_start: 0.7751 (m-70) cc_final: 0.6812 (t70) REVERT: C 214 GLN cc_start: 0.6990 (mm-40) cc_final: 0.6728 (tp40) REVERT: C 293 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: C 396 SER cc_start: 0.7769 (t) cc_final: 0.7525 (m) REVERT: C 411 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7540 (t0) REVERT: D 126 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7074 (mtm-85) REVERT: D 130 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6557 (mm110) REVERT: D 296 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7579 (p90) REVERT: D 372 GLU cc_start: 0.7519 (pm20) cc_final: 0.7118 (pm20) REVERT: D 407 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7819 (mtmm) REVERT: D 443 LYS cc_start: 0.7841 (mttt) cc_final: 0.7426 (mtpm) REVERT: D 451 GLN cc_start: 0.7016 (mm110) cc_final: 0.6658 (mm-40) REVERT: E 126 ARG cc_start: 0.7664 (mmp80) cc_final: 0.6988 (mtm-85) REVERT: E 130 GLN cc_start: 0.7428 (pt0) cc_final: 0.6823 (tp40) REVERT: E 333 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: E 443 LYS cc_start: 0.7778 (mttt) cc_final: 0.7386 (mtpm) REVERT: E 451 GLN cc_start: 0.6793 (mm110) cc_final: 0.6348 (mm-40) REVERT: F 83 MET cc_start: 0.7796 (mmp) cc_final: 0.7505 (mmt) REVERT: F 110 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6815 (ttt-90) REVERT: F 210 HIS cc_start: 0.7577 (m-70) cc_final: 0.6607 (t70) REVERT: F 267 MET cc_start: 0.8755 (mtt) cc_final: 0.8389 (mtp) REVERT: F 293 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: F 369 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7644 (pp20) REVERT: F 396 SER cc_start: 0.7800 (t) cc_final: 0.7548 (m) REVERT: F 442 GLU cc_start: 0.7471 (tt0) cc_final: 0.7246 (mm-30) REVERT: G 205 GLN cc_start: 0.6560 (mt0) cc_final: 0.6353 (mt0) REVERT: H 9 LEU cc_start: 0.7503 (mm) cc_final: 0.7215 (mm) REVERT: H 71 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: H 236 GLN cc_start: 0.6604 (tt0) cc_final: 0.6153 (tt0) outliers start: 40 outliers final: 21 residues processed: 362 average time/residue: 1.6324 time to fit residues: 664.7646 Evaluate side-chains 360 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 328 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 174 ASN Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 333 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 262 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 284 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 219 optimal weight: 0.0370 chunk 257 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 240 GLN C 174 ASN C 352 HIS C 413 GLN D 236 GLN E 142 GLN F 174 ASN F 214 GLN G 236 GLN H 202 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116332 restraints weight = 24086.383| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.82 r_work: 0.3205 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24983 Z= 0.215 Angle : 0.616 9.420 33823 Z= 0.332 Chirality : 0.045 0.210 3706 Planarity : 0.005 0.060 4369 Dihedral : 7.004 76.335 3402 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.70 % Allowed : 14.77 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 2979 helix: 1.66 (0.15), residues: 1209 sheet: -0.38 (0.21), residues: 517 loop : -0.61 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 199 HIS 0.009 0.001 HIS B 352 PHE 0.027 0.002 PHE E 296 TYR 0.017 0.002 TYR B 193 ARG 0.008 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.06593 ( 1107) hydrogen bonds : angle 4.50868 ( 3084) covalent geometry : bond 0.00522 (24983) covalent geometry : angle 0.61590 (33823) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 2.644 Fit side-chains REVERT: A 203 LEU cc_start: 0.3412 (OUTLIER) cc_final: 0.2580 (mt) REVERT: B 32 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (m110) REVERT: B 85 MET cc_start: 0.8774 (ttm) cc_final: 0.8307 (ttm) REVERT: B 134 ARG cc_start: 0.8318 (mtp180) cc_final: 0.8071 (mtp180) REVERT: B 248 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 1 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (ttt) REVERT: C 18 ASP cc_start: 0.7980 (p0) cc_final: 0.7672 (p0) REVERT: C 110 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.7005 (ttt-90) REVERT: C 126 ARG cc_start: 0.7180 (mmp80) cc_final: 0.6217 (mtm180) REVERT: C 210 HIS cc_start: 0.7847 (m-70) cc_final: 0.6882 (t70) REVERT: C 214 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6779 (tp40) REVERT: C 293 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: C 396 SER cc_start: 0.7754 (t) cc_final: 0.7478 (m) REVERT: C 411 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7565 (t0) REVERT: D 126 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7096 (mtm-85) REVERT: D 130 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6673 (mm110) REVERT: D 230 ARG cc_start: 0.6886 (mtm110) cc_final: 0.6622 (mtm110) REVERT: D 296 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7723 (p90) REVERT: D 372 GLU cc_start: 0.7437 (pm20) cc_final: 0.7185 (pm20) REVERT: D 407 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7783 (mtmm) REVERT: D 443 LYS cc_start: 0.7874 (mttt) cc_final: 0.7458 (mtpm) REVERT: D 451 GLN cc_start: 0.7141 (mm110) cc_final: 0.6773 (mm-40) REVERT: E 126 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7053 (mtm-85) REVERT: E 130 GLN cc_start: 0.7548 (pt0) cc_final: 0.6914 (tp40) REVERT: E 443 LYS cc_start: 0.7806 (mttt) cc_final: 0.7415 (mtpm) REVERT: E 451 GLN cc_start: 0.6912 (mm110) cc_final: 0.6462 (mm-40) REVERT: F 83 MET cc_start: 0.7875 (mmp) cc_final: 0.7293 (mmt) REVERT: F 110 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.6998 (ttt-90) REVERT: F 126 ARG cc_start: 0.7061 (mmp80) cc_final: 0.6109 (mtt180) REVERT: F 210 HIS cc_start: 0.7618 (m-70) cc_final: 0.6604 (t70) REVERT: F 267 MET cc_start: 0.8775 (mtt) cc_final: 0.8425 (mtp) REVERT: F 369 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: F 396 SER cc_start: 0.7860 (t) cc_final: 0.7601 (m) REVERT: F 442 GLU cc_start: 0.7467 (tt0) cc_final: 0.7260 (mm-30) REVERT: G 27 GLN cc_start: 0.7484 (mt0) cc_final: 0.7244 (mt0) REVERT: G 205 GLN cc_start: 0.6661 (mt0) cc_final: 0.6459 (mt0) REVERT: H 9 LEU cc_start: 0.7544 (mm) cc_final: 0.7246 (mm) REVERT: H 71 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: H 236 GLN cc_start: 0.6648 (tt0) cc_final: 0.6182 (tt0) outliers start: 45 outliers final: 24 residues processed: 356 average time/residue: 1.7015 time to fit residues: 686.2943 Evaluate side-chains 363 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 330 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 126 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 240 GLN C 174 ASN C 413 GLN G 202 GLN G 236 GLN H 202 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117120 restraints weight = 24122.791| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.83 r_work: 0.3222 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24983 Z= 0.179 Angle : 0.579 10.014 33823 Z= 0.314 Chirality : 0.043 0.234 3706 Planarity : 0.005 0.060 4369 Dihedral : 6.974 75.852 3402 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.52 % Allowed : 15.00 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 2979 helix: 1.69 (0.15), residues: 1209 sheet: -0.37 (0.21), residues: 521 loop : -0.58 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 199 HIS 0.008 0.001 HIS B 352 PHE 0.024 0.002 PHE E 296 TYR 0.015 0.001 TYR B 193 ARG 0.007 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.06152 ( 1107) hydrogen bonds : angle 4.47969 ( 3084) covalent geometry : bond 0.00426 (24983) covalent geometry : angle 0.57917 (33823) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 2.667 Fit side-chains REVERT: A 203 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.2593 (mt) REVERT: A 248 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8177 (tm-30) REVERT: B 32 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.9058 (m110) REVERT: B 85 MET cc_start: 0.8759 (ttm) cc_final: 0.8298 (ttm) REVERT: B 248 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 1 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8151 (ttt) REVERT: C 18 ASP cc_start: 0.7969 (p0) cc_final: 0.7667 (p0) REVERT: C 110 ARG cc_start: 0.7283 (ttm-80) cc_final: 0.7021 (ttt-90) REVERT: C 126 ARG cc_start: 0.7206 (mmp80) cc_final: 0.6262 (mtm180) REVERT: C 210 HIS cc_start: 0.7847 (m-70) cc_final: 0.6900 (t70) REVERT: C 293 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: C 396 SER cc_start: 0.7901 (t) cc_final: 0.7637 (m) REVERT: C 411 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7585 (t0) REVERT: D 126 ARG cc_start: 0.7785 (mmp80) cc_final: 0.7107 (mtm-85) REVERT: D 130 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6687 (mm110) REVERT: D 230 ARG cc_start: 0.6870 (mtm110) cc_final: 0.6607 (mtm110) REVERT: D 296 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7636 (p90) REVERT: D 372 GLU cc_start: 0.7459 (pm20) cc_final: 0.7211 (pm20) REVERT: D 407 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7882 (mtmm) REVERT: D 443 LYS cc_start: 0.7888 (mttt) cc_final: 0.7465 (mtpm) REVERT: D 451 GLN cc_start: 0.7164 (mm110) cc_final: 0.6802 (mm-40) REVERT: E 126 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7059 (mtm-85) REVERT: E 130 GLN cc_start: 0.7511 (pt0) cc_final: 0.6927 (tp40) REVERT: E 214 GLN cc_start: 0.4177 (OUTLIER) cc_final: 0.3689 (mm-40) REVERT: E 443 LYS cc_start: 0.7819 (mttt) cc_final: 0.7424 (mtpm) REVERT: E 451 GLN cc_start: 0.6925 (mm110) cc_final: 0.6467 (mm-40) REVERT: F 83 MET cc_start: 0.7828 (mmp) cc_final: 0.7471 (mmt) REVERT: F 110 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6974 (ttt-90) REVERT: F 126 ARG cc_start: 0.7075 (mmp80) cc_final: 0.6175 (mtt180) REVERT: F 210 HIS cc_start: 0.7626 (m-70) cc_final: 0.6621 (t70) REVERT: F 267 MET cc_start: 0.8776 (mtt) cc_final: 0.8428 (mtp) REVERT: F 369 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7608 (pp20) REVERT: F 396 SER cc_start: 0.7883 (t) cc_final: 0.7636 (m) REVERT: F 442 GLU cc_start: 0.7472 (tt0) cc_final: 0.7267 (mm-30) REVERT: G 27 GLN cc_start: 0.7470 (mt0) cc_final: 0.7228 (mt0) REVERT: G 205 GLN cc_start: 0.6685 (mt0) cc_final: 0.6475 (mt0) REVERT: H 9 LEU cc_start: 0.7539 (mm) cc_final: 0.7237 (mm) REVERT: H 71 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: H 236 GLN cc_start: 0.6663 (tt0) cc_final: 0.6199 (tt0) outliers start: 40 outliers final: 23 residues processed: 349 average time/residue: 1.6834 time to fit residues: 661.7884 Evaluate side-chains 357 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 296 PHE Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain G residue 193 HIS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 193 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 71 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN B 240 GLN C 413 GLN G 202 GLN G 236 GLN H 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.183510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124400 restraints weight = 24192.469| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.04 r_work: 0.3276 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24983 Z= 0.119 Angle : 0.500 9.460 33823 Z= 0.274 Chirality : 0.040 0.181 3706 Planarity : 0.004 0.055 4369 Dihedral : 6.774 79.571 3402 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 15.27 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 2979 helix: 1.97 (0.15), residues: 1209 sheet: -0.15 (0.21), residues: 546 loop : -0.53 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 252 HIS 0.005 0.001 HIS A 352 PHE 0.019 0.001 PHE D 296 TYR 0.010 0.001 TYR A 200 ARG 0.006 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 1107) hydrogen bonds : angle 4.31622 ( 3084) covalent geometry : bond 0.00260 (24983) covalent geometry : angle 0.50004 (33823) =============================================================================== Job complete usr+sys time: 27232.32 seconds wall clock time: 476 minutes 45.79 seconds (28605.79 seconds total)