Starting phenix.real_space_refine on Sun Aug 24 01:18:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hau_34609/08_2025/8hau_34609.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.222 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 18 5.49 5 S 66 5.16 5 C 10184 2.51 5 N 2805 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2681 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 333} Chain breaks: 1 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2689 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2631 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2649 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2649 Classifications: {'peptide': 345} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 2672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2672 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} 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: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 4.62, per 1000 atoms: 0.29 Number of scatterers: 16157 At special positions: 0 Unit cell: (120.7, 119.28, 105.08, 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 66 16.00 P 18 15.00 O 3084 8.00 N 2805 7.00 C 10184 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: 1.15 Conformation dependent library (CDL) restraints added in 549.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 19 sheets defined 17.8% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.535A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 4.180A pdb=" N PHE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.778A pdb=" N THR A 305 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 removed outlier: 4.253A pdb=" N LEU A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.274A pdb=" N THR B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'C' and resid 93 through 104 removed outlier: 3.640A pdb=" N LEU C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.822A pdb=" N THR C 305 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 removed outlier: 4.184A pdb=" N LEU C 331 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.630A pdb=" N LEU D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 removed outlier: 4.214A pdb=" N PHE D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 158 through 160 No H-bonds generated for 'chain 'D' and resid 158 through 160' Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.164A pdb=" N LEU D 331 " --> pdb=" O PRO D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'E' and resid 93 through 104 removed outlier: 3.509A pdb=" N LEU E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 removed outlier: 4.421A pdb=" N PHE E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.552A pdb=" N THR E 305 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 331 Processing helix chain 'E' and resid 432 through 440 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 104 through 111 removed outlier: 4.191A pdb=" N PHE F 111 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 146 through 150 removed outlier: 3.502A pdb=" N CYS F 150 " --> pdb=" O PRO F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 186 through 193 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 272 through 277 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.909A pdb=" N THR F 305 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 removed outlier: 4.189A pdb=" N LEU F 331 " --> pdb=" O PRO F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 3.635A pdb=" N GLY A 114 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 129 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ARG A 122 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 127 " --> pdb=" O ARG A 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 136 current: chain 'A' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 171 current: chain 'A' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 227 through 231 current: chain 'A' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 286 through 296 current: chain 'A' and resid 344 through 358 removed outlier: 5.463A pdb=" N THR A 349 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY A 373 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 351 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL A 371 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR A 353 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE A 369 " --> pdb=" O TYR A 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 364 through 373 current: chain 'A' and resid 400 through 407 Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.572A pdb=" N GLY A 261 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS A 248 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N TYR A 259 " --> pdb=" O HIS A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 122 removed outlier: 5.519A pdb=" N ILE B 129 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ARG B 122 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR B 127 " --> pdb=" O ARG B 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 136 current: chain 'B' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 162 through 171 current: chain 'B' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 227 through 231 current: chain 'B' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 286 through 296 current: chain 'B' and resid 344 through 358 removed outlier: 5.561A pdb=" N THR B 349 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY B 373 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET B 351 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N VAL B 371 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TYR B 353 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B 369 " --> pdb=" O TYR B 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 373 current: chain 'B' and resid 400 through 408 Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.083A pdb=" N ILE B 199 " --> pdb=" O THR B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.577A pdb=" N MET B 246 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 122 removed outlier: 3.764A pdb=" N GLY C 114 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 129 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG C 122 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 127 " --> pdb=" O ARG C 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 136 current: chain 'C' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 171 current: chain 'C' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 227 through 231 current: chain 'C' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 296 current: chain 'C' and resid 344 through 358 removed outlier: 6.694A pdb=" N LEU C 370 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 353 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP C 368 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 355 " --> pdb=" O PHE C 366 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE C 366 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR C 357 " --> pdb=" O CYS C 364 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS C 364 " --> pdb=" O TYR C 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 364 through 373 current: chain 'C' and resid 401 through 407 Processing sheet with id=AA9, first strand: chain 'C' and resid 211 through 213 removed outlier: 7.053A pdb=" N GLN C 204 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET C 246 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 122 removed outlier: 3.786A pdb=" N GLY D 114 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE D 129 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ARG D 122 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 127 " --> pdb=" O ARG D 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 136 current: chain 'D' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 162 through 171 current: chain 'D' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 227 through 231 current: chain 'D' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 286 through 296 current: chain 'D' and resid 344 through 358 removed outlier: 5.547A pdb=" N THR D 349 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY D 373 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET D 351 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL D 371 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR D 353 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 369 " --> pdb=" O TYR D 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 373 current: chain 'D' and resid 400 through 405 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 400 through 405 current: chain 'D' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 249 removed outlier: 6.567A pdb=" N MET D 246 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.936A pdb=" N GLY E 114 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU E 133 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA E 116 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA E 131 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY E 118 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE E 129 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARG E 120 " --> pdb=" O THR E 127 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 136 current: chain 'E' and resid 162 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 171 current: chain 'E' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 227 through 231 current: chain 'E' and resid 287 through 296 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 287 through 296 current: chain 'E' and resid 344 through 358 removed outlier: 3.568A pdb=" N MET E 351 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU E 370 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TYR E 353 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP E 368 " --> pdb=" O TYR E 353 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU E 355 " --> pdb=" O PHE E 366 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE E 366 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR E 357 " --> pdb=" O CYS E 364 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS E 364 " --> pdb=" O TYR E 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 364 through 373 current: chain 'E' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 401 through 408 current: chain 'E' and resid 423 through 424 Processing sheet with id=AB5, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AB6, first strand: chain 'E' and resid 245 through 249 removed outlier: 6.572A pdb=" N MET E 246 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 114 through 122 removed outlier: 5.624A pdb=" N ILE F 129 " --> pdb=" O ARG F 120 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG F 122 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR F 127 " --> pdb=" O ARG F 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 125 through 136 current: chain 'F' and resid 162 through 169 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 162 through 169 current: chain 'F' and resid 227 through 231 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 227 through 231 current: chain 'F' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 286 through 296 current: chain 'F' and resid 344 through 358 removed outlier: 7.105A pdb=" N LEU F 370 " --> pdb=" O MET F 351 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TYR F 353 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP F 368 " --> pdb=" O TYR F 353 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 355 " --> pdb=" O PHE F 366 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE F 366 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR F 357 " --> pdb=" O CYS F 364 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS F 364 " --> pdb=" O TYR F 357 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 364 through 373 current: chain 'F' and resid 400 through 407 removed outlier: 7.730A pdb=" N SER F 428 " --> pdb=" O TRP F 406 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AB9, first strand: chain 'F' and resid 245 through 249 removed outlier: 6.541A pdb=" N MET F 246 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 415 through 416 removed outlier: 3.501A pdb=" N LEU F 415 " --> pdb=" O GLU F 424 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 642 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: 2.72 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 31 1.22 - 1.37: 5489 1.37 - 1.52: 4964 1.52 - 1.66: 5914 1.66 - 1.81: 90 Bond restraints: 16488 Sorted by residual: bond pdb=" C GLU F 285 " pdb=" O GLU F 285 " ideal model delta sigma weight residual 1.233 1.078 0.156 1.38e-02 5.25e+03 1.27e+02 bond pdb=" C GLU C 285 " pdb=" O GLU C 285 " ideal model delta sigma weight residual 1.231 1.092 0.138 1.24e-02 6.50e+03 1.25e+02 bond pdb=" CA GLU C 285 " pdb=" C GLU C 285 " ideal model delta sigma weight residual 1.531 1.420 0.112 1.12e-02 7.97e+03 9.93e+01 bond pdb=" C GLU E 285 " pdb=" O GLU E 285 " ideal model delta sigma weight residual 1.235 1.135 0.100 1.14e-02 7.69e+03 7.67e+01 bond pdb=" C GLU B 285 " pdb=" O GLU B 285 " ideal model delta sigma weight residual 1.234 1.135 0.098 1.19e-02 7.06e+03 6.84e+01 ... (remaining 16483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 22295 3.56 - 7.12: 94 7.12 - 10.68: 16 10.68 - 14.24: 5 14.24 - 17.80: 1 Bond angle restraints: 22411 Sorted by residual: angle pdb=" C GLU E 285 " pdb=" N THR E 286 " pdb=" CA THR E 286 " ideal model delta sigma weight residual 122.74 140.54 -17.80 1.54e+00 4.22e-01 1.34e+02 angle pdb=" C ASN D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.47 132.63 -13.16 1.16e+00 7.43e-01 1.29e+02 angle pdb=" C ASN A 283 " pdb=" N PRO A 284 " pdb=" CA PRO A 284 " ideal model delta sigma weight residual 119.28 130.87 -11.59 1.10e+00 8.26e-01 1.11e+02 angle pdb=" N GLU F 285 " pdb=" CA GLU F 285 " pdb=" C GLU F 285 " ideal model delta sigma weight residual 113.20 100.49 12.71 1.36e+00 5.41e-01 8.73e+01 angle pdb=" C ASN F 283 " pdb=" N PRO F 284 " pdb=" CA PRO F 284 " ideal model delta sigma weight residual 119.84 129.99 -10.15 1.25e+00 6.40e-01 6.60e+01 ... (remaining 22406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8297 17.94 - 35.87: 1128 35.87 - 53.81: 313 53.81 - 71.74: 44 71.74 - 89.68: 19 Dihedral angle restraints: 9801 sinusoidal: 3992 harmonic: 5809 Sorted by residual: dihedral pdb=" C ASN B 283 " pdb=" N ASN B 283 " pdb=" CA ASN B 283 " pdb=" CB ASN B 283 " ideal model delta harmonic sigma weight residual -122.60 -109.66 -12.94 0 2.50e+00 1.60e-01 2.68e+01 dihedral pdb=" N ASN A 283 " pdb=" C ASN A 283 " pdb=" CA ASN A 283 " pdb=" CB ASN A 283 " ideal model delta harmonic sigma weight residual 122.80 110.37 12.43 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" N ASN D 283 " pdb=" C ASN D 283 " pdb=" CA ASN D 283 " pdb=" CB ASN D 283 " ideal model delta harmonic sigma weight residual 122.80 110.58 12.22 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2224 0.080 - 0.160: 291 0.160 - 0.239: 6 0.239 - 0.319: 19 0.319 - 0.399: 3 Chirality restraints: 2543 Sorted by residual: chirality pdb=" CA GLU B 285 " pdb=" N GLU B 285 " pdb=" C GLU B 285 " pdb=" CB GLU B 285 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA PRO D 284 " pdb=" N PRO D 284 " pdb=" C PRO D 284 " pdb=" CB PRO D 284 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA PRO A 284 " pdb=" N PRO A 284 " pdb=" C PRO A 284 " pdb=" CB PRO A 284 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 2540 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 282 " 0.050 2.00e-02 2.50e+03 9.90e-02 9.81e+01 pdb=" C THR F 282 " -0.171 2.00e-02 2.50e+03 pdb=" O THR F 282 " 0.064 2.00e-02 2.50e+03 pdb=" N ASN F 283 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 282 " -0.048 2.00e-02 2.50e+03 9.73e-02 9.47e+01 pdb=" C THR C 282 " 0.168 2.00e-02 2.50e+03 pdb=" O THR C 282 " -0.064 2.00e-02 2.50e+03 pdb=" N ASN C 283 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 282 " 0.040 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C THR A 282 " -0.133 2.00e-02 2.50e+03 pdb=" O THR A 282 " 0.048 2.00e-02 2.50e+03 pdb=" N ASN A 283 " 0.046 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 95 2.48 - 3.09: 11025 3.09 - 3.69: 23582 3.69 - 4.30: 34224 4.30 - 4.90: 59086 Nonbonded interactions: 128012 Sorted by model distance: nonbonded pdb=" O ASN C 283 " pdb=" OG1 THR C 286 " model vdw 1.876 3.040 nonbonded pdb=" OG1 THR E 409 " pdb=" O TRP E 426 " model vdw 1.972 3.040 nonbonded pdb=" OG1 THR C 409 " pdb=" O TRP C 426 " model vdw 1.980 3.040 nonbonded pdb=" OG1 THR A 409 " pdb=" O TRP A 426 " model vdw 1.983 3.040 nonbonded pdb=" OG1 THR B 409 " pdb=" O TRP B 426 " model vdw 2.014 3.040 ... (remaining 128007 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 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'B' and (resid 91 through 171 or resid 184 through 444 or resid 501)) selection = (chain 'C' and resid 91 through 501) selection = (chain 'D' and (resid 91 through 171 or resid 184 through 501)) selection = (chain 'E' and (resid 91 through 171 or resid 184 through 501)) selection = (chain 'F' and (resid 91 through 171 or resid 184 through 444 or resid 501)) } 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 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 : 0.006 0.156 16488 Z= 0.377 Angle : 0.624 17.795 22411 Z= 0.375 Chirality : 0.050 0.399 2543 Planarity : 0.006 0.106 2880 Dihedral : 17.463 89.681 6097 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 0.46 % Allowed : 24.11 % Favored : 75.43 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2056 helix: 2.25 (0.42), residues: 208 sheet: -0.02 (0.22), residues: 501 loop : 0.81 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 101 TYR 0.017 0.000 TYR E 241 PHE 0.006 0.000 PHE D 229 TRP 0.007 0.001 TRP E 275 HIS 0.002 0.000 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00630 (16488) covalent geometry : angle 0.62422 (22411) hydrogen bonds : bond 0.18543 ( 239) hydrogen bonds : angle 8.30446 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.5736 (t-90) REVERT: B 351 MET cc_start: 0.6233 (ptp) cc_final: 0.6027 (ptp) REVERT: F 285 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6199 (mt-10) outliers start: 8 outliers final: 4 residues processed: 268 average time/residue: 0.1222 time to fit residues: 49.8507 Evaluate side-chains 268 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain F residue 285 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN D 89 GLN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 ASN F 248 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.188958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.157753 restraints weight = 17156.016| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.23 r_work: 0.3523 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16488 Z= 0.173 Angle : 0.627 10.937 22411 Z= 0.331 Chirality : 0.047 0.188 2543 Planarity : 0.005 0.049 2880 Dihedral : 9.714 83.182 2444 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 5.12 % Allowed : 19.22 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2056 helix: 0.55 (0.37), residues: 210 sheet: -0.41 (0.22), residues: 462 loop : 0.47 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 120 TYR 0.016 0.002 TYR E 241 PHE 0.023 0.002 PHE F 379 TRP 0.021 0.002 TRP A 406 HIS 0.010 0.001 HIS E 248 Details of bonding type rmsd covalent geometry : bond 0.00385 (16488) covalent geometry : angle 0.62745 (22411) hydrogen bonds : bond 0.04489 ( 239) hydrogen bonds : angle 7.13358 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 321 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8246 (mtt) cc_final: 0.8006 (mtt) REVERT: A 227 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (t) REVERT: A 323 ASP cc_start: 0.6496 (m-30) cc_final: 0.5823 (t70) REVERT: A 335 GLN cc_start: 0.8302 (tt0) cc_final: 0.7771 (tt0) REVERT: B 103 PHE cc_start: 0.6517 (t80) cc_final: 0.6173 (t80) REVERT: B 123 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7096 (mtmm) REVERT: B 164 ASP cc_start: 0.7620 (m-30) cc_final: 0.7277 (m-30) REVERT: B 169 GLU cc_start: 0.7451 (tt0) cc_final: 0.7211 (tt0) REVERT: B 183 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: B 225 LYS cc_start: 0.7455 (mtmm) cc_final: 0.6234 (tmtt) REVERT: B 283 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7470 (m-40) REVERT: B 308 THR cc_start: 0.7627 (p) cc_final: 0.7392 (m) REVERT: B 311 ARG cc_start: 0.7484 (mmt180) cc_final: 0.6931 (mtm180) REVERT: C 169 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7537 (tt0) REVERT: C 196 ASP cc_start: 0.7042 (t0) cc_final: 0.6299 (p0) REVERT: C 431 ASP cc_start: 0.8162 (t0) cc_final: 0.7922 (t0) REVERT: D 136 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7751 (m) REVERT: D 334 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7478 (ttp-170) REVERT: E 240 ASP cc_start: 0.6138 (p0) cc_final: 0.5916 (p0) REVERT: E 283 ASN cc_start: 0.7265 (m110) cc_final: 0.7022 (m-40) REVERT: F 123 LYS cc_start: 0.7267 (mttp) cc_final: 0.7046 (mtmm) REVERT: F 144 TRP cc_start: 0.6900 (m-90) cc_final: 0.6667 (m-90) REVERT: F 191 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7181 (mtpt) REVERT: F 219 LYS cc_start: 0.6660 (mtmt) cc_final: 0.6439 (mtpp) REVERT: F 245 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7807 (mtmt) REVERT: F 260 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7435 (mt) REVERT: F 377 GLN cc_start: 0.4870 (OUTLIER) cc_final: 0.4374 (pt0) REVERT: F 438 ARG cc_start: 0.6766 (tpp-160) cc_final: 0.6288 (mmt-90) outliers start: 89 outliers final: 49 residues processed: 382 average time/residue: 0.1252 time to fit residues: 71.5925 Evaluate side-chains 335 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 280 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 377 GLN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 409 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 131 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 HIS C 224 ASN D 89 GLN D 253 ASN D 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.180730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149306 restraints weight = 17518.523| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.22 r_work: 0.3395 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16488 Z= 0.142 Angle : 0.549 11.044 22411 Z= 0.286 Chirality : 0.045 0.174 2543 Planarity : 0.004 0.052 2880 Dihedral : 9.195 86.011 2429 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 5.29 % Allowed : 21.29 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2056 helix: 0.57 (0.38), residues: 197 sheet: -0.40 (0.21), residues: 512 loop : 0.34 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 438 TYR 0.017 0.002 TYR E 241 PHE 0.024 0.002 PHE C 170 TRP 0.011 0.002 TRP D 406 HIS 0.004 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00340 (16488) covalent geometry : angle 0.54864 (22411) hydrogen bonds : bond 0.03706 ( 239) hydrogen bonds : angle 6.82688 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 312 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.8272 (mtt) cc_final: 0.8043 (mtt) REVERT: A 103 PHE cc_start: 0.6325 (t80) cc_final: 0.6070 (t80) REVERT: A 128 ASP cc_start: 0.6966 (p0) cc_final: 0.6710 (p0) REVERT: A 155 LEU cc_start: 0.7313 (mt) cc_final: 0.7094 (mp) REVERT: A 184 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6629 (mtp) REVERT: A 199 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 211 PHE cc_start: 0.7673 (m-10) cc_final: 0.7453 (m-10) REVERT: A 323 ASP cc_start: 0.6682 (m-30) cc_final: 0.6087 (t70) REVERT: B 164 ASP cc_start: 0.7671 (m-30) cc_final: 0.7416 (m-30) REVERT: B 191 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7179 (mmmt) REVERT: B 196 ASP cc_start: 0.8124 (t0) cc_final: 0.7798 (t0) REVERT: B 283 ASN cc_start: 0.8029 (m-40) cc_final: 0.7407 (t0) REVERT: B 285 GLU cc_start: 0.8200 (pt0) cc_final: 0.7929 (pt0) REVERT: B 311 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6708 (mtm180) REVERT: C 142 LYS cc_start: 0.7611 (tmmt) cc_final: 0.6923 (tttm) REVERT: C 149 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: C 198 CYS cc_start: 0.8035 (p) cc_final: 0.7814 (p) REVERT: D 156 GLU cc_start: 0.5482 (tm-30) cc_final: 0.5232 (tp30) REVERT: D 245 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8210 (mtmt) REVERT: E 438 ARG cc_start: 0.7044 (mmt180) cc_final: 0.6679 (mmt180) REVERT: F 144 TRP cc_start: 0.7461 (m-90) cc_final: 0.7092 (m-90) REVERT: F 184 MET cc_start: 0.7650 (mmm) cc_final: 0.7428 (mmm) REVERT: F 191 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7377 (mtpt) REVERT: F 209 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7057 (pm20) REVERT: F 219 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7190 (mtpp) REVERT: F 245 LYS cc_start: 0.8246 (mtmm) cc_final: 0.8021 (mtmt) REVERT: F 409 THR cc_start: 0.2796 (OUTLIER) cc_final: 0.2557 (m) REVERT: F 443 ILE cc_start: 0.7252 (tt) cc_final: 0.6981 (tt) outliers start: 92 outliers final: 62 residues processed: 373 average time/residue: 0.1127 time to fit residues: 62.9098 Evaluate side-chains 357 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 GLN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 132 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 179 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** D 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN E 224 ASN F 183 GLN F 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.174803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.141166 restraints weight = 17269.592| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.35 r_work: 0.3317 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16488 Z= 0.130 Angle : 0.547 11.726 22411 Z= 0.284 Chirality : 0.045 0.169 2543 Planarity : 0.004 0.050 2880 Dihedral : 8.724 78.463 2429 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 5.01 % Allowed : 21.40 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.18), residues: 2056 helix: 0.25 (0.38), residues: 209 sheet: -0.46 (0.22), residues: 481 loop : 0.25 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 109 TYR 0.017 0.002 TYR A 259 PHE 0.026 0.002 PHE C 170 TRP 0.011 0.002 TRP A 406 HIS 0.003 0.001 HIS E 234 Details of bonding type rmsd covalent geometry : bond 0.00312 (16488) covalent geometry : angle 0.54696 (22411) hydrogen bonds : bond 0.03277 ( 239) hydrogen bonds : angle 6.51814 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 314 time to evaluate : 0.401 Fit side-chains REVERT: A 103 PHE cc_start: 0.6630 (t80) cc_final: 0.6274 (t80) REVERT: A 128 ASP cc_start: 0.6953 (p0) cc_final: 0.6624 (p0) REVERT: A 184 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6917 (mtp) REVERT: A 244 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: A 323 ASP cc_start: 0.6843 (m-30) cc_final: 0.6213 (t70) REVERT: A 335 GLN cc_start: 0.8315 (tt0) cc_final: 0.7820 (tt0) REVERT: A 356 GLU cc_start: 0.7481 (tt0) cc_final: 0.7262 (tt0) REVERT: B 104 HIS cc_start: 0.7390 (m90) cc_final: 0.7020 (m-70) REVERT: B 156 GLU cc_start: 0.7129 (tp30) cc_final: 0.6647 (mm-30) REVERT: B 164 ASP cc_start: 0.7716 (m-30) cc_final: 0.7435 (m-30) REVERT: B 190 ASP cc_start: 0.8603 (m-30) cc_final: 0.8304 (m-30) REVERT: B 197 GLU cc_start: 0.7432 (mp0) cc_final: 0.7205 (pm20) REVERT: B 199 ILE cc_start: 0.8192 (tt) cc_final: 0.7967 (tt) REVERT: B 209 GLU cc_start: 0.6446 (pm20) cc_final: 0.6114 (pm20) REVERT: B 283 ASN cc_start: 0.7917 (m-40) cc_final: 0.7508 (t0) REVERT: B 311 ARG cc_start: 0.7207 (mmt180) cc_final: 0.6414 (mtm180) REVERT: C 105 SER cc_start: 0.7571 (t) cc_final: 0.7125 (t) REVERT: C 149 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: C 185 PHE cc_start: 0.8238 (m-80) cc_final: 0.8026 (m-80) REVERT: C 225 LYS cc_start: 0.7390 (mttp) cc_final: 0.5962 (tmtt) REVERT: C 323 ASP cc_start: 0.6340 (m-30) cc_final: 0.5508 (t70) REVERT: D 282 THR cc_start: 0.8964 (m) cc_final: 0.8675 (p) REVERT: D 351 MET cc_start: 0.8076 (ptp) cc_final: 0.7725 (ptp) REVERT: D 442 ASP cc_start: 0.7086 (OUTLIER) cc_final: 0.6755 (t0) REVERT: E 273 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: E 283 ASN cc_start: 0.7702 (m110) cc_final: 0.7365 (t0) REVERT: E 438 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6792 (mmt180) REVERT: F 191 LYS cc_start: 0.7829 (mmtp) cc_final: 0.7464 (mtpt) REVERT: F 209 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7131 (pm20) REVERT: F 219 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7452 (ptmt) REVERT: F 245 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7947 (mtmt) REVERT: F 265 ARG cc_start: 0.6219 (tpt170) cc_final: 0.5810 (tpt170) REVERT: F 443 ILE cc_start: 0.7358 (tt) cc_final: 0.7043 (tt) outliers start: 87 outliers final: 59 residues processed: 367 average time/residue: 0.1166 time to fit residues: 65.0854 Evaluate side-chains 350 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 198 CYS Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 148 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 194 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN E 234 HIS F 283 ASN F 375 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.169260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135729 restraints weight = 17250.299| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.35 r_work: 0.3239 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16488 Z= 0.164 Angle : 0.599 11.574 22411 Z= 0.310 Chirality : 0.046 0.178 2543 Planarity : 0.004 0.048 2880 Dihedral : 9.374 76.846 2429 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 5.81 % Allowed : 20.20 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2056 helix: 0.06 (0.37), residues: 208 sheet: -0.65 (0.22), residues: 482 loop : 0.03 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.014 0.002 TYR E 276 PHE 0.030 0.002 PHE C 170 TRP 0.015 0.002 TRP A 144 HIS 0.006 0.001 HIS C 248 Details of bonding type rmsd covalent geometry : bond 0.00400 (16488) covalent geometry : angle 0.59879 (22411) hydrogen bonds : bond 0.03715 ( 239) hydrogen bonds : angle 6.75462 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 300 time to evaluate : 0.496 Fit side-chains REVERT: A 122 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6971 (ttm170) REVERT: A 184 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.7050 (mtt) REVERT: A 282 THR cc_start: 0.8798 (m) cc_final: 0.8399 (p) REVERT: A 323 ASP cc_start: 0.6996 (m-30) cc_final: 0.6254 (t70) REVERT: A 356 GLU cc_start: 0.7900 (tt0) cc_final: 0.7637 (tt0) REVERT: A 431 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8097 (t0) REVERT: B 156 GLU cc_start: 0.7352 (tp30) cc_final: 0.6690 (mm-30) REVERT: B 164 ASP cc_start: 0.7871 (m-30) cc_final: 0.7524 (m-30) REVERT: B 190 ASP cc_start: 0.8741 (m-30) cc_final: 0.8511 (m-30) REVERT: B 283 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7593 (m-40) REVERT: B 311 ARG cc_start: 0.7295 (mmt180) cc_final: 0.6536 (mtm180) REVERT: C 105 SER cc_start: 0.7947 (t) cc_final: 0.7619 (t) REVERT: C 149 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: C 263 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8196 (t) REVERT: C 323 ASP cc_start: 0.6254 (m-30) cc_final: 0.5468 (t70) REVERT: C 438 ARG cc_start: 0.7413 (tpp-160) cc_final: 0.7119 (tpp-160) REVERT: D 245 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8379 (mtmt) REVERT: D 282 THR cc_start: 0.8714 (m) cc_final: 0.8454 (p) REVERT: D 335 GLN cc_start: 0.8346 (tt0) cc_final: 0.8081 (tt0) REVERT: D 431 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: D 442 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6705 (t0) REVERT: E 191 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7660 (mtpt) REVERT: E 198 CYS cc_start: 0.7940 (p) cc_final: 0.7323 (m) REVERT: F 156 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6791 (tm-30) REVERT: F 191 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7502 (mtpt) REVERT: F 265 ARG cc_start: 0.6221 (tpt170) cc_final: 0.5632 (ttt90) REVERT: F 374 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7517 (mt-10) REVERT: F 443 ILE cc_start: 0.7675 (tt) cc_final: 0.7460 (tt) outliers start: 101 outliers final: 76 residues processed: 369 average time/residue: 0.1190 time to fit residues: 65.1156 Evaluate side-chains 362 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 278 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 382 GLU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 382 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 211 PHE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN D 208 HIS E 90 GLN E 244 GLN F 183 GLN F 283 ASN F 325 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.167138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.136362 restraints weight = 17187.605| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.13 r_work: 0.3267 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16488 Z= 0.158 Angle : 0.576 7.662 22411 Z= 0.300 Chirality : 0.046 0.176 2543 Planarity : 0.004 0.047 2880 Dihedral : 9.162 77.241 2429 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.35 % Allowed : 21.58 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2056 helix: 0.10 (0.38), residues: 208 sheet: -0.77 (0.22), residues: 483 loop : -0.04 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 438 TYR 0.022 0.002 TYR E 241 PHE 0.022 0.002 PHE C 170 TRP 0.014 0.002 TRP D 144 HIS 0.004 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00391 (16488) covalent geometry : angle 0.57571 (22411) hydrogen bonds : bond 0.03572 ( 239) hydrogen bonds : angle 6.69843 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 297 time to evaluate : 0.606 Fit side-chains REVERT: A 103 PHE cc_start: 0.7238 (t80) cc_final: 0.6902 (t80) REVERT: A 122 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7056 (ttm170) REVERT: A 128 ASP cc_start: 0.6983 (p0) cc_final: 0.6662 (p0) REVERT: A 184 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: A 282 THR cc_start: 0.8611 (m) cc_final: 0.8252 (p) REVERT: A 323 ASP cc_start: 0.6985 (m-30) cc_final: 0.6280 (t70) REVERT: A 356 GLU cc_start: 0.7776 (tt0) cc_final: 0.7529 (tt0) REVERT: A 361 LYS cc_start: 0.5620 (mttt) cc_final: 0.5094 (mttm) REVERT: A 431 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8153 (t0) REVERT: B 92 ASN cc_start: 0.6089 (t0) cc_final: 0.5811 (p0) REVERT: B 128 ASP cc_start: 0.7362 (t70) cc_final: 0.6893 (p0) REVERT: B 156 GLU cc_start: 0.7404 (tp30) cc_final: 0.6717 (mm-30) REVERT: B 164 ASP cc_start: 0.7837 (m-30) cc_final: 0.7481 (m-30) REVERT: B 190 ASP cc_start: 0.8748 (m-30) cc_final: 0.8501 (m-30) REVERT: B 197 GLU cc_start: 0.7403 (mp0) cc_final: 0.7057 (mp0) REVERT: B 283 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7619 (m-40) REVERT: B 311 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6596 (mtm180) REVERT: B 438 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7004 (mmt-90) REVERT: C 98 MET cc_start: 0.8524 (mtt) cc_final: 0.8300 (mtt) REVERT: C 105 SER cc_start: 0.7995 (t) cc_final: 0.7490 (t) REVERT: C 263 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8221 (t) REVERT: C 282 THR cc_start: 0.8436 (m) cc_final: 0.8123 (p) REVERT: C 285 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 323 ASP cc_start: 0.6339 (m-30) cc_final: 0.5593 (t70) REVERT: C 374 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 90 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: D 245 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8417 (mtmt) REVERT: D 282 THR cc_start: 0.8721 (m) cc_final: 0.8473 (p) REVERT: D 318 ASP cc_start: 0.7419 (m-30) cc_final: 0.6462 (p0) REVERT: D 335 GLN cc_start: 0.8254 (tt0) cc_final: 0.7969 (tt0) REVERT: D 431 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: D 442 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6745 (t0) REVERT: E 149 GLN cc_start: 0.8348 (mt0) cc_final: 0.8001 (mt0) REVERT: E 191 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7655 (mtpt) REVERT: E 198 CYS cc_start: 0.8015 (p) cc_final: 0.7368 (m) REVERT: E 211 PHE cc_start: 0.8384 (p90) cc_final: 0.8157 (p90) REVERT: E 253 ASN cc_start: 0.8560 (p0) cc_final: 0.8244 (p0) REVERT: F 120 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7512 (ttm110) REVERT: F 149 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6914 (tp40) REVERT: F 156 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7005 (tm-30) REVERT: F 191 LYS cc_start: 0.7932 (mmtp) cc_final: 0.7349 (mtpt) REVERT: F 196 ASP cc_start: 0.7019 (t0) cc_final: 0.6645 (p0) REVERT: F 245 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8072 (mtmt) REVERT: F 265 ARG cc_start: 0.6114 (tpt170) cc_final: 0.5596 (ttt90) REVERT: F 374 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7469 (mt-10) REVERT: F 424 GLU cc_start: 0.6541 (mt-10) cc_final: 0.5961 (tt0) REVERT: F 443 ILE cc_start: 0.7898 (tt) cc_final: 0.7694 (tt) outliers start: 93 outliers final: 71 residues processed: 364 average time/residue: 0.1103 time to fit residues: 60.4400 Evaluate side-chains 377 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 296 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 155 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.168371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.137861 restraints weight = 17117.118| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.12 r_work: 0.3282 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16488 Z= 0.126 Angle : 0.530 7.088 22411 Z= 0.277 Chirality : 0.045 0.167 2543 Planarity : 0.004 0.044 2880 Dihedral : 8.840 79.965 2429 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.06 % Allowed : 21.75 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.18), residues: 2056 helix: 0.33 (0.39), residues: 202 sheet: -0.78 (0.22), residues: 483 loop : -0.06 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 110 TYR 0.013 0.001 TYR D 357 PHE 0.018 0.002 PHE C 170 TRP 0.011 0.001 TRP A 144 HIS 0.005 0.001 HIS E 248 Details of bonding type rmsd covalent geometry : bond 0.00307 (16488) covalent geometry : angle 0.53017 (22411) hydrogen bonds : bond 0.03199 ( 239) hydrogen bonds : angle 6.58762 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 302 time to evaluate : 0.476 Fit side-chains REVERT: A 103 PHE cc_start: 0.7220 (t80) cc_final: 0.6879 (t80) REVERT: A 122 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7111 (ttm170) REVERT: A 128 ASP cc_start: 0.6971 (p0) cc_final: 0.6657 (p0) REVERT: A 169 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7560 (tt0) REVERT: A 184 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7062 (mtp) REVERT: A 196 ASP cc_start: 0.8168 (t0) cc_final: 0.7965 (t0) REVERT: A 197 GLU cc_start: 0.7289 (mp0) cc_final: 0.6990 (pm20) REVERT: A 199 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8110 (mt) REVERT: A 282 THR cc_start: 0.8605 (m) cc_final: 0.8251 (p) REVERT: A 323 ASP cc_start: 0.6974 (m-30) cc_final: 0.6280 (t70) REVERT: A 341 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7041 (ppt90) REVERT: A 356 GLU cc_start: 0.7725 (tt0) cc_final: 0.7466 (tt0) REVERT: A 431 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8154 (t0) REVERT: B 128 ASP cc_start: 0.7179 (t70) cc_final: 0.6617 (p0) REVERT: B 156 GLU cc_start: 0.7406 (tp30) cc_final: 0.6714 (mm-30) REVERT: B 164 ASP cc_start: 0.7781 (m-30) cc_final: 0.7417 (m-30) REVERT: B 190 ASP cc_start: 0.8711 (m-30) cc_final: 0.8498 (m-30) REVERT: B 197 GLU cc_start: 0.7570 (mp0) cc_final: 0.7240 (mp0) REVERT: B 209 GLU cc_start: 0.6531 (pm20) cc_final: 0.6169 (pm20) REVERT: B 283 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7395 (t0) REVERT: B 311 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6670 (mpp80) REVERT: C 98 MET cc_start: 0.8458 (mtt) cc_final: 0.8201 (mtt) REVERT: C 105 SER cc_start: 0.7970 (t) cc_final: 0.7458 (t) REVERT: C 263 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8235 (t) REVERT: C 282 THR cc_start: 0.8448 (m) cc_final: 0.8100 (p) REVERT: C 323 ASP cc_start: 0.6356 (m-30) cc_final: 0.5621 (t70) REVERT: C 374 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7770 (mt-10) REVERT: D 90 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: D 245 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8429 (mtmm) REVERT: D 282 THR cc_start: 0.8753 (m) cc_final: 0.8500 (p) REVERT: D 318 ASP cc_start: 0.7445 (m-30) cc_final: 0.7071 (t0) REVERT: D 335 GLN cc_start: 0.8226 (tt0) cc_final: 0.7930 (tt0) REVERT: D 442 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6750 (t0) REVERT: E 149 GLN cc_start: 0.8353 (mt0) cc_final: 0.8015 (mt0) REVERT: E 191 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7709 (mtpt) REVERT: E 198 CYS cc_start: 0.7958 (p) cc_final: 0.7265 (m) REVERT: E 253 ASN cc_start: 0.8572 (p0) cc_final: 0.8293 (p0) REVERT: F 120 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7470 (ttm110) REVERT: F 144 TRP cc_start: 0.7908 (m-90) cc_final: 0.7557 (m-90) REVERT: F 156 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6954 (tm-30) REVERT: F 191 LYS cc_start: 0.7917 (mmtp) cc_final: 0.7330 (mtpt) REVERT: F 196 ASP cc_start: 0.7079 (t0) cc_final: 0.6621 (p0) REVERT: F 265 ARG cc_start: 0.6748 (tpt170) cc_final: 0.6104 (ttt90) REVERT: F 361 LYS cc_start: 0.6161 (mttt) cc_final: 0.5857 (mmtt) REVERT: F 374 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7585 (mt-10) REVERT: F 424 GLU cc_start: 0.6512 (mt-10) cc_final: 0.5921 (tt0) outliers start: 88 outliers final: 66 residues processed: 365 average time/residue: 0.1199 time to fit residues: 65.4059 Evaluate side-chains 366 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 290 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 120 ARG Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 31 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 181 optimal weight: 0.0770 chunk 131 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN D 183 GLN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132932 restraints weight = 17296.305| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.31 r_work: 0.3232 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16488 Z= 0.161 Angle : 0.583 9.380 22411 Z= 0.302 Chirality : 0.046 0.177 2543 Planarity : 0.004 0.043 2880 Dihedral : 9.251 80.751 2429 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.52 % Allowed : 21.29 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2056 helix: 0.13 (0.38), residues: 207 sheet: -1.00 (0.22), residues: 493 loop : -0.13 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 438 TYR 0.015 0.002 TYR D 357 PHE 0.021 0.002 PHE C 170 TRP 0.016 0.002 TRP D 144 HIS 0.003 0.001 HIS E 208 Details of bonding type rmsd covalent geometry : bond 0.00399 (16488) covalent geometry : angle 0.58337 (22411) hydrogen bonds : bond 0.03620 ( 239) hydrogen bonds : angle 6.72004 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 0.591 Fit side-chains REVERT: A 122 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: A 128 ASP cc_start: 0.6953 (p0) cc_final: 0.6643 (p0) REVERT: A 184 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: A 282 THR cc_start: 0.8717 (m) cc_final: 0.8293 (p) REVERT: A 323 ASP cc_start: 0.6982 (m-30) cc_final: 0.6262 (t70) REVERT: A 341 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7025 (ppt90) REVERT: A 356 GLU cc_start: 0.7734 (tt0) cc_final: 0.7494 (tt0) REVERT: A 431 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.7854 (t0) REVERT: B 128 ASP cc_start: 0.7092 (t70) cc_final: 0.6493 (p0) REVERT: B 156 GLU cc_start: 0.7472 (tp30) cc_final: 0.6788 (mm-30) REVERT: B 164 ASP cc_start: 0.7811 (m-30) cc_final: 0.7441 (m-30) REVERT: B 190 ASP cc_start: 0.8508 (m-30) cc_final: 0.8278 (m-30) REVERT: B 197 GLU cc_start: 0.7545 (mp0) cc_final: 0.7227 (mp0) REVERT: B 283 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7257 (t0) REVERT: B 438 ARG cc_start: 0.6973 (mmt-90) cc_final: 0.6635 (mmt-90) REVERT: C 105 SER cc_start: 0.7992 (t) cc_final: 0.7516 (t) REVERT: C 263 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8169 (t) REVERT: C 282 THR cc_start: 0.8533 (m) cc_final: 0.8154 (p) REVERT: C 323 ASP cc_start: 0.6440 (m-30) cc_final: 0.5644 (t70) REVERT: C 374 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 438 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7237 (tpp-160) REVERT: D 92 ASN cc_start: 0.7444 (t0) cc_final: 0.6845 (p0) REVERT: D 133 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7400 (mt) REVERT: D 245 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8430 (mtmm) REVERT: D 254 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 282 THR cc_start: 0.8569 (m) cc_final: 0.8322 (p) REVERT: D 318 ASP cc_start: 0.7147 (m-30) cc_final: 0.6869 (t0) REVERT: D 335 GLN cc_start: 0.8238 (tt0) cc_final: 0.7947 (tt0) REVERT: D 431 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: D 442 ASP cc_start: 0.7188 (OUTLIER) cc_final: 0.6838 (t0) REVERT: E 149 GLN cc_start: 0.8360 (mt0) cc_final: 0.8073 (mt0) REVERT: E 191 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7659 (mtpt) REVERT: E 198 CYS cc_start: 0.8215 (p) cc_final: 0.7294 (m) REVERT: E 253 ASN cc_start: 0.8544 (p0) cc_final: 0.8266 (p0) REVERT: E 320 LYS cc_start: 0.7433 (tttt) cc_final: 0.7193 (tttt) REVERT: F 149 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7082 (tp40) REVERT: F 156 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7156 (tm-30) REVERT: F 191 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7085 (mtpt) REVERT: F 196 ASP cc_start: 0.7255 (t0) cc_final: 0.6719 (p0) REVERT: F 245 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8084 (mtmt) REVERT: F 265 ARG cc_start: 0.6455 (tpt170) cc_final: 0.6011 (ttt90) REVERT: F 374 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7924 (mt-10) outliers start: 96 outliers final: 72 residues processed: 356 average time/residue: 0.1158 time to fit residues: 62.0974 Evaluate side-chains 363 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 149 GLN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 116 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.167919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135620 restraints weight = 17217.601| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.28 r_work: 0.3264 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16488 Z= 0.126 Angle : 0.529 7.691 22411 Z= 0.276 Chirality : 0.045 0.167 2543 Planarity : 0.004 0.042 2880 Dihedral : 8.809 82.079 2429 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.95 % Allowed : 21.81 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2056 helix: 0.30 (0.39), residues: 206 sheet: -0.95 (0.22), residues: 487 loop : -0.10 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 438 TYR 0.012 0.002 TYR D 357 PHE 0.018 0.002 PHE C 170 TRP 0.012 0.001 TRP D 144 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00306 (16488) covalent geometry : angle 0.52938 (22411) hydrogen bonds : bond 0.03198 ( 239) hydrogen bonds : angle 6.56652 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 0.623 Fit side-chains REVERT: A 122 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.7116 (ttm170) REVERT: A 128 ASP cc_start: 0.6948 (p0) cc_final: 0.6637 (p0) REVERT: A 184 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7199 (mtt) REVERT: A 199 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 282 THR cc_start: 0.8570 (m) cc_final: 0.8238 (p) REVERT: A 323 ASP cc_start: 0.6965 (m-30) cc_final: 0.6255 (t70) REVERT: A 341 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7035 (ppt90) REVERT: A 431 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 128 ASP cc_start: 0.7146 (t70) cc_final: 0.6686 (p0) REVERT: B 156 GLU cc_start: 0.7429 (tp30) cc_final: 0.6760 (mm-30) REVERT: B 164 ASP cc_start: 0.7700 (m-30) cc_final: 0.7443 (m-30) REVERT: B 197 GLU cc_start: 0.7551 (mp0) cc_final: 0.7236 (mp0) REVERT: B 209 GLU cc_start: 0.6672 (pm20) cc_final: 0.6362 (pm20) REVERT: B 283 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7178 (t0) REVERT: C 105 SER cc_start: 0.7918 (t) cc_final: 0.7440 (t) REVERT: C 156 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7345 (mm-30) REVERT: C 263 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8198 (t) REVERT: C 282 THR cc_start: 0.8535 (m) cc_final: 0.8161 (p) REVERT: C 323 ASP cc_start: 0.6551 (m-30) cc_final: 0.5789 (t70) REVERT: D 92 ASN cc_start: 0.7306 (t0) cc_final: 0.6758 (p0) REVERT: D 133 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7383 (mt) REVERT: D 184 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6676 (ptp) REVERT: D 244 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.5791 (mp10) REVERT: D 245 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8414 (mtmm) REVERT: D 282 THR cc_start: 0.8568 (m) cc_final: 0.8311 (p) REVERT: D 318 ASP cc_start: 0.7148 (m-30) cc_final: 0.6891 (t0) REVERT: D 335 GLN cc_start: 0.8203 (tt0) cc_final: 0.7906 (tt0) REVERT: D 442 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6849 (t0) REVERT: E 149 GLN cc_start: 0.8364 (mt0) cc_final: 0.8074 (mt0) REVERT: E 191 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7741 (mtpt) REVERT: E 198 CYS cc_start: 0.8045 (p) cc_final: 0.7201 (m) REVERT: E 320 LYS cc_start: 0.7421 (tttt) cc_final: 0.7194 (tttt) REVERT: F 156 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7040 (tm-30) REVERT: F 165 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8083 (t) REVERT: F 191 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7255 (mtpt) REVERT: F 196 ASP cc_start: 0.7847 (t0) cc_final: 0.7149 (p0) REVERT: F 245 LYS cc_start: 0.8370 (mtmm) cc_final: 0.8038 (mtmt) REVERT: F 265 ARG cc_start: 0.6523 (tpt170) cc_final: 0.6074 (tpt-90) REVERT: F 374 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7923 (mt-10) outliers start: 86 outliers final: 68 residues processed: 339 average time/residue: 0.1092 time to fit residues: 56.1320 Evaluate side-chains 362 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 282 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 244 GLN Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 135 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 0.0670 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 283 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.137041 restraints weight = 17194.050| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.27 r_work: 0.3270 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16488 Z= 0.110 Angle : 0.509 7.586 22411 Z= 0.265 Chirality : 0.044 0.159 2543 Planarity : 0.004 0.042 2880 Dihedral : 8.405 83.795 2429 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.49 % Allowed : 22.32 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 2056 helix: 0.43 (0.39), residues: 206 sheet: -0.85 (0.22), residues: 491 loop : -0.05 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 438 TYR 0.011 0.001 TYR D 357 PHE 0.015 0.001 PHE C 170 TRP 0.011 0.001 TRP A 144 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00262 (16488) covalent geometry : angle 0.50940 (22411) hydrogen bonds : bond 0.03125 ( 239) hydrogen bonds : angle 6.48645 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6943 (p0) cc_final: 0.6630 (p0) REVERT: A 169 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7393 (tt0) REVERT: A 197 GLU cc_start: 0.7296 (mp0) cc_final: 0.7073 (pm20) REVERT: A 282 THR cc_start: 0.8556 (m) cc_final: 0.8233 (p) REVERT: A 323 ASP cc_start: 0.6950 (m-30) cc_final: 0.6243 (t70) REVERT: A 356 GLU cc_start: 0.7770 (tt0) cc_final: 0.7494 (tt0) REVERT: A 431 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8172 (t0) REVERT: B 128 ASP cc_start: 0.7255 (t70) cc_final: 0.6758 (p0) REVERT: B 156 GLU cc_start: 0.7394 (tp30) cc_final: 0.6736 (mm-30) REVERT: B 164 ASP cc_start: 0.7695 (m-30) cc_final: 0.7480 (m-30) REVERT: B 197 GLU cc_start: 0.7446 (mp0) cc_final: 0.7107 (mp0) REVERT: B 209 GLU cc_start: 0.6787 (pm20) cc_final: 0.6481 (pm20) REVERT: B 283 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7054 (t0) REVERT: C 98 MET cc_start: 0.8297 (mtt) cc_final: 0.7974 (mtt) REVERT: C 105 SER cc_start: 0.7905 (t) cc_final: 0.7390 (t) REVERT: C 263 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8199 (t) REVERT: C 282 THR cc_start: 0.8576 (m) cc_final: 0.8205 (p) REVERT: C 323 ASP cc_start: 0.6565 (m-30) cc_final: 0.5776 (t70) REVERT: D 92 ASN cc_start: 0.7308 (t0) cc_final: 0.6763 (p0) REVERT: D 133 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7312 (mt) REVERT: D 184 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6609 (ptp) REVERT: D 244 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.5738 (mp10) REVERT: D 245 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8370 (mtmm) REVERT: D 282 THR cc_start: 0.8586 (m) cc_final: 0.8245 (p) REVERT: D 318 ASP cc_start: 0.7149 (m-30) cc_final: 0.6901 (t0) REVERT: D 335 GLN cc_start: 0.8222 (tt0) cc_final: 0.7919 (tt0) REVERT: D 442 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6807 (t0) REVERT: E 149 GLN cc_start: 0.8225 (mt0) cc_final: 0.7953 (mt0) REVERT: E 191 LYS cc_start: 0.7994 (mtpt) cc_final: 0.7713 (mtpt) REVERT: E 198 CYS cc_start: 0.8215 (p) cc_final: 0.7095 (m) REVERT: E 320 LYS cc_start: 0.7413 (tttt) cc_final: 0.7203 (tttt) REVERT: F 156 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7063 (tm-30) REVERT: F 165 VAL cc_start: 0.8288 (OUTLIER) cc_final: 0.8071 (t) REVERT: F 191 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7257 (mtpt) REVERT: F 196 ASP cc_start: 0.7860 (t0) cc_final: 0.7122 (p0) REVERT: F 245 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8046 (mtmt) REVERT: F 265 ARG cc_start: 0.6334 (tpt170) cc_final: 0.5928 (tpt-90) REVERT: F 374 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7866 (mt-10) outliers start: 78 outliers final: 66 residues processed: 349 average time/residue: 0.1101 time to fit residues: 58.3489 Evaluate side-chains 361 residues out of total 1738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 244 GLN Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 442 ASP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 341 ARG Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 304 SER Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 0.0770 chunk 142 optimal weight: 1.9990 chunk 90 optimal weight: 0.0570 chunk 3 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.168778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136701 restraints weight = 17146.139| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.27 r_work: 0.3281 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16488 Z= 0.115 Angle : 0.512 7.601 22411 Z= 0.267 Chirality : 0.045 0.181 2543 Planarity : 0.004 0.042 2880 Dihedral : 8.376 81.477 2429 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.66 % Allowed : 22.21 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 2056 helix: 0.38 (0.39), residues: 207 sheet: -0.88 (0.23), residues: 471 loop : 0.01 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 438 TYR 0.012 0.001 TYR D 357 PHE 0.017 0.001 PHE C 170 TRP 0.012 0.001 TRP A 144 HIS 0.006 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00277 (16488) covalent geometry : angle 0.51195 (22411) hydrogen bonds : bond 0.03090 ( 239) hydrogen bonds : angle 6.47975 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.68 seconds wall clock time: 56 minutes 42.22 seconds (3402.22 seconds total)