Starting phenix.real_space_refine on Sat Mar 7 07:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235.map" model { file = "/net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6smh_10235/03_2026/6smh_10235_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 25093 2.51 5 N 7133 2.21 5 O 7342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39744 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "G" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "H" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "J" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1523 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 179} Chain: "K" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "L" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "M" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1465 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "N" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "P" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1479 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Time building chain proxies: 8.69, per 1000 atoms: 0.22 Number of scatterers: 39744 At special positions: 0 Unit cell: (167.5, 165, 132.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 7342 8.00 N 7133 7.00 C 25093 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=23, symmetry=0 Number of additional bonds: simple=23, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.8 seconds 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9232 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 28 sheets defined 44.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.794A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 430 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 348 removed outlier: 4.167A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 409 through 430 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.503A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.660A pdb=" N GLY C 193 " --> pdb=" O CYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.842A pdb=" N ARG C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 409 through 431 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.603A pdb=" N ALA D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.044A pdb=" N PHE D 215 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 383 through 392 Processing helix chain 'D' and resid 409 through 431 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.546A pdb=" N CYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 193 " --> pdb=" O CYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.776A pdb=" N ALA E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 282 Processing helix chain 'E' and resid 307 through 319 Processing helix chain 'E' and resid 332 through 345 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.793A pdb=" N GLU E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.535A pdb=" N GLU E 437 " --> pdb=" O ASP E 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY E 439 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP E 440 " --> pdb=" O ARG E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.922A pdb=" N GLY F 193 " --> pdb=" O CYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.897A pdb=" N PHE F 215 " --> pdb=" O TRP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 4.286A pdb=" N GLU F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 307 through 318 Processing helix chain 'F' and resid 332 through 344 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 409 through 430 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 178 through 192 removed outlier: 4.354A pdb=" N GLY G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 removed outlier: 3.601A pdb=" N ALA G 254 " --> pdb=" O ARG G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 391 removed outlier: 4.419A pdb=" N GLU G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 390 " --> pdb=" O ALA G 386 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 430 Processing helix chain 'G' and resid 437 through 446 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA H 50 " --> pdb=" O PRO H 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 178 through 192 Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 295 through 300 removed outlier: 3.733A pdb=" N ASP H 299 " --> pdb=" O HIS H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 348 removed outlier: 4.220A pdb=" N MET H 346 " --> pdb=" O PHE H 342 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG H 347 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 392 Processing helix chain 'H' and resid 409 through 430 Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP H 459 " --> pdb=" O ALA H 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.536A pdb=" N LEU I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 34 removed outlier: 3.695A pdb=" N ALA I 32 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 48 removed outlier: 3.675A pdb=" N LEU I 48 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 67 through 75 removed outlier: 3.653A pdb=" N ILE I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU I 73 " --> pdb=" O TYR I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 121 through 130 removed outlier: 4.319A pdb=" N ALA I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP I 130 " --> pdb=" O LYS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.530A pdb=" N CYS I 153 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 168 Processing helix chain 'I' and resid 179 through 185 removed outlier: 3.733A pdb=" N LEU I 185 " --> pdb=" O GLY I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.773A pdb=" N LEU J 48 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE J 49 " --> pdb=" O PRO J 45 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.535A pdb=" N VAL J 64 " --> pdb=" O ASN J 60 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.527A pdb=" N LEU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.676A pdb=" N ALA J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 3.792A pdb=" N GLU J 113 " --> pdb=" O GLN J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 removed outlier: 3.561A pdb=" N ALA J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.902A pdb=" N VAL J 149 " --> pdb=" O PRO J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 removed outlier: 4.010A pdb=" N CYS J 153 " --> pdb=" O ALA J 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 153' Processing helix chain 'J' and resid 179 through 187 removed outlier: 3.766A pdb=" N ARG J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU J 187 " --> pdb=" O ARG J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 removed outlier: 3.893A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 24 removed outlier: 3.721A pdb=" N LEU K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 22 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 38 removed outlier: 3.723A pdb=" N ALA K 32 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 44 through 52 removed outlier: 3.997A pdb=" N LEU K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE K 49 " --> pdb=" O PRO K 45 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 72 removed outlier: 4.126A pdb=" N ALA K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.614A pdb=" N LEU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.723A pdb=" N SER K 105 " --> pdb=" O GLN K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 112 No H-bonds generated for 'chain 'K' and resid 110 through 112' Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 144 through 156 removed outlier: 4.114A pdb=" N CYS K 153 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TRP K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.506A pdb=" N ARG K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 28 through 39 removed outlier: 4.069A pdb=" N ALA L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.985A pdb=" N LEU L 48 " --> pdb=" O ASN L 44 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 44 through 49' Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 64 through 72 Processing helix chain 'L' and resid 89 through 96 removed outlier: 3.794A pdb=" N LEU L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 115 removed outlier: 4.744A pdb=" N SER L 105 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 132 removed outlier: 3.595A pdb=" N ALA L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 153 removed outlier: 3.580A pdb=" N CYS L 153 " --> pdb=" O VAL L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 166 removed outlier: 3.995A pdb=" N ARG L 166 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 186 removed outlier: 3.526A pdb=" N ARG L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 23 Processing helix chain 'M' and resid 28 through 39 removed outlier: 4.023A pdb=" N ALA M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.794A pdb=" N LEU M 48 " --> pdb=" O ASN M 44 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE M 49 " --> pdb=" O PRO M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.638A pdb=" N GLN M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR M 63 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.914A pdb=" N LEU M 96 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 115 removed outlier: 4.095A pdb=" N SER M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 removed outlier: 3.776A pdb=" N LEU M 134 " --> pdb=" O ASP M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 163 through 168 removed outlier: 3.784A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 163 through 168' Processing helix chain 'M' and resid 179 through 185 removed outlier: 3.940A pdb=" N ARG M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 190 removed outlier: 3.544A pdb=" N LEU M 190 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 24 removed outlier: 4.123A pdb=" N LEU N 21 " --> pdb=" O LEU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 4.064A pdb=" N ALA N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.843A pdb=" N LEU N 48 " --> pdb=" O ASN N 44 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 44 through 52' Processing helix chain 'N' and resid 60 through 72 removed outlier: 3.691A pdb=" N ALA N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET N 66 " --> pdb=" O ILE N 62 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 96 removed outlier: 3.572A pdb=" N LEU N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 114 Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 144 through 156 removed outlier: 3.560A pdb=" N ALA N 148 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 149 " --> pdb=" O PRO N 145 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS N 153 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP N 154 " --> pdb=" O ALA N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 167 removed outlier: 3.901A pdb=" N SER N 167 " --> pdb=" O LEU N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 186 Processing helix chain 'N' and resid 187 through 190 Processing helix chain 'O' and resid 18 through 23 Processing helix chain 'O' and resid 28 through 39 removed outlier: 4.001A pdb=" N ALA O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 49 removed outlier: 3.816A pdb=" N LEU O 48 " --> pdb=" O ASN O 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE O 49 " --> pdb=" O PRO O 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 44 through 49' Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.531A pdb=" N VAL O 64 " --> pdb=" O ASN O 60 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET O 66 " --> pdb=" O ILE O 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.738A pdb=" N TYR O 85 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN O 86 " --> pdb=" O GLU O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.691A pdb=" N LEU O 96 " --> pdb=" O LEU O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 115 removed outlier: 3.687A pdb=" N LEU O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 129 through 132 Processing helix chain 'O' and resid 144 through 151 Processing helix chain 'O' and resid 179 through 185 removed outlier: 3.810A pdb=" N ARG O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'P' and resid 18 through 24 Processing helix chain 'P' and resid 28 through 39 removed outlier: 4.016A pdb=" N ALA P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 52 removed outlier: 3.804A pdb=" N LEU P 48 " --> pdb=" O ASN P 44 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 44 through 52' Processing helix chain 'P' and resid 60 through 72 removed outlier: 4.237A pdb=" N ALA P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET P 66 " --> pdb=" O ILE P 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN P 67 " --> pdb=" O THR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 96 Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.892A pdb=" N SER P 105 " --> pdb=" O GLN P 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 108 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN P 109 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU P 110 " --> pdb=" O LEU P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 removed outlier: 3.573A pdb=" N ALA P 125 " --> pdb=" O ILE P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 151 Processing helix chain 'P' and resid 162 through 167 removed outlier: 3.636A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 185 removed outlier: 3.574A pdb=" N ARG P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 133 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.293A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 323 " --> pdb=" O VAL A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.775A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 133 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.987A pdb=" N ASP C 134 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG C 38 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 132 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER C 40 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 130 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198 removed outlier: 6.499A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET C 166 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 237 through 238 removed outlier: 6.206A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 86 removed outlier: 4.001A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 97 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 39 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 35 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 133 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.354A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N PHE D 399 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY D 168 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 196 through 198 removed outlier: 6.919A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN D 238 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS D 235 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET D 263 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 237 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA E 36 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 133 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET E 166 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 323 " --> pdb=" O VAL E 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB9, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.666A pdb=" N GLU F 85 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA F 36 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU F 133 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLY F 305 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU F 130 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET F 166 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU F 323 " --> pdb=" O VAL F 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 237 through 238 removed outlier: 5.759A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC4, first strand: chain 'G' and resid 36 through 39 Processing sheet with id=AC5, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 234 through 235 removed outlier: 3.670A pdb=" N THR G 197 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 261 through 263 removed outlier: 6.319A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 85 through 86 removed outlier: 3.865A pdb=" N PHE H 39 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA H 36 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 133 " --> pdb=" O ALA H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS H 235 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET H 263 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR H 197 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN H 238 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU H 323 " --> pdb=" O VAL H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 350 through 351 1366 hydrogen bonds defined for protein. 3972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.59 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11298 1.33 - 1.45: 7612 1.45 - 1.57: 21483 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 40657 Sorted by residual: bond pdb=" C GLN I 137 " pdb=" N PRO I 138 " ideal model delta sigma weight residual 1.333 1.367 -0.034 7.80e-03 1.64e+04 1.94e+01 bond pdb=" N GLN D 206 " pdb=" CA GLN D 206 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N VAL E 239 " pdb=" CA VAL E 239 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.35e+01 bond pdb=" N ILE C 379 " pdb=" CA ILE C 379 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N HIS O 144 " pdb=" CA HIS O 144 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.04e-02 9.25e+03 1.02e+01 ... (remaining 40652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 52713 2.83 - 5.65: 2123 5.65 - 8.48: 168 8.48 - 11.30: 52 11.30 - 14.13: 15 Bond angle restraints: 55071 Sorted by residual: angle pdb=" N ILE P 170 " pdb=" CA ILE P 170 " pdb=" C ILE P 170 " ideal model delta sigma weight residual 113.71 107.30 6.41 9.50e-01 1.11e+00 4.55e+01 angle pdb=" N ILE M 170 " pdb=" CA ILE M 170 " pdb=" C ILE M 170 " ideal model delta sigma weight residual 113.22 104.94 8.28 1.23e+00 6.61e-01 4.53e+01 angle pdb=" N ILE K 170 " pdb=" CA ILE K 170 " pdb=" C ILE K 170 " ideal model delta sigma weight residual 113.53 107.13 6.40 9.80e-01 1.04e+00 4.26e+01 angle pdb=" C SER E 367 " pdb=" N MET E 368 " pdb=" CA MET E 368 " ideal model delta sigma weight residual 121.61 113.22 8.39 1.39e+00 5.18e-01 3.64e+01 angle pdb=" C SER B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 121.61 113.23 8.38 1.39e+00 5.18e-01 3.63e+01 ... (remaining 55066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 22451 26.44 - 52.87: 1473 52.87 - 79.31: 288 79.31 - 105.74: 30 105.74 - 132.18: 1 Dihedral angle restraints: 24243 sinusoidal: 9890 harmonic: 14353 Sorted by residual: dihedral pdb=" CA LYS D 172 " pdb=" C LYS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta harmonic sigma weight residual 180.00 47.82 132.18 0 5.00e+00 4.00e-02 6.99e+02 dihedral pdb=" CD ARG J 27 " pdb=" NE ARG J 27 " pdb=" CZ ARG J 27 " pdb=" NH1 ARG J 27 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG H 191 " pdb=" NE ARG H 191 " pdb=" CZ ARG H 191 " pdb=" NH1 ARG H 191 " ideal model delta sinusoidal sigma weight residual 0.00 -89.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 24240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3767 0.062 - 0.125: 1665 0.125 - 0.187: 433 0.187 - 0.250: 35 0.250 - 0.312: 17 Chirality restraints: 5917 Sorted by residual: chirality pdb=" CB VAL I 81 " pdb=" CA VAL I 81 " pdb=" CG1 VAL I 81 " pdb=" CG2 VAL I 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE H 203 " pdb=" CA ILE H 203 " pdb=" CG1 ILE H 203 " pdb=" CG2 ILE H 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 5914 not shown) Planarity restraints: 7264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 27 " -1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG J 27 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 27 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG J 27 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 191 " -1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG H 191 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 191 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 191 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG H 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 428 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG E 428 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 428 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 428 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 428 " 0.016 2.00e-02 2.50e+03 ... (remaining 7261 not shown) Histogram of nonbonded interaction distances: 0.29 - 1.21: 46 1.21 - 2.14: 468 2.14 - 3.06: 26640 3.06 - 3.98: 105874 3.98 - 4.90: 185538 Warning: very small nonbonded interaction distances. Nonbonded interactions: 318566 Sorted by model distance: nonbonded pdb=" C ILE C 351 " pdb=" CG2 THR C 362 " model vdw 0.292 3.690 nonbonded pdb=" O HIS F 295 " pdb=" CG ASP F 299 " model vdw 0.375 3.270 nonbonded pdb=" CE2 TYR E 236 " pdb=" CE1 HIS E 289 " model vdw 0.502 3.560 nonbonded pdb=" CE2 TYR H 187 " pdb=" CE LYS H 224 " model vdw 0.550 3.740 nonbonded pdb=" O PHE J 141 " pdb=" OD2 ASP J 147 " model vdw 0.557 3.040 ... (remaining 318561 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 13 through 191) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 13 through 191) selection = (chain 'N' and resid 13 through 191) selection = (chain 'O' and resid 13 through 191) selection = (chain 'P' and resid 13 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.300 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.014 0.947 40680 Z= 1.225 Angle : 1.334 14.129 55071 Z= 0.867 Chirality : 0.072 0.312 5917 Planarity : 0.039 0.494 7264 Dihedral : 17.186 132.177 15011 Min Nonbonded Distance : 0.292 Molprobity Statistics. All-atom Clashscore : 54.30 Ramachandran Plot: Outliers : 2.20 % Allowed : 11.94 % Favored : 85.86 % Rotamer: Outliers : 14.61 % Allowed : 9.71 % Favored : 75.68 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.09), residues: 4993 helix: -2.91 (0.08), residues: 2050 sheet: -3.44 (0.19), residues: 440 loop : -3.67 (0.10), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 82 TYR 0.027 0.003 TYR J 69 PHE 0.034 0.003 PHE I 131 TRP 0.028 0.002 TRP M 28 HIS 0.020 0.002 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00865 (40657) covalent geometry : angle 1.33419 (55071) hydrogen bonds : bond 0.20243 ( 1364) hydrogen bonds : angle 8.31151 ( 3972) Misc. bond : bond 0.45752 ( 23) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2047 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 603 poor density : 1444 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.7885 (t80) cc_final: 0.6973 (t80) REVERT: A 146 GLN cc_start: 0.8718 (tp40) cc_final: 0.8483 (tp-100) REVERT: A 155 GLU cc_start: 0.7930 (tt0) cc_final: 0.7697 (tt0) REVERT: A 184 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8102 (mtp180) REVERT: A 250 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8153 (mtm-85) REVERT: A 255 LYS cc_start: 0.9274 (tmtt) cc_final: 0.8534 (tptp) REVERT: A 321 ASP cc_start: 0.8143 (m-30) cc_final: 0.7740 (m-30) REVERT: A 336 LYS cc_start: 0.9182 (tttm) cc_final: 0.8940 (tptt) REVERT: B 122 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 184 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7774 (mtt180) REVERT: B 197 THR cc_start: 0.8943 (p) cc_final: 0.8734 (p) REVERT: B 229 THR cc_start: 0.8209 (p) cc_final: 0.7978 (t) REVERT: B 250 ARG cc_start: 0.8708 (mtt180) cc_final: 0.8247 (mtm-85) REVERT: B 255 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8645 (tptp) REVERT: B 321 ASP cc_start: 0.8440 (m-30) cc_final: 0.8197 (m-30) REVERT: B 389 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7772 (pt0) REVERT: B 390 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9094 (mm) REVERT: C 26 TYR cc_start: 0.7763 (t80) cc_final: 0.7152 (t80) REVERT: C 75 ASP cc_start: 0.8187 (t0) cc_final: 0.7883 (t0) REVERT: C 76 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8104 (ttp80) REVERT: C 91 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6862 (tm-30) REVERT: C 180 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7581 (tppp) REVERT: C 237 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6511 (tt) REVERT: C 240 THR cc_start: 0.9065 (m) cc_final: 0.8765 (m) REVERT: C 259 MET cc_start: 0.9131 (mmp) cc_final: 0.8890 (mmp) REVERT: C 281 CYS cc_start: 0.8695 (m) cc_final: 0.8477 (m) REVERT: C 301 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8494 (mm-40) REVERT: C 321 ASP cc_start: 0.8127 (m-30) cc_final: 0.7830 (m-30) REVERT: C 331 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7313 (mmmt) REVERT: C 363 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: C 380 HIS cc_start: 0.7240 (OUTLIER) cc_final: 0.6534 (p-80) REVERT: C 382 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6188 (m100) REVERT: C 425 VAL cc_start: 0.8863 (t) cc_final: 0.8650 (t) REVERT: C 459 TRP cc_start: 0.7318 (m-90) cc_final: 0.7025 (m-90) REVERT: D 26 TYR cc_start: 0.7975 (t80) cc_final: 0.6988 (t80) REVERT: D 57 GLU cc_start: 0.8300 (tp30) cc_final: 0.7816 (mm-30) REVERT: D 67 TRP cc_start: 0.7786 (p-90) cc_final: 0.7485 (p-90) REVERT: D 146 GLN cc_start: 0.8706 (tp40) cc_final: 0.8445 (tp-100) REVERT: D 162 TYR cc_start: 0.7972 (m-10) cc_final: 0.6990 (m-10) REVERT: D 206 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7852 (mt0) REVERT: D 249 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9114 (ttpp) REVERT: D 259 MET cc_start: 0.8959 (mmp) cc_final: 0.8730 (mmm) REVERT: D 331 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.6688 (mmmt) REVERT: D 365 TRP cc_start: 0.9367 (m100) cc_final: 0.8726 (m100) REVERT: D 428 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8546 (tmm-80) REVERT: E 26 TYR cc_start: 0.7815 (t80) cc_final: 0.6947 (t80) REVERT: E 67 TRP cc_start: 0.7907 (p-90) cc_final: 0.7666 (p-90) REVERT: E 76 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7499 (ttt90) REVERT: E 81 CYS cc_start: 0.7311 (t) cc_final: 0.7073 (t) REVERT: E 133 GLU cc_start: 0.8362 (tp30) cc_final: 0.7400 (tp30) REVERT: E 134 ASP cc_start: 0.7315 (m-30) cc_final: 0.6970 (m-30) REVERT: E 180 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8407 (mmmt) REVERT: E 191 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7909 (ttp-110) REVERT: E 205 SER cc_start: 0.8615 (t) cc_final: 0.8289 (t) REVERT: E 237 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8197 (tt) REVERT: E 279 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8933 (ttmm) REVERT: E 282 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7789 (tpp80) REVERT: E 360 PHE cc_start: 0.7313 (m-80) cc_final: 0.6996 (m-80) REVERT: F 26 TYR cc_start: 0.7659 (t80) cc_final: 0.6859 (t80) REVERT: F 81 CYS cc_start: 0.7215 (t) cc_final: 0.6962 (t) REVERT: F 133 GLU cc_start: 0.8238 (tp30) cc_final: 0.7164 (tp30) REVERT: F 141 LEU cc_start: 0.8883 (tp) cc_final: 0.8673 (tt) REVERT: F 210 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.6564 (mmt-90) REVERT: F 248 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.4719 (mtm) REVERT: F 277 LEU cc_start: 0.9456 (tp) cc_final: 0.9144 (mm) REVERT: F 321 ASP cc_start: 0.8528 (m-30) cc_final: 0.8110 (m-30) REVERT: F 354 ASP cc_start: 0.7921 (t0) cc_final: 0.6658 (t0) REVERT: F 360 PHE cc_start: 0.7671 (m-10) cc_final: 0.7470 (m-80) REVERT: F 368 MET cc_start: 0.8360 (ttt) cc_final: 0.8143 (ttt) REVERT: F 444 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: G 30 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (t0) REVERT: G 57 GLU cc_start: 0.8365 (tp30) cc_final: 0.8030 (mm-30) REVERT: G 146 GLN cc_start: 0.8750 (tp40) cc_final: 0.8423 (tp-100) REVERT: G 197 THR cc_start: 0.8924 (p) cc_final: 0.8672 (p) REVERT: G 315 LEU cc_start: 0.9371 (tp) cc_final: 0.9063 (tt) REVERT: G 321 ASP cc_start: 0.8297 (m-30) cc_final: 0.7688 (m-30) REVERT: G 331 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6855 (mmmt) REVERT: G 363 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: G 434 LEU cc_start: 0.8423 (tt) cc_final: 0.7529 (mp) REVERT: G 441 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8432 (mm) REVERT: G 443 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7792 (ttt-90) REVERT: G 444 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8984 (pp20) REVERT: H 106 GLU cc_start: 0.8433 (tt0) cc_final: 0.7912 (tt0) REVERT: H 146 GLN cc_start: 0.8610 (tp40) cc_final: 0.8323 (tp-100) REVERT: H 184 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7391 (mpt180) REVERT: H 255 LYS cc_start: 0.9206 (tmtt) cc_final: 0.8417 (tptp) REVERT: H 259 MET cc_start: 0.8669 (mmp) cc_final: 0.8392 (mmm) REVERT: H 301 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8638 (mm-40) REVERT: H 321 ASP cc_start: 0.8377 (m-30) cc_final: 0.8137 (m-30) REVERT: H 465 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: I 110 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6485 (mp) REVERT: J 58 GLN cc_start: 0.8299 (pm20) cc_final: 0.6902 (tt0) REVERT: J 60 ASN cc_start: 0.6852 (t160) cc_final: 0.6515 (t0) REVERT: J 112 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5553 (mt) REVERT: J 113 GLU cc_start: 0.2851 (OUTLIER) cc_final: 0.1994 (mm-30) REVERT: J 114 ARG cc_start: 0.5584 (tpt90) cc_final: 0.4399 (mpt180) REVERT: J 163 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (mp) REVERT: K 28 TRP cc_start: 0.6898 (t60) cc_final: 0.6454 (t60) REVERT: K 66 MET cc_start: 0.7665 (tmm) cc_final: 0.7138 (tmm) REVERT: K 97 ARG cc_start: 0.6388 (mtm-85) cc_final: 0.5362 (mtm-85) REVERT: K 98 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5547 (tt0) REVERT: K 114 ARG cc_start: 0.5908 (tpt170) cc_final: 0.4786 (mtt-85) REVERT: K 187 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: K 191 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6420 (mt) REVERT: L 27 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7635 (mpp80) REVERT: L 55 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6358 (mt-10) REVERT: L 58 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.6748 (tt0) REVERT: L 59 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: L 60 ASN cc_start: 0.7093 (OUTLIER) cc_final: 0.6678 (t0) REVERT: L 72 ILE cc_start: 0.8292 (pp) cc_final: 0.8055 (tt) REVERT: L 86 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6464 (mm-40) REVERT: L 97 ARG cc_start: 0.6098 (mtm180) cc_final: 0.5295 (ptt90) REVERT: L 98 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5736 (tp30) REVERT: L 102 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6566 (tp30) REVERT: L 106 LEU cc_start: 0.8462 (mp) cc_final: 0.8081 (mt) REVERT: L 113 GLU cc_start: 0.7017 (pt0) cc_final: 0.6406 (tp30) REVERT: L 139 GLU cc_start: 0.7358 (tt0) cc_final: 0.7022 (pm20) REVERT: L 158 GLN cc_start: 0.5184 (OUTLIER) cc_final: 0.4548 (tp40) REVERT: L 168 ARG cc_start: 0.5480 (tpt170) cc_final: 0.5277 (tpp-160) REVERT: L 172 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.4496 (tpp-160) REVERT: M 27 ARG cc_start: 0.7861 (mpt-90) cc_final: 0.7241 (mpp80) REVERT: M 58 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: M 87 GLU cc_start: 0.4943 (OUTLIER) cc_final: 0.4700 (tp30) REVERT: M 113 GLU cc_start: 0.6725 (pt0) cc_final: 0.6281 (tp30) REVERT: M 139 GLU cc_start: 0.7695 (tt0) cc_final: 0.6882 (pp20) REVERT: M 160 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.6988 (ptt-90) REVERT: N 27 ARG cc_start: 0.8060 (mpt-90) cc_final: 0.7317 (mpp80) REVERT: N 49 PHE cc_start: 0.7456 (t80) cc_final: 0.6993 (t80) REVERT: N 60 ASN cc_start: 0.7258 (t160) cc_final: 0.6898 (t0) REVERT: N 66 MET cc_start: 0.8317 (tmm) cc_final: 0.8115 (tmm) REVERT: N 122 ARG cc_start: 0.6172 (ttp80) cc_final: 0.4222 (ttp80) REVERT: N 172 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7493 (tpm170) REVERT: O 27 ARG cc_start: 0.8100 (mpt-90) cc_final: 0.7770 (mpt-90) REVERT: O 60 ASN cc_start: 0.7071 (t160) cc_final: 0.6616 (t0) REVERT: O 64 VAL cc_start: 0.9281 (p) cc_final: 0.8856 (t) REVERT: O 110 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5500 (tm) REVERT: O 114 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.5190 (tpp-160) REVERT: P 13 GLU cc_start: 0.6989 (pp20) cc_final: 0.4218 (mp0) REVERT: P 14 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.4707 (tpt-90) REVERT: P 122 ARG cc_start: 0.5964 (ttp80) cc_final: 0.4482 (ttp80) REVERT: P 155 ARG cc_start: 0.4603 (OUTLIER) cc_final: 0.3922 (mtp85) REVERT: P 165 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6412 (pt0) outliers start: 603 outliers final: 366 residues processed: 1898 average time/residue: 0.2470 time to fit residues: 735.0556 Evaluate side-chains 1279 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 417 poor density : 862 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.0970 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 6.9990 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 112 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 146 GLN C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN D 112 ASN D 146 GLN D 160 ASN D 202 ASN D 284 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN E 83 HIS E 112 ASN E 160 ASN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN F 83 HIS F 150 HIS F 160 ASN F 209 GLN F 274 ASN F 304 HIS F 324 HIS G 83 HIS G 112 ASN G 146 GLN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 426 GLN H 112 ASN H 146 GLN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 HIS J 86 GLN K 86 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN M 46 GLN M 86 GLN M 152 GLN N 67 GLN O 46 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 152 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.161243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127989 restraints weight = 80980.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131367 restraints weight = 44545.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133491 restraints weight = 29439.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134848 restraints weight = 22735.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135619 restraints weight = 19482.306| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 40680 Z= 0.178 Angle : 0.831 15.205 55071 Z= 0.425 Chirality : 0.049 0.341 5917 Planarity : 0.007 0.147 7264 Dihedral : 7.035 168.864 5490 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.13 % Favored : 90.51 % Rotamer: Outliers : 0.34 % Allowed : 4.70 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.10), residues: 4993 helix: -1.38 (0.10), residues: 2113 sheet: -2.67 (0.24), residues: 328 loop : -3.14 (0.10), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 292 TYR 0.023 0.002 TYR I 69 PHE 0.034 0.003 PHE D 215 TRP 0.036 0.002 TRP M 28 HIS 0.013 0.001 HIS G 383 Details of bonding type rmsd covalent geometry : bond 0.00405 (40657) covalent geometry : angle 0.83129 (55071) hydrogen bonds : bond 0.04314 ( 1364) hydrogen bonds : angle 5.43316 ( 3972) Misc. bond : bond 0.00765 ( 23) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1261 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7254 (m-80) cc_final: 0.6511 (m-80) REVERT: A 26 TYR cc_start: 0.7472 (t80) cc_final: 0.6918 (t80) REVERT: A 67 TRP cc_start: 0.7296 (p-90) cc_final: 0.6564 (p-90) REVERT: A 106 GLU cc_start: 0.8338 (tt0) cc_final: 0.8069 (tt0) REVERT: A 184 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7929 (mtp180) REVERT: A 228 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 246 GLU cc_start: 0.8579 (tp30) cc_final: 0.8251 (tp30) REVERT: A 248 MET cc_start: 0.8633 (mmp) cc_final: 0.8360 (mmt) REVERT: A 284 ASN cc_start: 0.8687 (t0) cc_final: 0.8168 (t0) REVERT: A 344 ASP cc_start: 0.8137 (t70) cc_final: 0.7593 (t70) REVERT: A 422 GLU cc_start: 0.7971 (pt0) cc_final: 0.7412 (mm-30) REVERT: A 424 CYS cc_start: 0.8982 (m) cc_final: 0.7761 (t) REVERT: B 34 LEU cc_start: 0.7676 (tp) cc_final: 0.7008 (tp) REVERT: B 122 PHE cc_start: 0.7296 (m-80) cc_final: 0.6988 (m-80) REVERT: B 240 THR cc_start: 0.9163 (m) cc_final: 0.8492 (p) REVERT: B 248 MET cc_start: 0.6441 (mtt) cc_final: 0.6165 (mpp) REVERT: B 259 MET cc_start: 0.9105 (mmp) cc_final: 0.8658 (mmt) REVERT: B 364 ASP cc_start: 0.9117 (t70) cc_final: 0.8813 (t0) REVERT: B 389 GLU cc_start: 0.8426 (tt0) cc_final: 0.7682 (tp30) REVERT: C 30 ASP cc_start: 0.8014 (p0) cc_final: 0.7762 (t0) REVERT: C 106 GLU cc_start: 0.8119 (tt0) cc_final: 0.7811 (tt0) REVERT: C 125 LYS cc_start: 0.7695 (mmpt) cc_final: 0.6657 (pttm) REVERT: C 247 MET cc_start: 0.8703 (tpp) cc_final: 0.8131 (tpp) REVERT: C 291 HIS cc_start: 0.8946 (t-90) cc_final: 0.7970 (t-90) REVERT: C 301 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8439 (mm-40) REVERT: C 344 ASP cc_start: 0.8704 (t0) cc_final: 0.8131 (t0) REVERT: D 22 TYR cc_start: 0.7357 (m-80) cc_final: 0.6910 (m-80) REVERT: D 26 TYR cc_start: 0.7708 (t80) cc_final: 0.7243 (t80) REVERT: D 57 GLU cc_start: 0.8250 (tp30) cc_final: 0.7876 (mm-30) REVERT: D 106 GLU cc_start: 0.8099 (tt0) cc_final: 0.7791 (tt0) REVERT: D 162 TYR cc_start: 0.7885 (m-10) cc_final: 0.7458 (m-10) REVERT: D 166 MET cc_start: 0.7505 (mtp) cc_final: 0.6669 (mtp) REVERT: D 181 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.6509 (p0) REVERT: D 247 MET cc_start: 0.9037 (ttm) cc_final: 0.8389 (tmm) REVERT: D 255 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8730 (tptt) REVERT: D 281 CYS cc_start: 0.9267 (m) cc_final: 0.8959 (m) REVERT: D 344 ASP cc_start: 0.7996 (t0) cc_final: 0.7700 (t0) REVERT: D 452 LEU cc_start: 0.8986 (tp) cc_final: 0.8750 (tp) REVERT: E 22 TYR cc_start: 0.7305 (m-80) cc_final: 0.6651 (m-80) REVERT: E 26 TYR cc_start: 0.7701 (t80) cc_final: 0.6849 (t80) REVERT: E 125 LYS cc_start: 0.7886 (mmpt) cc_final: 0.6937 (pttm) REVERT: E 184 ARG cc_start: 0.8396 (mtt90) cc_final: 0.8111 (mtt-85) REVERT: E 205 SER cc_start: 0.8142 (t) cc_final: 0.7424 (t) REVERT: E 364 ASP cc_start: 0.9187 (t0) cc_final: 0.8956 (t0) REVERT: E 383 HIS cc_start: 0.8127 (m-70) cc_final: 0.7779 (m-70) REVERT: E 444 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8719 (pm20) REVERT: F 22 TYR cc_start: 0.7184 (m-80) cc_final: 0.6546 (m-80) REVERT: F 26 TYR cc_start: 0.7719 (t80) cc_final: 0.6824 (t80) REVERT: F 81 CYS cc_start: 0.6272 (t) cc_final: 0.5917 (t) REVERT: F 133 GLU cc_start: 0.8176 (tp30) cc_final: 0.7544 (tp30) REVERT: F 184 ARG cc_start: 0.8323 (mmt180) cc_final: 0.7825 (mmm-85) REVERT: F 209 GLN cc_start: 0.8608 (tm130) cc_final: 0.7866 (tm-30) REVERT: F 247 MET cc_start: 0.9036 (ttm) cc_final: 0.8645 (mmm) REVERT: F 291 HIS cc_start: 0.8398 (t-90) cc_final: 0.7776 (t-90) REVERT: F 344 ASP cc_start: 0.8534 (t0) cc_final: 0.7592 (t0) REVERT: G 22 TYR cc_start: 0.7582 (m-80) cc_final: 0.6918 (m-80) REVERT: G 34 LEU cc_start: 0.8561 (tp) cc_final: 0.8177 (tt) REVERT: G 57 GLU cc_start: 0.8371 (tp30) cc_final: 0.8096 (mm-30) REVERT: G 85 GLU cc_start: 0.7880 (tt0) cc_final: 0.7584 (mt-10) REVERT: G 106 GLU cc_start: 0.8367 (tt0) cc_final: 0.7861 (tt0) REVERT: G 133 GLU cc_start: 0.8309 (tp30) cc_final: 0.8107 (tp30) REVERT: G 203 ILE cc_start: 0.9173 (mm) cc_final: 0.8886 (mm) REVERT: G 204 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7765 (m-40) REVERT: G 246 GLU cc_start: 0.8658 (tp30) cc_final: 0.7700 (tm-30) REVERT: G 363 GLN cc_start: 0.8935 (pp30) cc_final: 0.8554 (pp30) REVERT: G 430 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7411 (mt-10) REVERT: H 22 TYR cc_start: 0.7032 (m-80) cc_final: 0.6546 (m-80) REVERT: H 184 ARG cc_start: 0.8315 (mmt90) cc_final: 0.7818 (mmt-90) REVERT: H 205 SER cc_start: 0.8386 (t) cc_final: 0.8038 (t) REVERT: H 247 MET cc_start: 0.8726 (ttm) cc_final: 0.8224 (mmm) REVERT: H 321 ASP cc_start: 0.8355 (m-30) cc_final: 0.8154 (m-30) REVERT: H 331 LYS cc_start: 0.7772 (mtpp) cc_final: 0.7404 (mmmt) REVERT: H 382 TRP cc_start: 0.8540 (m100) cc_final: 0.7925 (m100) REVERT: H 464 PHE cc_start: 0.5047 (t80) cc_final: 0.4688 (t80) REVERT: I 179 SER cc_start: 0.4773 (t) cc_final: 0.4341 (t) REVERT: K 39 LEU cc_start: 0.8618 (tp) cc_final: 0.8415 (mt) REVERT: K 62 ILE cc_start: 0.8175 (mm) cc_final: 0.7600 (pt) REVERT: K 63 THR cc_start: 0.9006 (m) cc_final: 0.8730 (m) REVERT: K 97 ARG cc_start: 0.6643 (mtm-85) cc_final: 0.5480 (mtm-85) REVERT: K 114 ARG cc_start: 0.6517 (tpt170) cc_final: 0.5864 (mtt-85) REVERT: L 27 ARG cc_start: 0.8070 (mpt-90) cc_final: 0.7655 (mpp80) REVERT: L 58 GLN cc_start: 0.8037 (mp10) cc_final: 0.7013 (tt0) REVERT: L 60 ASN cc_start: 0.7041 (t0) cc_final: 0.6800 (t0) REVERT: L 159 GLU cc_start: 0.5203 (tt0) cc_final: 0.4938 (tt0) REVERT: M 27 ARG cc_start: 0.8222 (mpt-90) cc_final: 0.5314 (tpp-160) REVERT: M 114 ARG cc_start: 0.4526 (tpp80) cc_final: 0.3866 (tpm170) REVERT: M 160 ARG cc_start: 0.7544 (mmt-90) cc_final: 0.6946 (ptt-90) REVERT: N 63 THR cc_start: 0.9200 (m) cc_final: 0.8942 (m) REVERT: N 67 GLN cc_start: 0.6848 (tt0) cc_final: 0.6404 (tm-30) REVERT: P 113 GLU cc_start: 0.7087 (tp30) cc_final: 0.6029 (pt0) REVERT: P 159 GLU cc_start: 0.6369 (tt0) cc_final: 0.6068 (mt-10) REVERT: P 165 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6406 (pm20) outliers start: 14 outliers final: 2 residues processed: 1271 average time/residue: 0.2280 time to fit residues: 467.6289 Evaluate side-chains 849 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 844 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 174 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 438 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 475 optimal weight: 20.0000 chunk 8 optimal weight: 0.0050 chunk 453 optimal weight: 20.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 291 HIS B 324 HIS C 112 ASN C 181 ASN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 202 ASN E 209 GLN E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 301 GLN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS H 324 HIS J 46 GLN ** J 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 178 GLN N 152 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121614 restraints weight = 83988.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125536 restraints weight = 48629.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126574 restraints weight = 31150.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127394 restraints weight = 25811.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127622 restraints weight = 24826.110| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 40680 Z= 0.198 Angle : 0.769 12.501 55071 Z= 0.394 Chirality : 0.047 0.239 5917 Planarity : 0.005 0.146 7264 Dihedral : 6.611 173.709 5490 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.03 % Favored : 89.69 % Rotamer: Outliers : 0.19 % Allowed : 4.80 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.11), residues: 4993 helix: -0.85 (0.11), residues: 2102 sheet: -2.62 (0.24), residues: 376 loop : -2.79 (0.11), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 104 TYR 0.027 0.002 TYR E 236 PHE 0.029 0.003 PHE M 49 TRP 0.026 0.002 TRP E 280 HIS 0.006 0.001 HIS C 289 Details of bonding type rmsd covalent geometry : bond 0.00461 (40657) covalent geometry : angle 0.76935 (55071) hydrogen bonds : bond 0.04014 ( 1364) hydrogen bonds : angle 5.01035 ( 3972) Misc. bond : bond 0.00608 ( 23) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1080 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7446 (m-80) cc_final: 0.6499 (m-80) REVERT: A 26 TYR cc_start: 0.7503 (t80) cc_final: 0.7060 (t80) REVERT: A 30 ASP cc_start: 0.7818 (p0) cc_final: 0.7450 (p0) REVERT: A 67 TRP cc_start: 0.7459 (p-90) cc_final: 0.6818 (p-90) REVERT: A 246 GLU cc_start: 0.8611 (tp30) cc_final: 0.8286 (tp30) REVERT: A 284 ASN cc_start: 0.8824 (t0) cc_final: 0.8371 (t0) REVERT: A 321 ASP cc_start: 0.8195 (m-30) cc_final: 0.7816 (m-30) REVERT: A 364 ASP cc_start: 0.9220 (t0) cc_final: 0.9004 (t0) REVERT: A 382 TRP cc_start: 0.8349 (m100) cc_final: 0.7924 (m-10) REVERT: A 422 GLU cc_start: 0.7920 (pt0) cc_final: 0.7601 (mm-30) REVERT: A 440 ASP cc_start: 0.8569 (t0) cc_final: 0.8127 (t0) REVERT: B 146 GLN cc_start: 0.8636 (tp40) cc_final: 0.8340 (tp-100) REVERT: B 184 ARG cc_start: 0.8360 (mtp180) cc_final: 0.8020 (mtt-85) REVERT: B 255 LYS cc_start: 0.9316 (tmmt) cc_final: 0.9050 (tptp) REVERT: B 351 ILE cc_start: 0.9332 (tt) cc_final: 0.9129 (tt) REVERT: B 389 GLU cc_start: 0.8517 (tt0) cc_final: 0.7862 (tp30) REVERT: C 22 TYR cc_start: 0.7596 (m-80) cc_final: 0.7317 (m-80) REVERT: C 106 GLU cc_start: 0.8274 (tt0) cc_final: 0.7967 (tt0) REVERT: C 184 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8159 (mmt180) REVERT: C 203 ILE cc_start: 0.8998 (tt) cc_final: 0.8758 (tp) REVERT: C 321 ASP cc_start: 0.8269 (m-30) cc_final: 0.7973 (m-30) REVERT: C 364 ASP cc_start: 0.9201 (t0) cc_final: 0.8856 (t0) REVERT: C 408 TRP cc_start: 0.7966 (t-100) cc_final: 0.7730 (t-100) REVERT: D 22 TYR cc_start: 0.7475 (m-80) cc_final: 0.6961 (m-80) REVERT: D 26 TYR cc_start: 0.7612 (t80) cc_final: 0.7216 (t80) REVERT: D 30 ASP cc_start: 0.8124 (p0) cc_final: 0.7576 (p0) REVERT: D 106 GLU cc_start: 0.8218 (tt0) cc_final: 0.7895 (tt0) REVERT: D 162 TYR cc_start: 0.8283 (m-10) cc_final: 0.7822 (m-80) REVERT: D 203 ILE cc_start: 0.8778 (tp) cc_final: 0.8431 (tp) REVERT: D 209 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8484 (tm-30) REVERT: D 228 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8491 (tm-30) REVERT: D 236 TYR cc_start: 0.7493 (m-10) cc_final: 0.7152 (m-10) REVERT: D 246 GLU cc_start: 0.8813 (tp30) cc_final: 0.8539 (tp30) REVERT: D 247 MET cc_start: 0.9100 (ttm) cc_final: 0.8398 (tmm) REVERT: D 255 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8723 (tptt) REVERT: D 281 CYS cc_start: 0.9401 (m) cc_final: 0.9166 (m) REVERT: D 364 ASP cc_start: 0.9076 (t0) cc_final: 0.8861 (t0) REVERT: E 22 TYR cc_start: 0.7493 (m-80) cc_final: 0.6830 (m-80) REVERT: E 26 TYR cc_start: 0.7491 (t80) cc_final: 0.6802 (t80) REVERT: E 34 LEU cc_start: 0.8740 (tp) cc_final: 0.8480 (tp) REVERT: E 77 TYR cc_start: 0.9010 (m-10) cc_final: 0.8691 (m-10) REVERT: E 81 CYS cc_start: 0.7272 (t) cc_final: 0.7058 (t) REVERT: E 125 LYS cc_start: 0.8007 (mmpt) cc_final: 0.7128 (pttm) REVERT: E 184 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8034 (mtt-85) REVERT: E 246 GLU cc_start: 0.8658 (tp30) cc_final: 0.8373 (tp30) REVERT: E 291 HIS cc_start: 0.8790 (t-90) cc_final: 0.8080 (t-90) REVERT: E 344 ASP cc_start: 0.8280 (t0) cc_final: 0.8060 (t0) REVERT: E 364 ASP cc_start: 0.9281 (t0) cc_final: 0.9050 (t0) REVERT: F 22 TYR cc_start: 0.7248 (m-80) cc_final: 0.6620 (m-80) REVERT: F 26 TYR cc_start: 0.7393 (t80) cc_final: 0.6846 (t80) REVERT: F 81 CYS cc_start: 0.6493 (t) cc_final: 0.6251 (t) REVERT: F 133 GLU cc_start: 0.8304 (tp30) cc_final: 0.7811 (tm-30) REVERT: F 177 LEU cc_start: 0.8680 (mm) cc_final: 0.8402 (mp) REVERT: F 205 SER cc_start: 0.8718 (t) cc_final: 0.8341 (t) REVERT: F 291 HIS cc_start: 0.8685 (t-90) cc_final: 0.7818 (t-90) REVERT: F 383 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8346 (m90) REVERT: F 389 GLU cc_start: 0.8236 (tt0) cc_final: 0.7777 (tp30) REVERT: F 408 TRP cc_start: 0.7060 (t60) cc_final: 0.6613 (t60) REVERT: F 424 CYS cc_start: 0.9053 (m) cc_final: 0.7655 (t) REVERT: G 22 TYR cc_start: 0.7755 (m-80) cc_final: 0.7045 (m-80) REVERT: G 34 LEU cc_start: 0.9184 (tp) cc_final: 0.8710 (tp) REVERT: G 67 TRP cc_start: 0.7223 (p-90) cc_final: 0.6803 (p-90) REVERT: G 77 TYR cc_start: 0.9053 (m-10) cc_final: 0.8739 (m-10) REVERT: G 85 GLU cc_start: 0.8101 (tt0) cc_final: 0.7670 (mt-10) REVERT: G 133 GLU cc_start: 0.8913 (tp30) cc_final: 0.8084 (tp30) REVERT: G 134 ASP cc_start: 0.7137 (t0) cc_final: 0.6905 (t0) REVERT: G 204 ASN cc_start: 0.8108 (m-40) cc_final: 0.7851 (m-40) REVERT: G 228 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 246 GLU cc_start: 0.8694 (tp30) cc_final: 0.7865 (tm-30) REVERT: G 363 GLN cc_start: 0.9087 (pp30) cc_final: 0.8789 (pp30) REVERT: H 22 TYR cc_start: 0.7081 (m-80) cc_final: 0.6497 (m-80) REVERT: H 154 VAL cc_start: 0.9243 (t) cc_final: 0.8950 (t) REVERT: H 247 MET cc_start: 0.8783 (ttm) cc_final: 0.8173 (mmm) REVERT: H 331 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7311 (mmmt) REVERT: H 351 ILE cc_start: 0.9372 (tp) cc_final: 0.9165 (tp) REVERT: H 364 ASP cc_start: 0.9212 (t0) cc_final: 0.8943 (t0) REVERT: H 382 TRP cc_start: 0.8483 (m100) cc_final: 0.8189 (m100) REVERT: H 464 PHE cc_start: 0.4877 (t80) cc_final: 0.4619 (t80) REVERT: I 179 SER cc_start: 0.4626 (t) cc_final: 0.4236 (t) REVERT: J 99 LEU cc_start: 0.4441 (pp) cc_final: 0.3950 (pp) REVERT: K 39 LEU cc_start: 0.8407 (tp) cc_final: 0.8120 (mt) REVERT: K 97 ARG cc_start: 0.6529 (mtm-85) cc_final: 0.5576 (mtm-85) REVERT: K 114 ARG cc_start: 0.6647 (tpt170) cc_final: 0.5757 (mtt180) REVERT: L 27 ARG cc_start: 0.7871 (mpt-90) cc_final: 0.7351 (mpp80) REVERT: L 62 ILE cc_start: 0.7789 (mm) cc_final: 0.7574 (mm) REVERT: L 159 GLU cc_start: 0.5344 (mt-10) cc_final: 0.4421 (mp0) REVERT: N 67 GLN cc_start: 0.6923 (tt0) cc_final: 0.6714 (tt0) REVERT: N 102 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8045 (mt-10) REVERT: N 113 GLU cc_start: 0.5711 (pm20) cc_final: 0.5339 (tp30) REVERT: O 50 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8261 (mm-30) REVERT: P 25 GLU cc_start: 0.7580 (tt0) cc_final: 0.7321 (tt0) outliers start: 8 outliers final: 1 residues processed: 1085 average time/residue: 0.2269 time to fit residues: 403.4963 Evaluate side-chains 808 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 806 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 482 optimal weight: 20.0000 chunk 229 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 428 optimal weight: 30.0000 chunk 216 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 209 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN B 83 HIS B 274 ASN B 324 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS F 112 ASN F 181 ASN F 274 ASN ** F 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS I 58 GLN K 101 GLN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN O 86 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117704 restraints weight = 83948.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121416 restraints weight = 48703.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123110 restraints weight = 30811.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123506 restraints weight = 24291.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123818 restraints weight = 23218.112| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 40680 Z= 0.229 Angle : 0.784 10.954 55071 Z= 0.401 Chirality : 0.047 0.290 5917 Planarity : 0.006 0.160 7264 Dihedral : 6.589 174.458 5490 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.93 % Favored : 89.79 % Rotamer: Outliers : 0.02 % Allowed : 5.18 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.11), residues: 4993 helix: -0.66 (0.11), residues: 2092 sheet: -2.51 (0.24), residues: 376 loop : -2.63 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 97 TYR 0.038 0.002 TYR E 236 PHE 0.031 0.003 PHE J 49 TRP 0.024 0.002 TRP I 28 HIS 0.014 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00527 (40657) covalent geometry : angle 0.78377 (55071) hydrogen bonds : bond 0.04043 ( 1364) hydrogen bonds : angle 4.98885 ( 3972) Misc. bond : bond 0.00628 ( 23) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 986 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7686 (m-80) cc_final: 0.6629 (m-80) REVERT: A 26 TYR cc_start: 0.7707 (t80) cc_final: 0.7230 (t80) REVERT: A 67 TRP cc_start: 0.7553 (p-90) cc_final: 0.7009 (p-90) REVERT: A 77 TYR cc_start: 0.9018 (m-10) cc_final: 0.8449 (m-10) REVERT: A 106 GLU cc_start: 0.8438 (tt0) cc_final: 0.7939 (tt0) REVERT: A 246 GLU cc_start: 0.8661 (tp30) cc_final: 0.8379 (tp30) REVERT: A 344 ASP cc_start: 0.8727 (t0) cc_final: 0.8290 (t0) REVERT: A 364 ASP cc_start: 0.9280 (t0) cc_final: 0.8960 (t0) REVERT: A 422 GLU cc_start: 0.7932 (pt0) cc_final: 0.7485 (mm-30) REVERT: A 440 ASP cc_start: 0.8569 (t0) cc_final: 0.8140 (t0) REVERT: B 130 LEU cc_start: 0.9412 (tp) cc_final: 0.9116 (tp) REVERT: B 184 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7997 (mtt-85) REVERT: B 228 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 236 TYR cc_start: 0.7659 (m-10) cc_final: 0.7458 (m-10) REVERT: B 246 GLU cc_start: 0.8894 (tp30) cc_final: 0.8543 (tp30) REVERT: B 364 ASP cc_start: 0.9083 (t0) cc_final: 0.8880 (t0) REVERT: C 22 TYR cc_start: 0.7727 (m-80) cc_final: 0.7259 (m-80) REVERT: C 106 GLU cc_start: 0.8133 (tt0) cc_final: 0.7565 (tt0) REVERT: C 247 MET cc_start: 0.8791 (tpp) cc_final: 0.7871 (tpp) REVERT: C 321 ASP cc_start: 0.8132 (m-30) cc_final: 0.7793 (m-30) REVERT: D 22 TYR cc_start: 0.7549 (m-80) cc_final: 0.7017 (m-80) REVERT: D 26 TYR cc_start: 0.7629 (t80) cc_final: 0.7206 (t80) REVERT: D 30 ASP cc_start: 0.7982 (p0) cc_final: 0.7603 (p0) REVERT: D 85 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 146 GLN cc_start: 0.8980 (tt0) cc_final: 0.8214 (tp-100) REVERT: D 162 TYR cc_start: 0.8342 (m-10) cc_final: 0.7892 (m-80) REVERT: D 203 ILE cc_start: 0.8668 (tp) cc_final: 0.8125 (tp) REVERT: D 209 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8501 (tm-30) REVERT: D 236 TYR cc_start: 0.7790 (m-10) cc_final: 0.7399 (m-10) REVERT: D 255 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8797 (tptt) REVERT: D 283 ASP cc_start: 0.8919 (t0) cc_final: 0.8709 (t70) REVERT: D 346 MET cc_start: 0.9141 (mpp) cc_final: 0.8900 (mpp) REVERT: D 364 ASP cc_start: 0.9149 (t0) cc_final: 0.8871 (t0) REVERT: D 440 ASP cc_start: 0.8663 (t0) cc_final: 0.8278 (p0) REVERT: E 22 TYR cc_start: 0.7398 (m-80) cc_final: 0.6656 (m-80) REVERT: E 26 TYR cc_start: 0.7646 (t80) cc_final: 0.7006 (t80) REVERT: E 125 LYS cc_start: 0.8243 (mmpt) cc_final: 0.7359 (pttm) REVERT: E 184 ARG cc_start: 0.8459 (mtt90) cc_final: 0.8115 (mtt-85) REVERT: E 246 GLU cc_start: 0.8651 (tp30) cc_final: 0.8440 (tp30) REVERT: E 344 ASP cc_start: 0.8348 (t0) cc_final: 0.8126 (t0) REVERT: E 364 ASP cc_start: 0.9309 (t0) cc_final: 0.9105 (t0) REVERT: E 440 ASP cc_start: 0.8840 (t0) cc_final: 0.8404 (t0) REVERT: F 22 TYR cc_start: 0.7216 (m-80) cc_final: 0.6607 (m-80) REVERT: F 26 TYR cc_start: 0.7575 (t80) cc_final: 0.7052 (t80) REVERT: F 106 GLU cc_start: 0.8110 (tt0) cc_final: 0.7637 (tt0) REVERT: F 133 GLU cc_start: 0.8537 (tp30) cc_final: 0.8034 (tm-30) REVERT: F 201 GLU cc_start: 0.7350 (mp0) cc_final: 0.7023 (mp0) REVERT: F 203 ILE cc_start: 0.8353 (mt) cc_final: 0.8131 (mt) REVERT: F 246 GLU cc_start: 0.8935 (tp30) cc_final: 0.8666 (tp30) REVERT: F 248 MET cc_start: 0.6687 (mtm) cc_final: 0.6129 (mtm) REVERT: F 294 MET cc_start: 0.8446 (ptt) cc_final: 0.7913 (ptt) REVERT: F 351 ILE cc_start: 0.9446 (mm) cc_final: 0.8600 (mm) REVERT: F 368 MET cc_start: 0.9202 (tpp) cc_final: 0.8511 (ttt) REVERT: G 22 TYR cc_start: 0.7686 (m-80) cc_final: 0.6996 (m-80) REVERT: G 34 LEU cc_start: 0.9222 (tp) cc_final: 0.8721 (tp) REVERT: G 77 TYR cc_start: 0.9016 (m-10) cc_final: 0.8710 (m-10) REVERT: G 85 GLU cc_start: 0.8033 (tt0) cc_final: 0.7610 (mt-10) REVERT: G 133 GLU cc_start: 0.9044 (tp30) cc_final: 0.8484 (tp30) REVERT: G 146 GLN cc_start: 0.8900 (tt0) cc_final: 0.8139 (tp40) REVERT: G 255 LYS cc_start: 0.9418 (tmmt) cc_final: 0.9141 (tptt) REVERT: G 291 HIS cc_start: 0.8503 (t-90) cc_final: 0.8296 (t-90) REVERT: G 321 ASP cc_start: 0.8325 (m-30) cc_final: 0.7846 (m-30) REVERT: G 343 VAL cc_start: 0.9439 (t) cc_final: 0.9166 (t) REVERT: G 346 MET cc_start: 0.9237 (mpp) cc_final: 0.8872 (mpp) REVERT: G 363 GLN cc_start: 0.9090 (pp30) cc_final: 0.8881 (pp30) REVERT: H 22 TYR cc_start: 0.7116 (m-80) cc_final: 0.6504 (m-80) REVERT: H 184 ARG cc_start: 0.8626 (mmt-90) cc_final: 0.7977 (mmt-90) REVERT: H 205 SER cc_start: 0.8663 (t) cc_final: 0.8186 (p) REVERT: H 247 MET cc_start: 0.8909 (ttm) cc_final: 0.8116 (mmm) REVERT: H 364 ASP cc_start: 0.9241 (t0) cc_final: 0.8938 (t0) REVERT: I 179 SER cc_start: 0.4730 (t) cc_final: 0.4287 (t) REVERT: J 28 TRP cc_start: 0.7381 (t60) cc_final: 0.7177 (t60) REVERT: K 28 TRP cc_start: 0.6637 (t60) cc_final: 0.5745 (t60) REVERT: K 67 GLN cc_start: 0.6481 (tt0) cc_final: 0.6083 (tt0) REVERT: K 114 ARG cc_start: 0.6580 (tpt170) cc_final: 0.5539 (mtt180) REVERT: K 191 LEU cc_start: 0.7496 (tt) cc_final: 0.7102 (mt) REVERT: L 27 ARG cc_start: 0.7983 (mpt-90) cc_final: 0.7428 (mpp80) REVERT: L 50 GLU cc_start: 0.8680 (tp30) cc_final: 0.8212 (tp30) REVERT: L 62 ILE cc_start: 0.7734 (mm) cc_final: 0.7483 (mm) REVERT: L 159 GLU cc_start: 0.5605 (mt-10) cc_final: 0.4761 (mp0) REVERT: M 27 ARG cc_start: 0.7816 (mpt-90) cc_final: 0.4825 (tpp-160) REVERT: M 28 TRP cc_start: 0.6841 (t60) cc_final: 0.6457 (t60) REVERT: M 66 MET cc_start: 0.5815 (ptt) cc_final: 0.5578 (ppp) REVERT: N 27 ARG cc_start: 0.7067 (mpp80) cc_final: 0.6805 (mpp80) REVERT: N 67 GLN cc_start: 0.7009 (tt0) cc_final: 0.6771 (tt0) REVERT: N 113 GLU cc_start: 0.6297 (pm20) cc_final: 0.5625 (tp30) outliers start: 1 outliers final: 0 residues processed: 986 average time/residue: 0.2209 time to fit residues: 357.4978 Evaluate side-chains 750 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 750 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 486 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 433 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 160 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN F 274 ASN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN H 204 ASN H 274 ASN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN K 46 GLN L 67 GLN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 GLN N 86 GLN P 46 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.156709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121949 restraints weight = 82952.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125418 restraints weight = 48764.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127762 restraints weight = 30836.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127593 restraints weight = 25476.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127901 restraints weight = 24202.624| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 40680 Z= 0.155 Angle : 0.726 10.211 55071 Z= 0.367 Chirality : 0.046 0.367 5917 Planarity : 0.006 0.153 7264 Dihedral : 6.737 177.113 5490 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.89 % Favored : 89.85 % Rotamer: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.11), residues: 4993 helix: -0.33 (0.11), residues: 2058 sheet: -2.72 (0.20), residues: 488 loop : -2.53 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 166 TYR 0.031 0.002 TYR E 236 PHE 0.033 0.002 PHE H 464 TRP 0.040 0.001 TRP I 28 HIS 0.014 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00361 (40657) covalent geometry : angle 0.72649 (55071) hydrogen bonds : bond 0.03566 ( 1364) hydrogen bonds : angle 4.75062 ( 3972) Misc. bond : bond 0.00643 ( 23) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1007 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7639 (m-80) cc_final: 0.6662 (m-80) REVERT: A 26 TYR cc_start: 0.7639 (t80) cc_final: 0.7216 (t80) REVERT: A 30 ASP cc_start: 0.7652 (p0) cc_final: 0.7219 (p0) REVERT: A 67 TRP cc_start: 0.7633 (p-90) cc_final: 0.6785 (p-90) REVERT: A 77 TYR cc_start: 0.8835 (m-10) cc_final: 0.8372 (m-10) REVERT: A 106 GLU cc_start: 0.8244 (tt0) cc_final: 0.7740 (tt0) REVERT: A 246 GLU cc_start: 0.8598 (tp30) cc_final: 0.8313 (tp30) REVERT: A 247 MET cc_start: 0.8624 (ttm) cc_final: 0.8346 (mmm) REVERT: A 248 MET cc_start: 0.8785 (mmp) cc_final: 0.8343 (mmt) REVERT: A 291 HIS cc_start: 0.8096 (t-90) cc_final: 0.7881 (t-90) REVERT: A 344 ASP cc_start: 0.8602 (t70) cc_final: 0.8201 (t0) REVERT: A 384 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (ttp) REVERT: A 422 GLU cc_start: 0.7905 (pt0) cc_final: 0.7406 (mm-30) REVERT: A 440 ASP cc_start: 0.8485 (t0) cc_final: 0.8041 (t0) REVERT: B 121 VAL cc_start: 0.9303 (p) cc_final: 0.9066 (t) REVERT: B 130 LEU cc_start: 0.9340 (tp) cc_final: 0.9034 (tp) REVERT: B 246 GLU cc_start: 0.8725 (tp30) cc_final: 0.8419 (tp30) REVERT: B 247 MET cc_start: 0.8766 (ttm) cc_final: 0.8441 (mmm) REVERT: B 364 ASP cc_start: 0.9082 (t0) cc_final: 0.8874 (t0) REVERT: C 22 TYR cc_start: 0.7661 (m-80) cc_final: 0.7194 (m-80) REVERT: C 106 GLU cc_start: 0.7883 (tt0) cc_final: 0.7544 (tt0) REVERT: C 199 ASP cc_start: 0.8138 (m-30) cc_final: 0.7913 (m-30) REVERT: C 259 MET cc_start: 0.9103 (mmp) cc_final: 0.8761 (mmp) REVERT: C 294 MET cc_start: 0.8477 (ptt) cc_final: 0.8010 (ptt) REVERT: D 22 TYR cc_start: 0.7446 (m-80) cc_final: 0.6874 (m-80) REVERT: D 26 TYR cc_start: 0.7511 (t80) cc_final: 0.7246 (t80) REVERT: D 30 ASP cc_start: 0.8155 (p0) cc_final: 0.7824 (p0) REVERT: D 85 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7354 (mt-10) REVERT: D 146 GLN cc_start: 0.8924 (tt0) cc_final: 0.8081 (tp-100) REVERT: D 184 ARG cc_start: 0.8493 (mmt180) cc_final: 0.8240 (mmt-90) REVERT: D 203 ILE cc_start: 0.8465 (tp) cc_final: 0.8037 (tp) REVERT: D 209 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 236 TYR cc_start: 0.7489 (m-10) cc_final: 0.7243 (m-10) REVERT: D 255 LYS cc_start: 0.9077 (tmtt) cc_final: 0.8741 (tptt) REVERT: D 283 ASP cc_start: 0.8954 (t0) cc_final: 0.8737 (t70) REVERT: D 343 VAL cc_start: 0.9498 (t) cc_final: 0.9221 (t) REVERT: D 346 MET cc_start: 0.9131 (mpp) cc_final: 0.8904 (mpp) REVERT: D 364 ASP cc_start: 0.9182 (t0) cc_final: 0.8928 (t0) REVERT: E 22 TYR cc_start: 0.7270 (m-80) cc_final: 0.6534 (m-80) REVERT: E 26 TYR cc_start: 0.7379 (t80) cc_final: 0.7004 (t80) REVERT: E 34 LEU cc_start: 0.8704 (tp) cc_final: 0.8402 (tp) REVERT: E 77 TYR cc_start: 0.8985 (m-10) cc_final: 0.8753 (m-10) REVERT: E 125 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7065 (pttm) REVERT: E 157 ASP cc_start: 0.8920 (m-30) cc_final: 0.8654 (m-30) REVERT: E 162 TYR cc_start: 0.8106 (m-80) cc_final: 0.7550 (m-80) REVERT: E 184 ARG cc_start: 0.8468 (mtt90) cc_final: 0.8028 (mtt-85) REVERT: E 247 MET cc_start: 0.8690 (ttm) cc_final: 0.8357 (tmm) REVERT: E 344 ASP cc_start: 0.8217 (t0) cc_final: 0.7959 (t0) REVERT: E 364 ASP cc_start: 0.9288 (t0) cc_final: 0.9079 (t0) REVERT: F 22 TYR cc_start: 0.7115 (m-80) cc_final: 0.6465 (m-80) REVERT: F 26 TYR cc_start: 0.7264 (t80) cc_final: 0.6948 (t80) REVERT: F 81 CYS cc_start: 0.6464 (t) cc_final: 0.6253 (t) REVERT: F 133 GLU cc_start: 0.8517 (tp30) cc_final: 0.8016 (tm-30) REVERT: F 246 GLU cc_start: 0.8876 (tp30) cc_final: 0.8601 (tp30) REVERT: F 248 MET cc_start: 0.6690 (mtm) cc_final: 0.5851 (mtm) REVERT: F 354 ASP cc_start: 0.8261 (t0) cc_final: 0.7562 (t0) REVERT: G 22 TYR cc_start: 0.7615 (m-80) cc_final: 0.6895 (m-80) REVERT: G 34 LEU cc_start: 0.9157 (tp) cc_final: 0.8641 (tp) REVERT: G 77 TYR cc_start: 0.8827 (m-10) cc_final: 0.8553 (m-10) REVERT: G 133 GLU cc_start: 0.8906 (tp30) cc_final: 0.8407 (tp30) REVERT: G 146 GLN cc_start: 0.8876 (tt0) cc_final: 0.8001 (tp-100) REVERT: G 184 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.7947 (mtt-85) REVERT: G 255 LYS cc_start: 0.9308 (tmmt) cc_final: 0.8916 (tttp) REVERT: G 284 ASN cc_start: 0.8539 (t0) cc_final: 0.7808 (t0) REVERT: G 321 ASP cc_start: 0.8215 (m-30) cc_final: 0.7995 (m-30) REVERT: G 343 VAL cc_start: 0.9523 (t) cc_final: 0.9094 (t) REVERT: G 346 MET cc_start: 0.9250 (mpp) cc_final: 0.8722 (mpp) REVERT: G 408 TRP cc_start: 0.7395 (t-100) cc_final: 0.7111 (t-100) REVERT: H 22 TYR cc_start: 0.7291 (m-80) cc_final: 0.6727 (m-80) REVERT: H 105 PHE cc_start: 0.8993 (m-80) cc_final: 0.8589 (m-80) REVERT: H 184 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8122 (mmt-90) REVERT: H 205 SER cc_start: 0.8629 (t) cc_final: 0.8127 (p) REVERT: H 239 VAL cc_start: 0.9555 (m) cc_final: 0.9315 (p) REVERT: H 247 MET cc_start: 0.8806 (ttm) cc_final: 0.8223 (mmm) REVERT: H 255 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8810 (tptp) REVERT: H 364 ASP cc_start: 0.9215 (t0) cc_final: 0.8950 (t0) REVERT: I 62 ILE cc_start: 0.7993 (mm) cc_final: 0.7731 (mm) REVERT: I 179 SER cc_start: 0.4972 (t) cc_final: 0.4626 (t) REVERT: K 67 GLN cc_start: 0.6411 (tt0) cc_final: 0.6044 (tt0) REVERT: K 114 ARG cc_start: 0.6726 (tpt170) cc_final: 0.5577 (mtt180) REVERT: K 189 LEU cc_start: 0.7650 (pt) cc_final: 0.7203 (pt) REVERT: K 191 LEU cc_start: 0.7564 (tt) cc_final: 0.7130 (mt) REVERT: L 27 ARG cc_start: 0.8007 (mpt-90) cc_final: 0.7564 (mpp80) REVERT: L 159 GLU cc_start: 0.5665 (mt-10) cc_final: 0.4785 (mp0) REVERT: L 168 ARG cc_start: 0.7343 (tmm-80) cc_final: 0.7086 (ttp-170) REVERT: M 27 ARG cc_start: 0.7784 (mpt-90) cc_final: 0.4807 (tpp-160) REVERT: N 27 ARG cc_start: 0.7166 (mpp80) cc_final: 0.6945 (mpp80) REVERT: N 67 GLN cc_start: 0.6993 (tt0) cc_final: 0.6736 (tt0) REVERT: N 113 GLU cc_start: 0.6144 (pm20) cc_final: 0.5682 (tp30) REVERT: O 28 TRP cc_start: 0.7280 (t60) cc_final: 0.6959 (t60) REVERT: O 97 ARG cc_start: 0.6859 (ptp-170) cc_final: 0.5294 (ptp-170) REVERT: O 159 GLU cc_start: 0.5652 (mt-10) cc_final: 0.4458 (mp0) REVERT: P 28 TRP cc_start: 0.7455 (t60) cc_final: 0.6653 (t60) REVERT: P 159 GLU cc_start: 0.5888 (mt-10) cc_final: 0.4419 (mp0) outliers start: 4 outliers final: 1 residues processed: 1009 average time/residue: 0.2153 time to fit residues: 358.8696 Evaluate side-chains 769 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 767 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 272 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 184 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 chunk 488 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 274 ASN B 291 HIS ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 181 ASN F 274 ASN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 HIS G 324 HIS G 363 GLN H 150 HIS H 274 ASN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 322 HIS I 58 GLN K 46 GLN L 60 ASN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN ** O 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.153130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119218 restraints weight = 81675.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.122807 restraints weight = 46891.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125193 restraints weight = 28894.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125020 restraints weight = 23238.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125252 restraints weight = 22133.332| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 40680 Z= 0.172 Angle : 0.727 11.615 55071 Z= 0.368 Chirality : 0.046 0.224 5917 Planarity : 0.007 0.426 7264 Dihedral : 6.484 176.545 5490 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.73 % Favored : 90.01 % Rotamer: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 4993 helix: -0.29 (0.11), residues: 2084 sheet: -2.65 (0.20), residues: 488 loop : -2.48 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 166 TYR 0.020 0.002 TYR I 69 PHE 0.035 0.002 PHE F 266 TRP 0.027 0.002 TRP A 408 HIS 0.012 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00398 (40657) covalent geometry : angle 0.72663 (55071) hydrogen bonds : bond 0.03583 ( 1364) hydrogen bonds : angle 4.68718 ( 3972) Misc. bond : bond 0.00660 ( 23) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 951 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7757 (m-80) cc_final: 0.6552 (m-80) REVERT: A 26 TYR cc_start: 0.7632 (t80) cc_final: 0.7273 (t80) REVERT: A 30 ASP cc_start: 0.7753 (p0) cc_final: 0.7320 (p0) REVERT: A 67 TRP cc_start: 0.7569 (p-90) cc_final: 0.6803 (p-90) REVERT: A 77 TYR cc_start: 0.8920 (m-10) cc_final: 0.8417 (m-10) REVERT: A 106 GLU cc_start: 0.8303 (tt0) cc_final: 0.7966 (tt0) REVERT: A 233 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8182 (mmmt) REVERT: A 246 GLU cc_start: 0.8644 (tp30) cc_final: 0.8314 (tp30) REVERT: A 248 MET cc_start: 0.8785 (mmp) cc_final: 0.8439 (mmt) REVERT: A 344 ASP cc_start: 0.8457 (t70) cc_final: 0.8215 (t0) REVERT: A 363 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8868 (tm-30) REVERT: A 422 GLU cc_start: 0.7893 (pt0) cc_final: 0.7651 (mm-30) REVERT: A 440 ASP cc_start: 0.8492 (t0) cc_final: 0.8041 (t0) REVERT: B 121 VAL cc_start: 0.9316 (p) cc_final: 0.9056 (t) REVERT: B 130 LEU cc_start: 0.9373 (tp) cc_final: 0.9059 (tp) REVERT: B 146 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8526 (tp-100) REVERT: B 190 LEU cc_start: 0.9447 (tt) cc_final: 0.9245 (tt) REVERT: B 246 GLU cc_start: 0.8742 (tp30) cc_final: 0.8523 (tp30) REVERT: B 247 MET cc_start: 0.8842 (ttm) cc_final: 0.8423 (mmm) REVERT: B 364 ASP cc_start: 0.9088 (t0) cc_final: 0.8861 (t0) REVERT: C 22 TYR cc_start: 0.7789 (m-80) cc_final: 0.7246 (m-80) REVERT: C 106 GLU cc_start: 0.7892 (tt0) cc_final: 0.7510 (tt0) REVERT: C 199 ASP cc_start: 0.8316 (m-30) cc_final: 0.8046 (m-30) REVERT: C 204 ASN cc_start: 0.8345 (m-40) cc_final: 0.7946 (m-40) REVERT: C 259 MET cc_start: 0.9049 (mmp) cc_final: 0.8777 (mmp) REVERT: C 294 MET cc_start: 0.8491 (ptt) cc_final: 0.8000 (ptt) REVERT: C 422 GLU cc_start: 0.8427 (pt0) cc_final: 0.8218 (mm-30) REVERT: D 22 TYR cc_start: 0.7540 (m-80) cc_final: 0.7135 (m-80) REVERT: D 26 TYR cc_start: 0.7514 (t80) cc_final: 0.7178 (t80) REVERT: D 30 ASP cc_start: 0.7910 (p0) cc_final: 0.7503 (p0) REVERT: D 146 GLN cc_start: 0.8984 (tt0) cc_final: 0.8123 (tp-100) REVERT: D 209 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8703 (tm-30) REVERT: D 236 TYR cc_start: 0.7588 (m-10) cc_final: 0.7298 (m-10) REVERT: D 283 ASP cc_start: 0.8954 (t0) cc_final: 0.8685 (t70) REVERT: D 364 ASP cc_start: 0.9177 (t0) cc_final: 0.8862 (t0) REVERT: D 440 ASP cc_start: 0.8492 (t0) cc_final: 0.8197 (p0) REVERT: E 22 TYR cc_start: 0.7316 (m-80) cc_final: 0.6413 (m-80) REVERT: E 26 TYR cc_start: 0.7269 (t80) cc_final: 0.6889 (t80) REVERT: E 34 LEU cc_start: 0.8767 (tp) cc_final: 0.8458 (tp) REVERT: E 77 TYR cc_start: 0.9044 (m-10) cc_final: 0.8742 (m-10) REVERT: E 125 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7181 (pttm) REVERT: E 309 ARG cc_start: 0.8636 (ptp-110) cc_final: 0.8128 (ptp-170) REVERT: E 351 ILE cc_start: 0.9287 (tt) cc_final: 0.9045 (mt) REVERT: E 440 ASP cc_start: 0.8883 (t0) cc_final: 0.8466 (t0) REVERT: F 22 TYR cc_start: 0.7219 (m-80) cc_final: 0.6464 (m-80) REVERT: F 26 TYR cc_start: 0.7216 (t80) cc_final: 0.6916 (t80) REVERT: F 81 CYS cc_start: 0.6446 (t) cc_final: 0.6238 (t) REVERT: F 133 GLU cc_start: 0.8599 (tp30) cc_final: 0.7971 (tm-30) REVERT: F 246 GLU cc_start: 0.8887 (tp30) cc_final: 0.8582 (tp30) REVERT: F 247 MET cc_start: 0.8813 (ttm) cc_final: 0.8578 (ttm) REVERT: F 248 MET cc_start: 0.6740 (mtm) cc_final: 0.5983 (mtm) REVERT: F 354 ASP cc_start: 0.8202 (t0) cc_final: 0.7504 (t0) REVERT: G 22 TYR cc_start: 0.7662 (m-80) cc_final: 0.6912 (m-80) REVERT: G 34 LEU cc_start: 0.9176 (tp) cc_final: 0.8650 (tp) REVERT: G 77 TYR cc_start: 0.8837 (m-10) cc_final: 0.8508 (m-10) REVERT: G 133 GLU cc_start: 0.8985 (tp30) cc_final: 0.8458 (tp30) REVERT: G 146 GLN cc_start: 0.8932 (tt0) cc_final: 0.8042 (tp-100) REVERT: G 228 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8497 (tm-30) REVERT: G 255 LYS cc_start: 0.9347 (tmmt) cc_final: 0.9080 (tttp) REVERT: G 284 ASN cc_start: 0.8718 (t0) cc_final: 0.7981 (t0) REVERT: G 321 ASP cc_start: 0.8311 (m-30) cc_final: 0.8032 (m-30) REVERT: G 343 VAL cc_start: 0.9552 (t) cc_final: 0.9155 (t) REVERT: G 346 MET cc_start: 0.9346 (mpp) cc_final: 0.8832 (mpp) REVERT: G 382 TRP cc_start: 0.8632 (m100) cc_final: 0.8349 (m100) REVERT: G 408 TRP cc_start: 0.7410 (t-100) cc_final: 0.7108 (t-100) REVERT: H 22 TYR cc_start: 0.7352 (m-80) cc_final: 0.6781 (m-80) REVERT: H 130 LEU cc_start: 0.9281 (tp) cc_final: 0.9075 (tp) REVERT: H 184 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8143 (mmt-90) REVERT: H 205 SER cc_start: 0.8773 (t) cc_final: 0.8177 (p) REVERT: H 247 MET cc_start: 0.8818 (ttm) cc_final: 0.8186 (mmm) REVERT: H 255 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8716 (tptp) REVERT: H 351 ILE cc_start: 0.9394 (tp) cc_final: 0.9151 (tt) REVERT: H 361 PHE cc_start: 0.7874 (m-80) cc_final: 0.7254 (m-80) REVERT: H 364 ASP cc_start: 0.9193 (t0) cc_final: 0.8944 (t0) REVERT: I 121 ILE cc_start: 0.7857 (tp) cc_final: 0.7651 (tp) REVERT: I 179 SER cc_start: 0.5264 (t) cc_final: 0.4880 (t) REVERT: K 67 GLN cc_start: 0.6418 (tt0) cc_final: 0.6048 (tt0) REVERT: K 114 ARG cc_start: 0.6747 (tpt170) cc_final: 0.5571 (mtt180) REVERT: K 191 LEU cc_start: 0.7760 (tt) cc_final: 0.7273 (mt) REVERT: L 27 ARG cc_start: 0.7990 (mpt-90) cc_final: 0.7378 (mpp80) REVERT: L 159 GLU cc_start: 0.5824 (mt-10) cc_final: 0.4857 (mp0) REVERT: M 27 ARG cc_start: 0.7880 (mpt-90) cc_final: 0.4935 (tpp-160) REVERT: N 27 ARG cc_start: 0.7325 (mpp80) cc_final: 0.4113 (tpp-160) REVERT: N 97 ARG cc_start: 0.5837 (mtm-85) cc_final: 0.4101 (mtm-85) REVERT: N 113 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5460 (tp30) REVERT: O 97 ARG cc_start: 0.6879 (ptp-170) cc_final: 0.5387 (ptp-170) REVERT: O 159 GLU cc_start: 0.5597 (mt-10) cc_final: 0.4411 (mp0) REVERT: P 28 TRP cc_start: 0.7168 (t60) cc_final: 0.6631 (t60) REVERT: P 159 GLU cc_start: 0.6039 (mt-10) cc_final: 0.4550 (mp0) outliers start: 8 outliers final: 0 residues processed: 957 average time/residue: 0.2176 time to fit residues: 343.1191 Evaluate side-chains 738 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 737 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 39 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 492 optimal weight: 30.0000 chunk 313 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 274 ASN B 291 HIS B 380 HIS ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN F 206 GLN F 274 ASN F 301 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 HIS ** G 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116181 restraints weight = 83574.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119673 restraints weight = 49246.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121075 restraints weight = 31276.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121359 restraints weight = 26531.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121557 restraints weight = 24981.243| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 40680 Z= 0.198 Angle : 0.764 12.771 55071 Z= 0.386 Chirality : 0.047 0.343 5917 Planarity : 0.007 0.433 7264 Dihedral : 6.421 176.279 5490 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.05 % Favored : 89.69 % Rotamer: Outliers : 0.12 % Allowed : 1.94 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.11), residues: 4993 helix: -0.32 (0.11), residues: 2056 sheet: -2.67 (0.20), residues: 472 loop : -2.46 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 292 TYR 0.020 0.002 TYR D 94 PHE 0.031 0.003 PHE O 49 TRP 0.029 0.002 TRP I 154 HIS 0.009 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00459 (40657) covalent geometry : angle 0.76415 (55071) hydrogen bonds : bond 0.03760 ( 1364) hydrogen bonds : angle 4.82059 ( 3972) Misc. bond : bond 0.00658 ( 23) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 916 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7822 (m-80) cc_final: 0.6623 (m-80) REVERT: A 26 TYR cc_start: 0.7484 (t80) cc_final: 0.7104 (t80) REVERT: A 30 ASP cc_start: 0.7735 (p0) cc_final: 0.7312 (p0) REVERT: A 67 TRP cc_start: 0.7540 (p-90) cc_final: 0.7081 (p-90) REVERT: A 77 TYR cc_start: 0.8986 (m-10) cc_final: 0.8554 (m-10) REVERT: A 106 GLU cc_start: 0.8272 (tt0) cc_final: 0.7974 (tt0) REVERT: A 246 GLU cc_start: 0.8648 (tp30) cc_final: 0.8325 (tp30) REVERT: A 248 MET cc_start: 0.8755 (mmp) cc_final: 0.8459 (mmt) REVERT: A 344 ASP cc_start: 0.8593 (t70) cc_final: 0.8152 (t0) REVERT: A 351 ILE cc_start: 0.9106 (mt) cc_final: 0.8902 (tt) REVERT: A 440 ASP cc_start: 0.8548 (t0) cc_final: 0.8117 (t0) REVERT: B 121 VAL cc_start: 0.9363 (p) cc_final: 0.9142 (t) REVERT: B 130 LEU cc_start: 0.9399 (tp) cc_final: 0.9052 (tp) REVERT: B 233 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8255 (mmmt) REVERT: B 246 GLU cc_start: 0.8782 (tp30) cc_final: 0.8517 (tp30) REVERT: B 247 MET cc_start: 0.8829 (ttm) cc_final: 0.8438 (mmm) REVERT: B 364 ASP cc_start: 0.9076 (t0) cc_final: 0.8813 (t0) REVERT: B 368 MET cc_start: 0.9344 (tpp) cc_final: 0.8733 (ttt) REVERT: C 22 TYR cc_start: 0.7808 (m-80) cc_final: 0.7408 (m-80) REVERT: C 84 ILE cc_start: 0.9287 (pt) cc_final: 0.9030 (mp) REVERT: C 106 GLU cc_start: 0.7885 (tt0) cc_final: 0.7591 (tt0) REVERT: C 199 ASP cc_start: 0.8387 (m-30) cc_final: 0.8184 (m-30) REVERT: C 204 ASN cc_start: 0.8182 (m-40) cc_final: 0.7623 (m110) REVERT: C 209 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8653 (tm-30) REVERT: C 240 THR cc_start: 0.8609 (m) cc_final: 0.7804 (p) REVERT: C 294 MET cc_start: 0.8481 (ptt) cc_final: 0.8054 (ptt) REVERT: D 22 TYR cc_start: 0.7551 (m-80) cc_final: 0.7112 (m-80) REVERT: D 26 TYR cc_start: 0.7551 (t80) cc_final: 0.7171 (t80) REVERT: D 30 ASP cc_start: 0.8060 (p0) cc_final: 0.7776 (p0) REVERT: D 146 GLN cc_start: 0.9022 (tt0) cc_final: 0.8129 (tp-100) REVERT: D 209 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8710 (tm-30) REVERT: D 236 TYR cc_start: 0.7683 (m-10) cc_final: 0.7340 (m-10) REVERT: D 283 ASP cc_start: 0.8987 (t0) cc_final: 0.8707 (t70) REVERT: D 364 ASP cc_start: 0.9222 (t0) cc_final: 0.8933 (t0) REVERT: D 440 ASP cc_start: 0.8428 (t0) cc_final: 0.8151 (p0) REVERT: E 22 TYR cc_start: 0.7483 (m-80) cc_final: 0.6668 (m-80) REVERT: E 26 TYR cc_start: 0.7440 (t80) cc_final: 0.6979 (t80) REVERT: E 34 LEU cc_start: 0.8799 (tp) cc_final: 0.8476 (tp) REVERT: E 77 TYR cc_start: 0.9075 (m-10) cc_final: 0.8759 (m-10) REVERT: E 125 LYS cc_start: 0.8111 (mmpt) cc_final: 0.7211 (pttm) REVERT: E 157 ASP cc_start: 0.8846 (m-30) cc_final: 0.8601 (m-30) REVERT: E 247 MET cc_start: 0.8850 (ttm) cc_final: 0.8447 (tmm) REVERT: E 440 ASP cc_start: 0.8866 (t0) cc_final: 0.8414 (t0) REVERT: F 22 TYR cc_start: 0.7226 (m-80) cc_final: 0.6451 (m-80) REVERT: F 26 TYR cc_start: 0.7340 (t80) cc_final: 0.6860 (t80) REVERT: F 81 CYS cc_start: 0.6427 (t) cc_final: 0.6221 (t) REVERT: F 133 GLU cc_start: 0.8633 (tp30) cc_final: 0.7921 (tm-30) REVERT: F 209 GLN cc_start: 0.8747 (pp30) cc_final: 0.8510 (pp30) REVERT: F 240 THR cc_start: 0.9150 (m) cc_final: 0.8513 (p) REVERT: F 246 GLU cc_start: 0.8889 (tp30) cc_final: 0.8558 (tp30) REVERT: F 248 MET cc_start: 0.6791 (mtm) cc_final: 0.6039 (mtm) REVERT: F 294 MET cc_start: 0.8439 (ptt) cc_final: 0.7609 (tmm) REVERT: F 354 ASP cc_start: 0.8107 (t0) cc_final: 0.7503 (t0) REVERT: F 368 MET cc_start: 0.9357 (tpp) cc_final: 0.8641 (ttt) REVERT: G 22 TYR cc_start: 0.7735 (m-80) cc_final: 0.7012 (m-80) REVERT: G 34 LEU cc_start: 0.9299 (tp) cc_final: 0.8804 (tp) REVERT: G 77 TYR cc_start: 0.8781 (m-10) cc_final: 0.8469 (m-10) REVERT: G 146 GLN cc_start: 0.8943 (tt0) cc_final: 0.8081 (tp-100) REVERT: G 203 ILE cc_start: 0.9130 (mm) cc_final: 0.8919 (mm) REVERT: G 228 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8614 (tm-30) REVERT: G 291 HIS cc_start: 0.8542 (t-90) cc_final: 0.8263 (t-90) REVERT: G 321 ASP cc_start: 0.8309 (m-30) cc_final: 0.8074 (m-30) REVERT: G 382 TRP cc_start: 0.8592 (m100) cc_final: 0.8381 (m100) REVERT: G 432 ARG cc_start: 0.7725 (mtp180) cc_final: 0.7510 (ptp-170) REVERT: H 22 TYR cc_start: 0.7420 (m-80) cc_final: 0.6829 (m-80) REVERT: H 85 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7530 (mt-10) REVERT: H 106 GLU cc_start: 0.8113 (tt0) cc_final: 0.7857 (tt0) REVERT: H 146 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8233 (tp-100) REVERT: H 204 ASN cc_start: 0.8418 (m110) cc_final: 0.7761 (m-40) REVERT: H 205 SER cc_start: 0.8749 (t) cc_final: 0.8109 (p) REVERT: H 240 THR cc_start: 0.8730 (m) cc_final: 0.7796 (p) REVERT: H 247 MET cc_start: 0.8861 (ttm) cc_final: 0.8206 (mmm) REVERT: H 255 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8753 (tptp) REVERT: H 351 ILE cc_start: 0.9415 (tp) cc_final: 0.9173 (tt) REVERT: H 361 PHE cc_start: 0.7940 (m-80) cc_final: 0.7271 (m-80) REVERT: H 364 ASP cc_start: 0.9189 (t0) cc_final: 0.8954 (t0) REVERT: I 62 ILE cc_start: 0.7691 (mm) cc_final: 0.7470 (mm) REVERT: I 179 SER cc_start: 0.5455 (t) cc_final: 0.5076 (t) REVERT: K 67 GLN cc_start: 0.6456 (tt0) cc_final: 0.6066 (tt0) REVERT: K 114 ARG cc_start: 0.6558 (tpt170) cc_final: 0.5267 (mtt180) REVERT: K 132 CYS cc_start: 0.6993 (m) cc_final: 0.5887 (p) REVERT: K 191 LEU cc_start: 0.7862 (tt) cc_final: 0.7290 (mt) REVERT: L 27 ARG cc_start: 0.7947 (mpt-90) cc_final: 0.7304 (mpp80) REVERT: L 62 ILE cc_start: 0.7519 (mm) cc_final: 0.7270 (mm) REVERT: L 159 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5146 (mp0) REVERT: M 27 ARG cc_start: 0.7874 (mpt-90) cc_final: 0.5073 (tpp-160) REVERT: N 97 ARG cc_start: 0.5754 (mtm-85) cc_final: 0.4063 (mtm-85) REVERT: N 113 GLU cc_start: 0.6591 (pm20) cc_final: 0.6103 (tp30) REVERT: N 132 CYS cc_start: 0.6762 (m) cc_final: 0.5919 (p) REVERT: O 28 TRP cc_start: 0.7083 (t60) cc_final: 0.6861 (t60) REVERT: O 97 ARG cc_start: 0.6935 (ptp-170) cc_final: 0.5592 (ptp-170) REVERT: P 27 ARG cc_start: 0.8110 (mpt-90) cc_final: 0.7299 (mpp80) REVERT: P 28 TRP cc_start: 0.7343 (t60) cc_final: 0.6721 (t60) REVERT: P 159 GLU cc_start: 0.6026 (mt-10) cc_final: 0.4910 (mp0) outliers start: 5 outliers final: 0 residues processed: 921 average time/residue: 0.2184 time to fit residues: 330.3078 Evaluate side-chains 706 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 165 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 431 optimal weight: 0.0020 chunk 449 optimal weight: 8.9990 chunk 456 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 380 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 HIS ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN F 324 HIS ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 HIS ** G 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN O 46 GLN ** O 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.149276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.115544 restraints weight = 82655.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118497 restraints weight = 45898.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120370 restraints weight = 30828.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121512 restraints weight = 24096.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122148 restraints weight = 21001.073| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 40680 Z= 0.212 Angle : 0.778 10.510 55071 Z= 0.395 Chirality : 0.048 0.341 5917 Planarity : 0.006 0.143 7264 Dihedral : 6.394 176.325 5490 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.55 % Favored : 89.20 % Rotamer: Outliers : 0.10 % Allowed : 1.84 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.11), residues: 4993 helix: -0.45 (0.11), residues: 2096 sheet: -2.67 (0.20), residues: 480 loop : -2.45 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG H 292 TYR 0.018 0.002 TYR D 94 PHE 0.028 0.003 PHE D 217 TRP 0.031 0.002 TRP F 67 HIS 0.009 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00491 (40657) covalent geometry : angle 0.77805 (55071) hydrogen bonds : bond 0.03860 ( 1364) hydrogen bonds : angle 4.84033 ( 3972) Misc. bond : bond 0.00609 ( 23) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 871 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7833 (m-80) cc_final: 0.6532 (m-80) REVERT: A 26 TYR cc_start: 0.7626 (t80) cc_final: 0.7243 (t80) REVERT: A 30 ASP cc_start: 0.7522 (p0) cc_final: 0.7307 (p0) REVERT: A 67 TRP cc_start: 0.7597 (p-90) cc_final: 0.7071 (p-90) REVERT: A 77 TYR cc_start: 0.8995 (m-10) cc_final: 0.8525 (m-10) REVERT: A 106 GLU cc_start: 0.8344 (tt0) cc_final: 0.8000 (tt0) REVERT: A 233 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8192 (mmmt) REVERT: A 246 GLU cc_start: 0.8724 (tp30) cc_final: 0.8413 (tp30) REVERT: A 248 MET cc_start: 0.8867 (mmp) cc_final: 0.8521 (mmt) REVERT: A 344 ASP cc_start: 0.8593 (t70) cc_final: 0.8133 (t0) REVERT: A 351 ILE cc_start: 0.9107 (mt) cc_final: 0.8903 (tt) REVERT: A 361 PHE cc_start: 0.8124 (m-80) cc_final: 0.7533 (m-80) REVERT: A 440 ASP cc_start: 0.8465 (t0) cc_final: 0.8018 (t0) REVERT: B 130 LEU cc_start: 0.9437 (tp) cc_final: 0.9072 (tp) REVERT: B 246 GLU cc_start: 0.8815 (tp30) cc_final: 0.8559 (tp30) REVERT: B 247 MET cc_start: 0.8851 (ttm) cc_final: 0.8394 (mmm) REVERT: B 364 ASP cc_start: 0.9068 (t0) cc_final: 0.8803 (t0) REVERT: C 22 TYR cc_start: 0.7859 (m-80) cc_final: 0.7467 (m-80) REVERT: C 34 LEU cc_start: 0.8662 (tp) cc_final: 0.8369 (tp) REVERT: C 84 ILE cc_start: 0.9271 (pt) cc_final: 0.9010 (mp) REVERT: C 85 GLU cc_start: 0.8874 (pp20) cc_final: 0.8555 (pp20) REVERT: C 106 GLU cc_start: 0.7955 (tt0) cc_final: 0.7637 (tt0) REVERT: C 199 ASP cc_start: 0.8457 (m-30) cc_final: 0.8129 (m-30) REVERT: C 204 ASN cc_start: 0.8223 (m-40) cc_final: 0.7982 (m110) REVERT: C 294 MET cc_start: 0.8514 (ptt) cc_final: 0.8083 (ptt) REVERT: D 22 TYR cc_start: 0.7568 (m-80) cc_final: 0.7129 (m-80) REVERT: D 26 TYR cc_start: 0.7490 (t80) cc_final: 0.7175 (t80) REVERT: D 30 ASP cc_start: 0.8174 (p0) cc_final: 0.7931 (p0) REVERT: D 85 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7435 (mt-10) REVERT: D 146 GLN cc_start: 0.9044 (tt0) cc_final: 0.8127 (tp-100) REVERT: D 203 ILE cc_start: 0.8715 (tp) cc_final: 0.8152 (mt) REVERT: D 209 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8663 (tm-30) REVERT: D 236 TYR cc_start: 0.7504 (m-10) cc_final: 0.7229 (m-10) REVERT: D 344 ASP cc_start: 0.8345 (t0) cc_final: 0.8093 (t70) REVERT: D 364 ASP cc_start: 0.9203 (t0) cc_final: 0.8914 (t0) REVERT: D 440 ASP cc_start: 0.8363 (t0) cc_final: 0.8136 (p0) REVERT: E 22 TYR cc_start: 0.7488 (m-80) cc_final: 0.6740 (m-80) REVERT: E 26 TYR cc_start: 0.7527 (t80) cc_final: 0.7004 (t80) REVERT: E 34 LEU cc_start: 0.8787 (tp) cc_final: 0.8423 (tp) REVERT: E 81 CYS cc_start: 0.7298 (t) cc_final: 0.7066 (t) REVERT: E 125 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7250 (pttp) REVERT: E 205 SER cc_start: 0.8385 (m) cc_final: 0.8169 (t) REVERT: E 440 ASP cc_start: 0.8768 (t0) cc_final: 0.8314 (t0) REVERT: F 22 TYR cc_start: 0.7316 (m-80) cc_final: 0.6505 (m-80) REVERT: F 26 TYR cc_start: 0.7445 (t80) cc_final: 0.6904 (t80) REVERT: F 81 CYS cc_start: 0.6588 (t) cc_final: 0.6319 (t) REVERT: F 133 GLU cc_start: 0.8627 (tp30) cc_final: 0.7886 (tm-30) REVERT: F 209 GLN cc_start: 0.8724 (pp30) cc_final: 0.8442 (pp30) REVERT: F 236 TYR cc_start: 0.7893 (m-10) cc_final: 0.7453 (m-10) REVERT: F 240 THR cc_start: 0.9167 (m) cc_final: 0.8522 (p) REVERT: F 246 GLU cc_start: 0.8820 (tp30) cc_final: 0.8573 (tp30) REVERT: F 248 MET cc_start: 0.6856 (mtm) cc_final: 0.5983 (mtm) REVERT: F 294 MET cc_start: 0.8562 (ptt) cc_final: 0.8345 (ptt) REVERT: F 354 ASP cc_start: 0.8161 (t0) cc_final: 0.7529 (t0) REVERT: F 368 MET cc_start: 0.9309 (tpp) cc_final: 0.8633 (ttt) REVERT: G 22 TYR cc_start: 0.7797 (m-80) cc_final: 0.7084 (m-80) REVERT: G 34 LEU cc_start: 0.9251 (tp) cc_final: 0.8980 (tp) REVERT: G 77 TYR cc_start: 0.8752 (m-10) cc_final: 0.8422 (m-10) REVERT: G 146 GLN cc_start: 0.8962 (tt0) cc_final: 0.8141 (tp-100) REVERT: G 203 ILE cc_start: 0.9063 (mm) cc_final: 0.8743 (mm) REVERT: G 209 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8490 (tm-30) REVERT: G 228 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8668 (tm-30) REVERT: G 321 ASP cc_start: 0.8403 (m-30) cc_final: 0.8118 (m-30) REVERT: G 382 TRP cc_start: 0.8539 (m100) cc_final: 0.8238 (m100) REVERT: G 432 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7718 (ptp-170) REVERT: H 22 TYR cc_start: 0.7424 (m-80) cc_final: 0.6767 (m-80) REVERT: H 146 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8283 (tp-100) REVERT: H 184 ARG cc_start: 0.8693 (mmt-90) cc_final: 0.8174 (mmt-90) REVERT: H 204 ASN cc_start: 0.8510 (m110) cc_final: 0.7850 (m-40) REVERT: H 205 SER cc_start: 0.8736 (t) cc_final: 0.8092 (p) REVERT: H 240 THR cc_start: 0.8736 (m) cc_final: 0.7850 (p) REVERT: H 247 MET cc_start: 0.8925 (ttm) cc_final: 0.8276 (mmm) REVERT: H 255 LYS cc_start: 0.9105 (tmtt) cc_final: 0.8769 (tptp) REVERT: H 351 ILE cc_start: 0.9405 (tp) cc_final: 0.9179 (tt) REVERT: H 364 ASP cc_start: 0.9186 (t0) cc_final: 0.8963 (t0) REVERT: I 66 MET cc_start: 0.4967 (ppp) cc_final: 0.3645 (ppp) REVERT: I 179 SER cc_start: 0.5683 (t) cc_final: 0.5338 (t) REVERT: J 58 GLN cc_start: 0.7636 (pm20) cc_final: 0.7094 (tt0) REVERT: J 154 TRP cc_start: 0.6215 (m-90) cc_final: 0.6007 (m100) REVERT: K 67 GLN cc_start: 0.6536 (tt0) cc_final: 0.6154 (tt0) REVERT: K 114 ARG cc_start: 0.6281 (tpt170) cc_final: 0.5091 (mtt180) REVERT: K 132 CYS cc_start: 0.6994 (m) cc_final: 0.5809 (p) REVERT: K 191 LEU cc_start: 0.7894 (tt) cc_final: 0.7233 (mt) REVERT: L 27 ARG cc_start: 0.8120 (mpt-90) cc_final: 0.7506 (mpp80) REVERT: L 66 MET cc_start: 0.7220 (tmm) cc_final: 0.6851 (tmm) REVERT: L 159 GLU cc_start: 0.5952 (mt-10) cc_final: 0.5136 (mp0) REVERT: M 27 ARG cc_start: 0.8051 (mpt-90) cc_final: 0.5065 (tpp-160) REVERT: M 114 ARG cc_start: 0.4473 (tpp80) cc_final: 0.3887 (tpm170) REVERT: N 67 GLN cc_start: 0.7132 (tt0) cc_final: 0.6752 (tt0) REVERT: N 113 GLU cc_start: 0.6365 (pm20) cc_final: 0.5830 (tp30) REVERT: N 132 CYS cc_start: 0.6761 (m) cc_final: 0.5910 (p) REVERT: O 28 TRP cc_start: 0.6717 (t60) cc_final: 0.6384 (t60) REVERT: O 97 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.5487 (ptp-170) REVERT: O 159 GLU cc_start: 0.5834 (mt-10) cc_final: 0.4606 (mp0) REVERT: P 27 ARG cc_start: 0.8210 (mpt-90) cc_final: 0.7373 (mpp80) REVERT: P 28 TRP cc_start: 0.7148 (t60) cc_final: 0.6762 (t60) REVERT: P 159 GLU cc_start: 0.6096 (mt-10) cc_final: 0.4988 (mp0) outliers start: 4 outliers final: 1 residues processed: 874 average time/residue: 0.2196 time to fit residues: 315.9432 Evaluate side-chains 690 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 689 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 429 optimal weight: 20.0000 chunk 402 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN C 146 GLN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS C 324 HIS C 363 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 324 HIS ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN F 274 ASN ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 GLN H 274 ASN H 322 HIS ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN L 46 GLN L 60 ASN M 60 ASN M 137 GLN N 67 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121445 restraints weight = 82852.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125076 restraints weight = 48357.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126604 restraints weight = 30896.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127142 restraints weight = 25772.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127518 restraints weight = 23501.456| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 40680 Z= 0.134 Angle : 0.728 10.695 55071 Z= 0.363 Chirality : 0.045 0.223 5917 Planarity : 0.005 0.136 7264 Dihedral : 6.173 178.011 5490 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.85 % Favored : 89.93 % Rotamer: Outliers : 0.17 % Allowed : 0.92 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.12), residues: 4993 helix: -0.15 (0.11), residues: 2093 sheet: -2.09 (0.24), residues: 344 loop : -2.32 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 292 TYR 0.021 0.001 TYR F 182 PHE 0.029 0.002 PHE D 39 TRP 0.038 0.002 TRP I 28 HIS 0.007 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00306 (40657) covalent geometry : angle 0.72783 (55071) hydrogen bonds : bond 0.03402 ( 1364) hydrogen bonds : angle 4.57837 ( 3972) Misc. bond : bond 0.00584 ( 23) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 975 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7692 (m-80) cc_final: 0.6442 (m-80) REVERT: A 67 TRP cc_start: 0.7623 (p-90) cc_final: 0.7044 (p-90) REVERT: A 146 GLN cc_start: 0.9012 (tt0) cc_final: 0.8651 (tp40) REVERT: A 233 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8178 (mmmt) REVERT: A 246 GLU cc_start: 0.8558 (tp30) cc_final: 0.8252 (tp30) REVERT: A 255 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8476 (ttpt) REVERT: A 284 ASN cc_start: 0.8238 (t0) cc_final: 0.7666 (t0) REVERT: A 291 HIS cc_start: 0.8012 (t-90) cc_final: 0.7521 (t-90) REVERT: A 344 ASP cc_start: 0.8473 (t70) cc_final: 0.8238 (t0) REVERT: A 361 PHE cc_start: 0.7934 (m-80) cc_final: 0.7494 (m-80) REVERT: A 440 ASP cc_start: 0.8491 (t0) cc_final: 0.8080 (t0) REVERT: B 130 LEU cc_start: 0.9359 (tp) cc_final: 0.9120 (tp) REVERT: B 246 GLU cc_start: 0.8765 (tp30) cc_final: 0.8512 (tp30) REVERT: B 247 MET cc_start: 0.8783 (ttm) cc_final: 0.8397 (mmm) REVERT: B 294 MET cc_start: 0.8560 (ptt) cc_final: 0.7749 (ptp) REVERT: C 22 TYR cc_start: 0.7762 (m-80) cc_final: 0.7353 (m-80) REVERT: C 34 LEU cc_start: 0.8564 (tp) cc_final: 0.8324 (tp) REVERT: C 84 ILE cc_start: 0.9102 (pt) cc_final: 0.8891 (mp) REVERT: C 180 LYS cc_start: 0.8414 (mmpt) cc_final: 0.7666 (mmmt) REVERT: C 184 ARG cc_start: 0.8471 (mmt180) cc_final: 0.8038 (mmt-90) REVERT: C 294 MET cc_start: 0.8383 (ptt) cc_final: 0.8007 (ptt) REVERT: C 383 HIS cc_start: 0.8277 (m-70) cc_final: 0.8077 (m90) REVERT: D 22 TYR cc_start: 0.7625 (m-80) cc_final: 0.7176 (m-80) REVERT: D 26 TYR cc_start: 0.7365 (t80) cc_final: 0.7159 (t80) REVERT: D 85 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 146 GLN cc_start: 0.9043 (tt0) cc_final: 0.8184 (tp-100) REVERT: D 184 ARG cc_start: 0.8438 (mmt180) cc_final: 0.8197 (mmt180) REVERT: D 203 ILE cc_start: 0.8635 (tp) cc_final: 0.8009 (mt) REVERT: D 209 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8840 (tm-30) REVERT: D 247 MET cc_start: 0.8710 (ttm) cc_final: 0.8413 (tmm) REVERT: D 324 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8542 (m-70) REVERT: D 351 ILE cc_start: 0.9297 (tp) cc_final: 0.9095 (mt) REVERT: D 364 ASP cc_start: 0.9180 (t0) cc_final: 0.8848 (t0) REVERT: D 440 ASP cc_start: 0.8349 (t0) cc_final: 0.7704 (t0) REVERT: E 22 TYR cc_start: 0.7590 (m-80) cc_final: 0.6816 (m-80) REVERT: E 26 TYR cc_start: 0.7304 (t80) cc_final: 0.7032 (t80) REVERT: E 64 THR cc_start: 0.8112 (p) cc_final: 0.7905 (p) REVERT: E 75 ASP cc_start: 0.7492 (t0) cc_final: 0.6834 (t70) REVERT: E 77 TYR cc_start: 0.9139 (m-10) cc_final: 0.8874 (m-10) REVERT: E 106 GLU cc_start: 0.8406 (tt0) cc_final: 0.8164 (tt0) REVERT: E 125 LYS cc_start: 0.7800 (mmpt) cc_final: 0.6946 (pttp) REVERT: E 184 ARG cc_start: 0.8528 (mmt180) cc_final: 0.8142 (mmt-90) REVERT: E 205 SER cc_start: 0.8228 (m) cc_final: 0.7931 (t) REVERT: E 351 ILE cc_start: 0.8914 (mt) cc_final: 0.8710 (tp) REVERT: E 440 ASP cc_start: 0.8756 (t0) cc_final: 0.8354 (t0) REVERT: F 22 TYR cc_start: 0.7118 (m-80) cc_final: 0.6340 (m-80) REVERT: F 26 TYR cc_start: 0.7215 (t80) cc_final: 0.6980 (t80) REVERT: F 106 GLU cc_start: 0.8175 (tt0) cc_final: 0.7936 (tt0) REVERT: F 133 GLU cc_start: 0.8470 (tp30) cc_final: 0.7819 (tm-30) REVERT: F 209 GLN cc_start: 0.8571 (pp30) cc_final: 0.8329 (pp30) REVERT: F 236 TYR cc_start: 0.7684 (m-10) cc_final: 0.7398 (m-10) REVERT: F 238 ASN cc_start: 0.8840 (t0) cc_final: 0.8491 (t0) REVERT: F 240 THR cc_start: 0.9117 (m) cc_final: 0.8218 (p) REVERT: F 294 MET cc_start: 0.8514 (ptt) cc_final: 0.7956 (ppp) REVERT: F 354 ASP cc_start: 0.8183 (t0) cc_final: 0.7646 (t0) REVERT: F 368 MET cc_start: 0.9299 (tpp) cc_final: 0.8656 (ttt) REVERT: G 22 TYR cc_start: 0.7685 (m-80) cc_final: 0.7099 (m-80) REVERT: G 34 LEU cc_start: 0.9154 (tp) cc_final: 0.8893 (tp) REVERT: G 77 TYR cc_start: 0.8702 (m-10) cc_final: 0.8341 (m-10) REVERT: G 146 GLN cc_start: 0.8989 (tt0) cc_final: 0.8260 (tp-100) REVERT: G 228 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8703 (tm-30) REVERT: G 321 ASP cc_start: 0.8229 (m-30) cc_final: 0.7843 (m-30) REVERT: G 351 ILE cc_start: 0.9145 (tp) cc_final: 0.8880 (tt) REVERT: G 382 TRP cc_start: 0.8533 (m100) cc_final: 0.8265 (m100) REVERT: G 408 TRP cc_start: 0.7539 (t-100) cc_final: 0.7282 (t-100) REVERT: H 22 TYR cc_start: 0.7377 (m-80) cc_final: 0.6846 (m-80) REVERT: H 76 ARG cc_start: 0.8418 (ttt-90) cc_final: 0.7900 (ttt180) REVERT: H 77 TYR cc_start: 0.9107 (m-80) cc_final: 0.8162 (m-80) REVERT: H 106 GLU cc_start: 0.7815 (tt0) cc_final: 0.7364 (tt0) REVERT: H 184 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.7812 (mpt180) REVERT: H 204 ASN cc_start: 0.8351 (m110) cc_final: 0.7868 (m110) REVERT: H 239 VAL cc_start: 0.9547 (m) cc_final: 0.9255 (p) REVERT: H 240 THR cc_start: 0.8852 (m) cc_final: 0.8026 (p) REVERT: H 247 MET cc_start: 0.8777 (ttm) cc_final: 0.8234 (mmm) REVERT: H 255 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8659 (tptp) REVERT: H 351 ILE cc_start: 0.9386 (tp) cc_final: 0.9173 (tt) REVERT: H 361 PHE cc_start: 0.7845 (m-80) cc_final: 0.7322 (m-80) REVERT: I 28 TRP cc_start: 0.7068 (t60) cc_final: 0.6806 (t60) REVERT: I 66 MET cc_start: 0.4991 (ppp) cc_final: 0.3670 (ppp) REVERT: I 159 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6316 (tt0) REVERT: I 179 SER cc_start: 0.6150 (t) cc_final: 0.5868 (t) REVERT: J 58 GLN cc_start: 0.7651 (pm20) cc_final: 0.6692 (tt0) REVERT: J 102 GLU cc_start: 0.5332 (mt-10) cc_final: 0.5045 (mp0) REVERT: K 114 ARG cc_start: 0.6121 (tpt170) cc_final: 0.5022 (mtt180) REVERT: K 132 CYS cc_start: 0.6898 (m) cc_final: 0.5817 (p) REVERT: K 133 ARG cc_start: 0.6317 (ttm110) cc_final: 0.6080 (ttm110) REVERT: K 191 LEU cc_start: 0.7940 (tt) cc_final: 0.7258 (mt) REVERT: L 27 ARG cc_start: 0.7816 (mpt-90) cc_final: 0.7203 (mpp80) REVERT: L 62 ILE cc_start: 0.7489 (mm) cc_final: 0.7261 (mm) REVERT: L 159 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5194 (mp0) REVERT: N 67 GLN cc_start: 0.6911 (tt0) cc_final: 0.6550 (tt0) REVERT: N 97 ARG cc_start: 0.5752 (mtm-85) cc_final: 0.3779 (mtm-85) REVERT: N 113 GLU cc_start: 0.5855 (pm20) cc_final: 0.5329 (tp30) REVERT: N 132 CYS cc_start: 0.6668 (m) cc_final: 0.5830 (p) REVERT: O 27 ARG cc_start: 0.7591 (mpt-90) cc_final: 0.4992 (tpp-160) REVERT: O 66 MET cc_start: 0.7695 (tmm) cc_final: 0.7321 (tmm) REVERT: O 97 ARG cc_start: 0.6944 (ptp-170) cc_final: 0.5680 (ptp-170) REVERT: O 159 GLU cc_start: 0.5785 (mt-10) cc_final: 0.4624 (mp0) REVERT: P 28 TRP cc_start: 0.7231 (t60) cc_final: 0.6883 (t60) REVERT: P 159 GLU cc_start: 0.5957 (mt-10) cc_final: 0.4931 (mp0) outliers start: 7 outliers final: 0 residues processed: 978 average time/residue: 0.2142 time to fit residues: 346.5708 Evaluate side-chains 748 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 747 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 379 optimal weight: 0.0570 chunk 252 optimal weight: 2.9990 chunk 229 optimal weight: 0.0170 chunk 213 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 442 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 HIS C 274 ASN C 291 HIS C 324 HIS C 363 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 GLN H 274 ASN I 58 GLN L 60 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 GLN ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122450 restraints weight = 82042.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125482 restraints weight = 46908.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.127429 restraints weight = 32082.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128624 restraints weight = 25428.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129266 restraints weight = 22291.871| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 40680 Z= 0.132 Angle : 0.732 14.244 55071 Z= 0.362 Chirality : 0.045 0.219 5917 Planarity : 0.005 0.143 7264 Dihedral : 6.061 178.361 5490 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.53 % Favored : 90.25 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4993 helix: -0.06 (0.11), residues: 2113 sheet: -2.15 (0.23), residues: 392 loop : -2.30 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.000 ARG J 104 TYR 0.024 0.002 TYR K 69 PHE 0.032 0.002 PHE C 266 TRP 0.035 0.002 TRP H 67 HIS 0.009 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00303 (40657) covalent geometry : angle 0.73199 (55071) hydrogen bonds : bond 0.03342 ( 1364) hydrogen bonds : angle 4.49432 ( 3972) Misc. bond : bond 0.00628 ( 23) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 949 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 TYR cc_start: 0.7716 (m-80) cc_final: 0.6601 (m-80) REVERT: A 26 TYR cc_start: 0.6448 (t80) cc_final: 0.6152 (t80) REVERT: A 67 TRP cc_start: 0.7540 (p-90) cc_final: 0.7081 (p-90) REVERT: A 77 TYR cc_start: 0.8665 (m-10) cc_final: 0.8049 (m-10) REVERT: A 106 GLU cc_start: 0.8469 (tt0) cc_final: 0.8256 (tt0) REVERT: A 184 ARG cc_start: 0.8535 (mtt-85) cc_final: 0.8325 (mtt90) REVERT: A 246 GLU cc_start: 0.8506 (tp30) cc_final: 0.8195 (tp30) REVERT: A 247 MET cc_start: 0.8496 (ttm) cc_final: 0.7917 (mmm) REVERT: A 259 MET cc_start: 0.8246 (mmp) cc_final: 0.7770 (mmp) REVERT: A 284 ASN cc_start: 0.8233 (t0) cc_final: 0.7812 (t0) REVERT: A 361 PHE cc_start: 0.7913 (m-80) cc_final: 0.7603 (m-80) REVERT: A 440 ASP cc_start: 0.8596 (t0) cc_final: 0.8257 (t0) REVERT: B 87 VAL cc_start: 0.8062 (t) cc_final: 0.7679 (p) REVERT: B 121 VAL cc_start: 0.9230 (p) cc_final: 0.9003 (t) REVERT: B 130 LEU cc_start: 0.9395 (tp) cc_final: 0.9069 (tp) REVERT: B 247 MET cc_start: 0.8734 (ttm) cc_final: 0.8452 (mmm) REVERT: B 294 MET cc_start: 0.8517 (ptt) cc_final: 0.8059 (ptt) REVERT: B 394 ASP cc_start: 0.8613 (m-30) cc_final: 0.7653 (p0) REVERT: B 422 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7793 (pt0) REVERT: C 22 TYR cc_start: 0.7753 (m-80) cc_final: 0.7374 (m-80) REVERT: C 34 LEU cc_start: 0.8605 (tp) cc_final: 0.8381 (tp) REVERT: C 84 ILE cc_start: 0.9083 (pt) cc_final: 0.8838 (mp) REVERT: C 91 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6788 (tm-30) REVERT: C 146 GLN cc_start: 0.8618 (tp40) cc_final: 0.8350 (tp-100) REVERT: C 180 LYS cc_start: 0.8307 (mmpt) cc_final: 0.7415 (mmmt) REVERT: C 184 ARG cc_start: 0.8506 (mmt180) cc_final: 0.7977 (mmt180) REVERT: C 197 THR cc_start: 0.8218 (p) cc_final: 0.7669 (p) REVERT: C 235 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6653 (p-80) REVERT: C 294 MET cc_start: 0.8497 (ptt) cc_final: 0.8161 (ptt) REVERT: D 22 TYR cc_start: 0.7623 (m-80) cc_final: 0.7233 (m-80) REVERT: D 106 GLU cc_start: 0.8071 (tt0) cc_final: 0.7596 (tt0) REVERT: D 146 GLN cc_start: 0.9016 (tt0) cc_final: 0.8061 (tp-100) REVERT: D 184 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8110 (mmt180) REVERT: D 203 ILE cc_start: 0.8571 (tp) cc_final: 0.7995 (mt) REVERT: D 236 TYR cc_start: 0.7512 (m-10) cc_final: 0.7272 (m-10) REVERT: D 364 ASP cc_start: 0.9153 (t0) cc_final: 0.8848 (t0) REVERT: D 440 ASP cc_start: 0.8283 (t0) cc_final: 0.7660 (t0) REVERT: E 22 TYR cc_start: 0.7595 (m-80) cc_final: 0.6812 (m-80) REVERT: E 75 ASP cc_start: 0.7398 (t0) cc_final: 0.6773 (t70) REVERT: E 77 TYR cc_start: 0.9073 (m-10) cc_final: 0.8708 (m-10) REVERT: E 125 LYS cc_start: 0.7616 (mmpt) cc_final: 0.6652 (pttp) REVERT: E 154 VAL cc_start: 0.9232 (t) cc_final: 0.9012 (t) REVERT: E 171 ILE cc_start: 0.9125 (mm) cc_final: 0.8859 (tp) REVERT: E 180 LYS cc_start: 0.8412 (mmpt) cc_final: 0.8121 (mmmt) REVERT: E 184 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8045 (mmt-90) REVERT: E 384 MET cc_start: 0.8352 (ppp) cc_final: 0.8002 (ttm) REVERT: E 440 ASP cc_start: 0.8642 (t0) cc_final: 0.8375 (t0) REVERT: F 22 TYR cc_start: 0.7254 (m-80) cc_final: 0.6460 (m-80) REVERT: F 81 CYS cc_start: 0.6531 (t) cc_final: 0.6265 (t) REVERT: F 133 GLU cc_start: 0.8498 (tp30) cc_final: 0.7797 (tm-30) REVERT: F 188 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8768 (mm-30) REVERT: F 209 GLN cc_start: 0.8499 (pp30) cc_final: 0.8200 (pp30) REVERT: F 236 TYR cc_start: 0.7587 (m-10) cc_final: 0.7158 (m-10) REVERT: F 238 ASN cc_start: 0.8761 (t0) cc_final: 0.8556 (t0) REVERT: F 240 THR cc_start: 0.9073 (m) cc_final: 0.8663 (m) REVERT: F 246 GLU cc_start: 0.8648 (tp30) cc_final: 0.8208 (tm-30) REVERT: F 263 MET cc_start: 0.8795 (ppp) cc_final: 0.8559 (ppp) REVERT: F 294 MET cc_start: 0.8447 (ptt) cc_final: 0.7933 (ppp) REVERT: F 354 ASP cc_start: 0.8093 (t0) cc_final: 0.7569 (t0) REVERT: F 368 MET cc_start: 0.9296 (tpp) cc_final: 0.8600 (ttt) REVERT: F 394 ASP cc_start: 0.8529 (m-30) cc_final: 0.8197 (m-30) REVERT: F 408 TRP cc_start: 0.7175 (t60) cc_final: 0.6262 (t60) REVERT: G 22 TYR cc_start: 0.7653 (m-80) cc_final: 0.7081 (m-80) REVERT: G 34 LEU cc_start: 0.9077 (tp) cc_final: 0.8874 (tp) REVERT: G 77 TYR cc_start: 0.8591 (m-10) cc_final: 0.8256 (m-10) REVERT: G 146 GLN cc_start: 0.8895 (tt0) cc_final: 0.8191 (tp-100) REVERT: G 204 ASN cc_start: 0.8061 (m110) cc_final: 0.7689 (m110) REVERT: G 228 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8732 (tm-30) REVERT: H 22 TYR cc_start: 0.7305 (m-80) cc_final: 0.6811 (m-80) REVERT: H 76 ARG cc_start: 0.8351 (ttt-90) cc_final: 0.7928 (ttt180) REVERT: H 77 TYR cc_start: 0.9118 (m-80) cc_final: 0.8147 (m-80) REVERT: H 106 GLU cc_start: 0.7801 (tt0) cc_final: 0.7489 (tt0) REVERT: H 184 ARG cc_start: 0.8283 (mmt-90) cc_final: 0.7961 (mmt-90) REVERT: H 239 VAL cc_start: 0.9528 (m) cc_final: 0.9290 (p) REVERT: H 247 MET cc_start: 0.8802 (ttm) cc_final: 0.8258 (mmm) REVERT: H 255 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8641 (tptp) REVERT: H 346 MET cc_start: 0.7699 (mtp) cc_final: 0.7053 (ttp) REVERT: H 351 ILE cc_start: 0.9395 (tp) cc_final: 0.9100 (tt) REVERT: H 361 PHE cc_start: 0.7840 (m-80) cc_final: 0.7526 (m-80) REVERT: H 364 ASP cc_start: 0.9153 (t70) cc_final: 0.8918 (t0) REVERT: I 66 MET cc_start: 0.5060 (ppp) cc_final: 0.3720 (ppp) REVERT: I 95 GLU cc_start: 0.8359 (tp30) cc_final: 0.8121 (tp30) REVERT: I 159 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6420 (tt0) REVERT: I 179 SER cc_start: 0.6150 (t) cc_final: 0.5932 (t) REVERT: J 28 TRP cc_start: 0.6750 (t60) cc_final: 0.6478 (t60) REVERT: J 58 GLN cc_start: 0.7278 (pm20) cc_final: 0.6747 (tt0) REVERT: J 63 THR cc_start: 0.8989 (m) cc_final: 0.8663 (p) REVERT: J 93 LEU cc_start: 0.6370 (mm) cc_final: 0.5725 (tp) REVERT: J 102 GLU cc_start: 0.6031 (mt-10) cc_final: 0.5764 (mp0) REVERT: K 72 ILE cc_start: 0.8034 (pt) cc_final: 0.7356 (mm) REVERT: K 114 ARG cc_start: 0.6185 (tpt170) cc_final: 0.5076 (mtt180) REVERT: K 132 CYS cc_start: 0.6930 (m) cc_final: 0.5861 (p) REVERT: K 133 ARG cc_start: 0.6354 (ttm110) cc_final: 0.6135 (ttm110) REVERT: K 191 LEU cc_start: 0.7905 (tt) cc_final: 0.7265 (mt) REVERT: L 27 ARG cc_start: 0.7916 (mpt-90) cc_final: 0.7479 (mpp80) REVERT: L 159 GLU cc_start: 0.5934 (mt-10) cc_final: 0.4960 (mp0) REVERT: M 24 LYS cc_start: 0.7654 (mmtm) cc_final: 0.6574 (tmtt) REVERT: M 160 ARG cc_start: 0.7320 (mmt-90) cc_final: 0.6839 (ptt-90) REVERT: N 132 CYS cc_start: 0.6348 (m) cc_final: 0.5444 (p) REVERT: O 69 TYR cc_start: 0.7826 (t80) cc_final: 0.7511 (t80) REVERT: O 97 ARG cc_start: 0.6955 (ptp-170) cc_final: 0.5657 (ptp-170) REVERT: O 159 GLU cc_start: 0.5797 (mt-10) cc_final: 0.4620 (mp0) REVERT: P 27 ARG cc_start: 0.7997 (mpt-90) cc_final: 0.7302 (mpp80) REVERT: P 28 TRP cc_start: 0.7031 (t60) cc_final: 0.6705 (t60) REVERT: P 159 GLU cc_start: 0.5921 (mt-10) cc_final: 0.4913 (mp0) outliers start: 8 outliers final: 1 residues processed: 953 average time/residue: 0.2145 time to fit residues: 339.3850 Evaluate side-chains 756 residues out of total 4128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 754 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 76 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 chunk 446 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 274 ASN B 291 HIS C 204 ASN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 291 HIS F 304 HIS ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN ** G 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 GLN ** G 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN H 274 ASN H 324 HIS I 58 GLN K 67 GLN L 60 ASN ** L 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120909 restraints weight = 81788.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124612 restraints weight = 47084.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126495 restraints weight = 29330.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126936 restraints weight = 23254.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127233 restraints weight = 21386.013| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 40680 Z= 0.170 Angle : 0.748 16.405 55071 Z= 0.373 Chirality : 0.046 0.294 5917 Planarity : 0.008 0.478 7264 Dihedral : 6.188 177.835 5490 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.23 % Favored : 89.53 % Rotamer: Outliers : 0.17 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4993 helix: -0.06 (0.11), residues: 2094 sheet: -2.08 (0.23), residues: 392 loop : -2.29 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG J 104 TYR 0.023 0.002 TYR H 26 PHE 0.035 0.003 PHE C 266 TRP 0.036 0.002 TRP I 28 HIS 0.009 0.001 HIS E 235 Details of bonding type rmsd covalent geometry : bond 0.00399 (40657) covalent geometry : angle 0.74806 (55071) hydrogen bonds : bond 0.03518 ( 1364) hydrogen bonds : angle 4.52955 ( 3972) Misc. bond : bond 0.00667 ( 23) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7668.26 seconds wall clock time: 133 minutes 11.23 seconds (7991.23 seconds total)