Starting phenix.real_space_refine on Sun Feb 8 03:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.map" model { file = "/net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ue7_64078/02_2026/9ue7_64078.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.015 sd= 0.508 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 195 5.16 5 C 24987 2.51 5 N 6459 2.21 5 O 7374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 246 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39015 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "B" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Time building chain proxies: 8.56, per 1000 atoms: 0.22 Number of scatterers: 39015 At special positions: 0 Unit cell: (154.712, 161.236, 246.98, 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 195 16.00 O 7374 8.00 N 6459 7.00 C 24987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9234 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 54 sheets defined 42.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'F' and resid 20 through 53 removed outlier: 4.112A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.528A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.535A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 108 " --> pdb=" O SER F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 144 through 154 removed outlier: 3.921A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.561A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 removed outlier: 3.791A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 218 through 252 Proline residue: F 235 - end of helix removed outlier: 4.153A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 278 through 283 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 318 removed outlier: 3.649A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.601A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 4.433A pdb=" N VAL F 339 " --> pdb=" O PRO F 336 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN F 340 " --> pdb=" O GLY F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 446 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 530 removed outlier: 4.308A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N CYS F 530 " --> pdb=" O GLN F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.902A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 575 removed outlier: 3.709A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 600 Proline residue: F 590 - end of helix removed outlier: 3.676A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.155A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.646A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.511A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.716A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 250 removed outlier: 3.633A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.163A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.040A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.661A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.570A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.666A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.903A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.557A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.731A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.629A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.323A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.668A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.627A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 173 removed outlier: 3.645A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.989A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 252 Proline residue: E 235 - end of helix removed outlier: 4.095A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 removed outlier: 4.155A pdb=" N SER E 280 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.684A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.566A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 446 through 448 No H-bonds generated for 'chain 'E' and resid 446 through 448' Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 472 through 485 removed outlier: 3.510A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.327A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.871A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 4.036A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 removed outlier: 3.664A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 600 Proline residue: E 590 - end of helix removed outlier: 3.699A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.670A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 371' Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.861A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.530A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.875A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.143A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.648A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.627A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1147 removed outlier: 3.823A pdb=" N SER A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.690A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.804A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.522A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.522A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.911A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.040A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.659A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 944 removed outlier: 3.676A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 978 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.619A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 3.564A pdb=" N SER B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.737A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.875A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.650A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.646A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 627 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.522A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.889A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.609A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.904A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1148 Processing sheet with id=AA1, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.098A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.770A pdb=" N THR F 347 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F 359 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP F 349 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG F 357 " --> pdb=" O TRP F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.682A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.783A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP D 349 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.712A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.812A pdb=" N THR E 347 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 359 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP E 349 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 357 " --> pdb=" O TRP E 349 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.607A pdb=" N LEU A 18 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.185A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.530A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.816A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.515A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.232A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.831A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.767A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.014A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.059A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.203A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.687A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.687A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.116A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.625A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.732A pdb=" N LEU B 18 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.470A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.921A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.392A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.778A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.196A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.849A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.675A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.087A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.549A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.323A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.140A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.738A pdb=" N LEU C 18 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.554A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.773A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.410A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.848A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.628A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.067A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.900A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.900A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.185A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.000A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1835 hydrogen bonds defined for protein. 5268 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: 9.74 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12531 1.35 - 1.46: 9859 1.46 - 1.58: 17342 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 40014 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.17e+00 bond pdb=" C GLY F 130 " pdb=" O GLY F 130 " ideal model delta sigma weight residual 1.243 1.232 0.011 9.30e-03 1.16e+04 1.35e+00 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.06e-01 bond pdb=" C PHE C 216 " pdb=" N PRO C 217 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.77e-01 bond pdb=" CA PHE A 216 " pdb=" C PHE A 216 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.49e-01 ... (remaining 40009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 53907 1.66 - 3.32: 447 3.32 - 4.98: 65 4.98 - 6.64: 9 6.64 - 8.30: 1 Bond angle restraints: 54429 Sorted by residual: angle pdb=" N VAL C 635 " pdb=" CA VAL C 635 " pdb=" C VAL C 635 " ideal model delta sigma weight residual 112.98 108.79 4.19 1.25e+00 6.40e-01 1.12e+01 angle pdb=" N VAL E 318 " pdb=" CA VAL E 318 " pdb=" C VAL E 318 " ideal model delta sigma weight residual 112.80 109.49 3.31 1.15e+00 7.56e-01 8.27e+00 angle pdb=" N VAL D 318 " pdb=" CA VAL D 318 " pdb=" C VAL D 318 " ideal model delta sigma weight residual 112.80 109.57 3.23 1.15e+00 7.56e-01 7.91e+00 angle pdb=" C CYS D 498 " pdb=" N ASP D 499 " pdb=" CA ASP D 499 " ideal model delta sigma weight residual 119.78 123.01 -3.23 1.24e+00 6.50e-01 6.78e+00 angle pdb=" C CYS F 498 " pdb=" N ASP F 499 " pdb=" CA ASP F 499 " ideal model delta sigma weight residual 119.78 122.93 -3.15 1.24e+00 6.50e-01 6.44e+00 ... (remaining 54424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 22934 16.43 - 32.86: 643 32.86 - 49.28: 151 49.28 - 65.71: 17 65.71 - 82.14: 6 Dihedral angle restraints: 23751 sinusoidal: 9414 harmonic: 14337 Sorted by residual: dihedral pdb=" CA LYS E 470 " pdb=" C LYS E 470 " pdb=" N ASP E 471 " pdb=" CA ASP E 471 " ideal model delta harmonic sigma weight residual 180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA LEU D 144 " pdb=" C LEU D 144 " pdb=" N GLU D 145 " pdb=" CA GLU D 145 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA LEU E 144 " pdb=" C LEU E 144 " pdb=" N GLU E 145 " pdb=" CA GLU E 145 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 23748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4037 0.031 - 0.061: 1320 0.061 - 0.092: 324 0.092 - 0.123: 306 0.123 - 0.154: 4 Chirality restraints: 5991 Sorted by residual: chirality pdb=" CG LEU B 18 " pdb=" CB LEU B 18 " pdb=" CD1 LEU B 18 " pdb=" CD2 LEU B 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA PRO F 469 " pdb=" N PRO F 469 " pdb=" C PRO F 469 " pdb=" CB PRO F 469 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 5988 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 582 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO F 583 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 583 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO B 987 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 582 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO E 583 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 583 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 583 " 0.021 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3785 2.75 - 3.29: 37978 3.29 - 3.82: 65192 3.82 - 4.36: 75330 4.36 - 4.90: 133351 Nonbonded interactions: 315636 Sorted by model distance: nonbonded pdb=" O VAL C 608 " pdb=" OH TYR C 636 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD2 ASP B 111 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" OD1 ASN A 914 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR F 41 " pdb=" OG1 THR C 500 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP F 494 " pdb=" OG1 THR F 496 " model vdw 2.266 3.040 ... (remaining 315631 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 35.920 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.001 0.034 40057 Z= 0.080 Angle : 0.411 8.296 54515 Z= 0.226 Chirality : 0.038 0.154 5991 Planarity : 0.003 0.041 7032 Dihedral : 7.914 82.139 14388 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 1.99 % Allowed : 4.26 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.11), residues: 4851 helix: 0.67 (0.12), residues: 1797 sheet: -0.56 (0.18), residues: 633 loop : -1.73 (0.11), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1000 TYR 0.015 0.001 TYR F 385 PHE 0.006 0.001 PHE C 133 TRP 0.010 0.000 TRP B 633 HIS 0.002 0.000 HIS F 373 Details of bonding type rmsd covalent geometry : bond 0.00146 (40014) covalent geometry : angle 0.41026 (54429) SS BOND : bond 0.00099 ( 43) SS BOND : angle 0.55161 ( 86) hydrogen bonds : bond 0.16070 ( 1811) hydrogen bonds : angle 6.78839 ( 5268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 459 time to evaluate : 1.454 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: F 455 MET cc_start: 0.4552 (tmm) cc_final: 0.4281 (tmm) REVERT: D 557 MET cc_start: 0.5046 (tmm) cc_final: 0.4186 (tmm) REVERT: D 579 MET cc_start: 0.1796 (mtm) cc_final: 0.1356 (mtm) REVERT: E 455 MET cc_start: 0.4850 (tmm) cc_final: 0.4590 (tmm) REVERT: B 1125 ASN cc_start: 0.6642 (p0) cc_final: 0.6237 (p0) outliers start: 86 outliers final: 29 residues processed: 532 average time/residue: 0.6881 time to fit residues: 446.2585 Evaluate side-chains 352 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 945 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.0470 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN F 102 GLN F 210 ASN F 388 GLN D 98 GLN D 102 GLN D 210 ASN D 373 HIS D 388 GLN D 524 GLN E 98 GLN E 102 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 HIS E 388 GLN E 493 HIS E 524 GLN E 599 ASN A 17 ASN A 30 ASN A 218 GLN A 493 GLN A 544 ASN A 563 GLN A 677 GLN A 901 GLN A 955 ASN A 960 ASN A 965 GLN A 992 GLN A1071 GLN A1074 ASN A1142 GLN B 87 ASN B 125 ASN B 321 GLN B 439 ASN B 493 GLN B 563 GLN B 580 GLN B 603 ASN B 628 GLN B 690 GLN B 872 GLN B 907 ASN B 913 GLN B 914 ASN B 935 GLN B 965 GLN B1071 GLN C 218 GLN C 314 GLN C 339 HIS C 493 GLN C 563 GLN C 603 ASN C 628 GLN C 872 GLN C 901 GLN C 914 ASN C 935 GLN C1002 GLN C1071 GLN C1142 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.228168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.182787 restraints weight = 72004.699| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 7.10 r_work: 0.2812 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 40057 Z= 0.196 Angle : 0.583 10.614 54515 Z= 0.306 Chirality : 0.045 0.286 5991 Planarity : 0.005 0.073 7032 Dihedral : 4.798 59.202 5321 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.31 % Allowed : 7.64 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4851 helix: 1.57 (0.12), residues: 1812 sheet: 0.04 (0.17), residues: 678 loop : -1.27 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1107 TYR 0.036 0.002 TYR C 28 PHE 0.024 0.002 PHE B 939 TRP 0.029 0.001 TRP B 633 HIS 0.009 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00459 (40014) covalent geometry : angle 0.57966 (54429) SS BOND : bond 0.00470 ( 43) SS BOND : angle 1.73109 ( 86) hydrogen bonds : bond 0.04389 ( 1811) hydrogen bonds : angle 5.17376 ( 5268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 320 time to evaluate : 1.099 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: F 203 TRP cc_start: -0.0144 (OUTLIER) cc_final: -0.0735 (m-10) REVERT: D 557 MET cc_start: 0.5278 (tmm) cc_final: 0.4121 (tmm) REVERT: D 579 MET cc_start: -0.0575 (mtm) cc_final: -0.1065 (mtm) REVERT: A 1113 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: B 122 ASN cc_start: 0.8247 (p0) cc_final: 0.7875 (p0) REVERT: B 633 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.7965 (p-90) REVERT: B 990 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8457 (tp30) REVERT: B 1119 ASN cc_start: 0.8351 (m-40) cc_final: 0.8029 (m110) outliers start: 100 outliers final: 43 residues processed: 389 average time/residue: 0.6312 time to fit residues: 303.0170 Evaluate side-chains 337 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 732 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 407 optimal weight: 0.9980 chunk 159 optimal weight: 40.0000 chunk 170 optimal weight: 30.0000 chunk 308 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 258 optimal weight: 0.9980 chunk 131 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 58 optimal weight: 30.0000 chunk 458 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 373 HIS E 149 ASN A 563 GLN A 703 ASN A 804 GLN A 935 GLN A1002 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 339 HIS C1002 GLN C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.224251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.174996 restraints weight = 70192.220| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 7.42 r_work: 0.2668 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.211 40057 Z= 0.426 Angle : 0.795 12.639 54515 Z= 0.422 Chirality : 0.055 0.296 5991 Planarity : 0.007 0.114 7032 Dihedral : 5.541 59.890 5313 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 3.66 % Allowed : 8.01 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4851 helix: 1.50 (0.12), residues: 1836 sheet: 0.05 (0.17), residues: 699 loop : -1.16 (0.12), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 815 TYR 0.037 0.002 TYR C 28 PHE 0.038 0.003 PHE B 939 TRP 0.038 0.001 TRP B 633 HIS 0.014 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01043 (40014) covalent geometry : angle 0.79139 (54429) SS BOND : bond 0.01026 ( 43) SS BOND : angle 2.14065 ( 86) hydrogen bonds : bond 0.05476 ( 1811) hydrogen bonds : angle 5.34620 ( 5268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 303 time to evaluate : 1.547 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: F 203 TRP cc_start: -0.0014 (OUTLIER) cc_final: -0.0665 (m-10) REVERT: D 480 MET cc_start: 0.1081 (mtp) cc_final: 0.0733 (mtp) REVERT: D 557 MET cc_start: 0.5353 (tmm) cc_final: 0.4195 (tmm) REVERT: D 579 MET cc_start: -0.0506 (mtm) cc_final: -0.0902 (mtm) REVERT: A 129 LYS cc_start: 0.8896 (ptmm) cc_final: 0.8687 (ptmm) REVERT: A 224 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8895 (mt-10) REVERT: A 980 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8587 (mt) REVERT: A 1113 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8447 (mm110) REVERT: B 19 ILE cc_start: 0.5816 (OUTLIER) cc_final: 0.5582 (pp) REVERT: B 314 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: B 633 TRP cc_start: 0.9153 (OUTLIER) cc_final: 0.7574 (p-90) REVERT: C 52 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.7940 (tm-30) outliers start: 158 outliers final: 83 residues processed: 421 average time/residue: 0.6923 time to fit residues: 357.4372 Evaluate side-chains 374 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 283 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1147 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 74 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 469 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 465 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 426 optimal weight: 10.0000 chunk 395 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 456 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 321 GLN A 563 GLN A 804 GLN A 935 GLN A1002 GLN A1142 GLN B 331 ASN B 779 GLN C 321 GLN C 339 HIS C 935 GLN C1002 GLN C1142 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.225541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.175898 restraints weight = 70254.391| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 7.93 r_work: 0.2671 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 40057 Z= 0.225 Angle : 0.607 10.026 54515 Z= 0.321 Chirality : 0.045 0.211 5991 Planarity : 0.005 0.077 7032 Dihedral : 5.239 59.500 5311 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.26 % Allowed : 8.82 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 4851 helix: 1.88 (0.12), residues: 1818 sheet: 0.19 (0.17), residues: 720 loop : -1.07 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.027 0.001 TYR C 265 PHE 0.035 0.002 PHE B 939 TRP 0.028 0.001 TRP B 633 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00537 (40014) covalent geometry : angle 0.60361 (54429) SS BOND : bond 0.00527 ( 43) SS BOND : angle 1.66668 ( 86) hydrogen bonds : bond 0.04386 ( 1811) hydrogen bonds : angle 5.04987 ( 5268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 299 time to evaluate : 1.483 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: F 203 TRP cc_start: -0.0023 (OUTLIER) cc_final: -0.0569 (m-10) REVERT: D 480 MET cc_start: 0.1053 (mtp) cc_final: 0.0812 (mtp) REVERT: D 557 MET cc_start: 0.5326 (tmm) cc_final: 0.4318 (tmm) REVERT: D 579 MET cc_start: -0.0683 (mtm) cc_final: -0.0981 (mtm) REVERT: E 579 MET cc_start: 0.1027 (mtm) cc_final: 0.0774 (ttm) REVERT: A 224 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8829 (mt-10) REVERT: A 229 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (pp) REVERT: A 418 ILE cc_start: 0.3682 (OUTLIER) cc_final: 0.3248 (pt) REVERT: A 1073 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9371 (ttpp) REVERT: A 1113 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8385 (mt0) REVERT: B 19 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5390 (pp) REVERT: B 190 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8084 (mtm-85) REVERT: B 314 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: B 633 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8066 (p-90) REVERT: C 52 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: C 314 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: C 726 ILE cc_start: 0.9635 (OUTLIER) cc_final: 0.9380 (mt) REVERT: C 990 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8444 (tt0) outliers start: 141 outliers final: 69 residues processed: 404 average time/residue: 0.6439 time to fit residues: 318.0595 Evaluate side-chains 365 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 357 optimal weight: 0.7980 chunk 361 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 429 optimal weight: 5.9990 chunk 440 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 779 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 339 HIS C1002 GLN C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.225639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.173363 restraints weight = 70449.583| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 9.31 r_work: 0.2724 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 40057 Z= 0.208 Angle : 0.596 10.031 54515 Z= 0.313 Chirality : 0.045 0.232 5991 Planarity : 0.005 0.077 7032 Dihedral : 5.200 59.913 5310 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.29 % Allowed : 9.28 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 4851 helix: 2.06 (0.12), residues: 1809 sheet: 0.20 (0.17), residues: 738 loop : -0.95 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 646 TYR 0.028 0.001 TYR C 28 PHE 0.036 0.002 PHE B 939 TRP 0.027 0.001 TRP B 633 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00497 (40014) covalent geometry : angle 0.59158 (54429) SS BOND : bond 0.00489 ( 43) SS BOND : angle 1.82348 ( 86) hydrogen bonds : bond 0.04238 ( 1811) hydrogen bonds : angle 4.97968 ( 5268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 290 time to evaluate : 1.378 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: F 203 TRP cc_start: -0.0426 (OUTLIER) cc_final: -0.1178 (m-10) REVERT: F 383 MET cc_start: 0.4107 (mtp) cc_final: 0.3507 (mtp) REVERT: D 557 MET cc_start: 0.5087 (tmm) cc_final: 0.3919 (tmm) REVERT: A 224 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: A 229 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 418 ILE cc_start: 0.3720 (OUTLIER) cc_final: 0.3248 (pt) REVERT: A 990 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 1073 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9340 (ttpp) REVERT: A 1113 GLN cc_start: 0.9264 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: B 19 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.5198 (pp) REVERT: B 314 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: B 633 TRP cc_start: 0.8947 (OUTLIER) cc_final: 0.8121 (p-90) REVERT: C 52 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: C 226 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 314 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 636 TYR cc_start: 0.5286 (t80) cc_final: 0.5083 (t80) REVERT: C 726 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9387 (mt) REVERT: C 990 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8405 (tt0) outliers start: 142 outliers final: 84 residues processed: 395 average time/residue: 0.7219 time to fit residues: 348.6385 Evaluate side-chains 384 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 285 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 140 optimal weight: 50.0000 chunk 204 optimal weight: 6.9990 chunk 465 optimal weight: 0.5980 chunk 441 optimal weight: 0.0770 chunk 392 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 474 optimal weight: 0.6980 chunk 450 optimal weight: 0.9990 chunk 412 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN A1142 GLN B 779 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 339 HIS C1142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.226826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.180241 restraints weight = 71308.815| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 7.20 r_work: 0.2792 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40057 Z= 0.125 Angle : 0.522 10.568 54515 Z= 0.272 Chirality : 0.042 0.189 5991 Planarity : 0.004 0.075 7032 Dihedral : 4.930 57.912 5309 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.80 % Allowed : 10.19 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 4851 helix: 2.26 (0.12), residues: 1806 sheet: 0.22 (0.17), residues: 768 loop : -0.80 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 646 TYR 0.025 0.001 TYR C 170 PHE 0.034 0.001 PHE B 939 TRP 0.018 0.001 TRP C 633 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00283 (40014) covalent geometry : angle 0.51990 (54429) SS BOND : bond 0.00279 ( 43) SS BOND : angle 1.27050 ( 86) hydrogen bonds : bond 0.03613 ( 1811) hydrogen bonds : angle 4.78437 ( 5268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 303 time to evaluate : 1.519 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: F 203 TRP cc_start: -0.0162 (OUTLIER) cc_final: -0.0742 (m-10) REVERT: D 557 MET cc_start: 0.5328 (tmm) cc_final: 0.4281 (tmm) REVERT: E 270 MET cc_start: 0.0910 (OUTLIER) cc_final: 0.0674 (tpp) REVERT: E 366 MET cc_start: 0.3718 (ttt) cc_final: 0.3461 (mtt) REVERT: E 579 MET cc_start: 0.0198 (ttm) cc_final: -0.0200 (ttm) REVERT: A 314 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: A 418 ILE cc_start: 0.3696 (OUTLIER) cc_final: 0.3273 (pt) REVERT: A 878 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 990 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 19 ILE cc_start: 0.5288 (OUTLIER) cc_final: 0.4919 (pp) REVERT: B 314 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: B 633 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.8209 (p-90) REVERT: B 904 TYR cc_start: 0.8452 (m-10) cc_final: 0.8250 (m-10) REVERT: C 52 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 226 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8536 (mp) REVERT: C 314 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: C 636 TYR cc_start: 0.5067 (t80) cc_final: 0.4821 (t80) REVERT: C 990 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8258 (tt0) outliers start: 121 outliers final: 66 residues processed: 391 average time/residue: 0.6520 time to fit residues: 313.1078 Evaluate side-chains 366 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 7 optimal weight: 50.0000 chunk 287 optimal weight: 3.9990 chunk 399 optimal weight: 0.7980 chunk 413 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 112 optimal weight: 50.0000 chunk 387 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 441 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 381 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 87 ASN C 339 HIS ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.226406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.179151 restraints weight = 70609.567| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 7.34 r_work: 0.2777 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work: 0.2732 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work: 0.2732 rms_B_bonded: 4.89 restraints_weight: 0.0625 r_work: 0.2732 rms_B_bonded: 4.89 restraints_weight: 0.0312 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 40057 Z= 0.154 Angle : 0.553 10.319 54515 Z= 0.289 Chirality : 0.043 0.205 5991 Planarity : 0.004 0.074 7032 Dihedral : 4.952 58.141 5308 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.99 % Allowed : 10.30 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 4851 helix: 2.28 (0.12), residues: 1806 sheet: 0.24 (0.17), residues: 768 loop : -0.76 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 995 TYR 0.024 0.001 TYR A 170 PHE 0.034 0.001 PHE B 939 TRP 0.023 0.001 TRP B 633 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (40014) covalent geometry : angle 0.54953 (54429) SS BOND : bond 0.00387 ( 43) SS BOND : angle 1.69050 ( 86) hydrogen bonds : bond 0.03838 ( 1811) hydrogen bonds : angle 4.80276 ( 5268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 296 time to evaluate : 1.486 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: F 203 TRP cc_start: -0.0079 (OUTLIER) cc_final: -0.0664 (m-10) REVERT: F 323 MET cc_start: 0.1846 (OUTLIER) cc_final: 0.1327 (tmm) REVERT: F 359 LEU cc_start: -0.6487 (OUTLIER) cc_final: -0.6769 (mt) REVERT: D 480 MET cc_start: 0.1039 (mtp) cc_final: 0.0714 (mtp) REVERT: D 557 MET cc_start: 0.5329 (tmm) cc_final: 0.4316 (tmm) REVERT: E 270 MET cc_start: 0.0849 (OUTLIER) cc_final: 0.0296 (tpp) REVERT: E 323 MET cc_start: -0.0211 (tmm) cc_final: -0.0806 (tmm) REVERT: E 366 MET cc_start: 0.3768 (ttt) cc_final: 0.3519 (mtt) REVERT: E 579 MET cc_start: 0.0295 (ttm) cc_final: -0.0110 (ttm) REVERT: A 226 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: A 418 ILE cc_start: 0.3660 (OUTLIER) cc_final: 0.3281 (pt) REVERT: A 563 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8686 (mt0) REVERT: A 878 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 990 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 1073 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9221 (ttpp) REVERT: A 1113 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: B 19 ILE cc_start: 0.5297 (OUTLIER) cc_final: 0.4897 (pp) REVERT: B 314 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: B 633 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.8210 (p-90) REVERT: C 52 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: C 226 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8575 (mp) REVERT: C 314 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: C 636 TYR cc_start: 0.5229 (t80) cc_final: 0.4995 (t80) REVERT: C 990 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: C 1106 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8795 (mt0) outliers start: 129 outliers final: 79 residues processed: 395 average time/residue: 0.6097 time to fit residues: 297.8229 Evaluate side-chains 385 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 286 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 62 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 280 optimal weight: 0.5980 chunk 149 optimal weight: 0.0770 chunk 236 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 259 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 422 optimal weight: 0.0670 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 218 GLN B 935 GLN B1119 ASN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.226628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.178838 restraints weight = 70688.865| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 7.60 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0625 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0312 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0156 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0078 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0039 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0020 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0010 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0005 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0002 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0001 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0001 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.0000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 40057 Z= 0.148 Angle : 0.552 12.030 54515 Z= 0.289 Chirality : 0.043 0.307 5991 Planarity : 0.004 0.088 7032 Dihedral : 4.937 58.626 5307 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.94 % Allowed : 10.79 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 4851 helix: 2.31 (0.12), residues: 1806 sheet: 0.27 (0.17), residues: 768 loop : -0.72 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1107 TYR 0.025 0.001 TYR C 170 PHE 0.034 0.001 PHE B 939 TRP 0.021 0.001 TRP B 633 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00347 (40014) covalent geometry : angle 0.54808 (54429) SS BOND : bond 0.00404 ( 43) SS BOND : angle 1.76555 ( 86) hydrogen bonds : bond 0.03734 ( 1811) hydrogen bonds : angle 4.78615 ( 5268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 291 time to evaluate : 1.577 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: F 203 TRP cc_start: -0.0086 (OUTLIER) cc_final: -0.0650 (m-10) REVERT: F 359 LEU cc_start: -0.6557 (OUTLIER) cc_final: -0.6852 (mt) REVERT: D 480 MET cc_start: 0.1035 (mtp) cc_final: 0.0741 (mtp) REVERT: D 557 MET cc_start: 0.5343 (tmm) cc_final: 0.4376 (tmm) REVERT: E 270 MET cc_start: 0.0734 (OUTLIER) cc_final: 0.0320 (tpp) REVERT: E 323 MET cc_start: -0.0039 (tmm) cc_final: -0.0597 (tmm) REVERT: E 366 MET cc_start: 0.3900 (ttt) cc_final: 0.3667 (mtt) REVERT: E 579 MET cc_start: 0.0362 (ttm) cc_final: -0.0115 (ttm) REVERT: A 226 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 314 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 418 ILE cc_start: 0.3770 (OUTLIER) cc_final: 0.3362 (pt) REVERT: A 878 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8876 (mm) REVERT: A 990 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 1113 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: B 19 ILE cc_start: 0.5286 (OUTLIER) cc_final: 0.4931 (pp) REVERT: B 314 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: B 633 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.8194 (p-90) REVERT: C 52 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: C 226 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 314 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: C 636 TYR cc_start: 0.5059 (t80) cc_final: 0.4808 (t80) REVERT: C 990 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8294 (tt0) outliers start: 127 outliers final: 80 residues processed: 386 average time/residue: 0.6939 time to fit residues: 330.9189 Evaluate side-chains 383 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 287 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 PRO Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1126 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 39 optimal weight: 30.0000 chunk 282 optimal weight: 0.0670 chunk 355 optimal weight: 2.9990 chunk 410 optimal weight: 1.9990 chunk 447 optimal weight: 2.9990 chunk 391 optimal weight: 0.4980 chunk 279 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 152 optimal weight: 0.0040 chunk 320 optimal weight: 0.0170 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 439 ASN A 563 GLN A 613 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 779 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 613 GLN C1119 ASN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.228111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.181901 restraints weight = 71899.642| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 7.52 r_work: 0.2848 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work: 0.2839 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work: 0.2839 rms_B_bonded: 4.22 restraints_weight: 0.0625 r_work: 0.2839 rms_B_bonded: 4.22 restraints_weight: 0.0312 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 40057 Z= 0.103 Angle : 0.516 11.848 54515 Z= 0.266 Chirality : 0.042 0.234 5991 Planarity : 0.004 0.076 7032 Dihedral : 4.727 59.153 5307 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.22 % Allowed : 11.60 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.05 (0.12), residues: 4851 helix: 2.43 (0.12), residues: 1806 sheet: 0.42 (0.17), residues: 738 loop : -0.64 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 237 TYR 0.027 0.001 TYR A 170 PHE 0.036 0.001 PHE A 168 TRP 0.018 0.001 TRP C 633 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00225 (40014) covalent geometry : angle 0.51436 (54429) SS BOND : bond 0.00209 ( 43) SS BOND : angle 1.28499 ( 86) hydrogen bonds : bond 0.03206 ( 1811) hydrogen bonds : angle 4.60524 ( 5268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 301 time to evaluate : 1.504 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: F 203 TRP cc_start: -0.0246 (OUTLIER) cc_final: -0.0854 (m-10) REVERT: F 323 MET cc_start: 0.1710 (OUTLIER) cc_final: 0.1078 (tmm) REVERT: F 359 LEU cc_start: -0.6597 (OUTLIER) cc_final: -0.6882 (mt) REVERT: D 480 MET cc_start: 0.1119 (mtp) cc_final: 0.0863 (mtp) REVERT: D 557 MET cc_start: 0.5283 (tmm) cc_final: 0.4380 (tmm) REVERT: E 152 MET cc_start: -0.0586 (mmm) cc_final: -0.0905 (mmm) REVERT: E 270 MET cc_start: 0.0845 (OUTLIER) cc_final: 0.0535 (tpp) REVERT: E 323 MET cc_start: 0.0005 (OUTLIER) cc_final: -0.0560 (tmm) REVERT: E 366 MET cc_start: 0.4063 (ttt) cc_final: 0.3835 (mtt) REVERT: E 579 MET cc_start: 0.0282 (ttm) cc_final: -0.0147 (ttm) REVERT: A 226 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 418 ILE cc_start: 0.3576 (OUTLIER) cc_final: 0.3234 (pt) REVERT: B 19 ILE cc_start: 0.5330 (OUTLIER) cc_final: 0.5005 (pp) REVERT: B 314 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: B 633 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7813 (p-90) REVERT: C 226 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8528 (mp) REVERT: C 314 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: C 636 TYR cc_start: 0.4813 (t80) cc_final: 0.4499 (t80) REVERT: C 990 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8175 (tt0) outliers start: 96 outliers final: 56 residues processed: 370 average time/residue: 0.6528 time to fit residues: 296.5511 Evaluate side-chains 364 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 PRO Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 117 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 478 optimal weight: 0.9980 chunk 325 optimal weight: 0.0980 chunk 94 optimal weight: 50.0000 chunk 165 optimal weight: 2.9990 chunk 451 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 314 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 87 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN C 613 GLN C 804 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.226318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.176860 restraints weight = 70580.966| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 8.31 r_work: 0.2720 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work: 0.2680 rms_B_bonded: 4.98 restraints_weight: 0.1250 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 40057 Z= 0.178 Angle : 0.590 11.280 54515 Z= 0.309 Chirality : 0.044 0.258 5991 Planarity : 0.005 0.074 7032 Dihedral : 4.961 59.204 5303 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.25 % Allowed : 11.88 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.97 (0.12), residues: 4851 helix: 2.37 (0.12), residues: 1806 sheet: 0.29 (0.17), residues: 768 loop : -0.66 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 237 TYR 0.040 0.001 TYR C 904 PHE 0.036 0.002 PHE B 939 TRP 0.027 0.001 TRP B 633 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00423 (40014) covalent geometry : angle 0.58600 (54429) SS BOND : bond 0.00474 ( 43) SS BOND : angle 1.72693 ( 86) hydrogen bonds : bond 0.03930 ( 1811) hydrogen bonds : angle 4.79224 ( 5268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 1.400 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: F 203 TRP cc_start: -0.0120 (OUTLIER) cc_final: -0.0673 (m-10) REVERT: F 323 MET cc_start: 0.1494 (OUTLIER) cc_final: 0.0870 (tmm) REVERT: F 359 LEU cc_start: -0.6590 (OUTLIER) cc_final: -0.6860 (mt) REVERT: D 480 MET cc_start: 0.1129 (mtp) cc_final: 0.0861 (mtp) REVERT: D 557 MET cc_start: 0.5287 (tmm) cc_final: 0.4418 (tmm) REVERT: E 152 MET cc_start: -0.0580 (mmm) cc_final: -0.0889 (mmm) REVERT: E 270 MET cc_start: 0.0760 (OUTLIER) cc_final: 0.0429 (tpp) REVERT: E 323 MET cc_start: -0.0281 (OUTLIER) cc_final: -0.0768 (tmm) REVERT: E 366 MET cc_start: 0.3756 (ttt) cc_final: 0.3520 (mtt) REVERT: E 579 MET cc_start: 0.0518 (ttm) cc_final: 0.0013 (ttm) REVERT: A 197 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 226 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8785 (mp) REVERT: A 418 ILE cc_start: 0.3443 (OUTLIER) cc_final: 0.3104 (pt) REVERT: A 1073 LYS cc_start: 0.9586 (OUTLIER) cc_final: 0.9216 (ttpp) REVERT: B 19 ILE cc_start: 0.5437 (OUTLIER) cc_final: 0.5039 (pp) REVERT: B 314 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: B 633 TRP cc_start: 0.8932 (OUTLIER) cc_final: 0.8138 (p-90) REVERT: C 168 PHE cc_start: 0.7539 (t80) cc_final: 0.7234 (t80) REVERT: C 226 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8572 (mp) REVERT: C 314 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: C 636 TYR cc_start: 0.5266 (t80) cc_final: 0.5034 (t80) REVERT: C 990 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8391 (tt0) outliers start: 97 outliers final: 66 residues processed: 357 average time/residue: 0.6693 time to fit residues: 293.2954 Evaluate side-chains 366 residues out of total 4320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 169 ARG Chi-restraints excluded: chain F residue 203 TRP Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 518 ARG Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 102 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 987 PRO Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 80 optimal weight: 10.0000 chunk 152 optimal weight: 40.0000 chunk 136 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 371 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 77 optimal weight: 40.0000 chunk 397 optimal weight: 2.9990 chunk 402 optimal weight: 0.9980 chunk 360 optimal weight: 0.9990 chunk 413 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 314 GLN A 613 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 804 GLN C1002 GLN C1119 ASN C1142 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.225577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.174804 restraints weight = 70406.720| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 8.57 r_work: 0.2671 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 40057 Z= 0.231 Angle : 0.639 11.502 54515 Z= 0.337 Chirality : 0.046 0.276 5991 Planarity : 0.005 0.111 7032 Dihedral : 5.123 59.325 5303 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.36 % Allowed : 11.90 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.88 (0.12), residues: 4851 helix: 2.30 (0.12), residues: 1806 sheet: 0.24 (0.17), residues: 768 loop : -0.73 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B1107 TYR 0.045 0.002 TYR B 904 PHE 0.026 0.002 PHE C 32 TRP 0.031 0.001 TRP B 633 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00555 (40014) covalent geometry : angle 0.63492 (54429) SS BOND : bond 0.00577 ( 43) SS BOND : angle 1.93858 ( 86) hydrogen bonds : bond 0.04235 ( 1811) hydrogen bonds : angle 4.90046 ( 5268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31208.65 seconds wall clock time: 527 minutes 4.67 seconds (31624.67 seconds total)