Starting phenix.real_space_refine on Mon Jul 6 13:05:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.map" model { file = "/net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1n_66464/07_2026/9x1n_66464.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 8 7.51 5 P 58 5.49 5 S 102 5.16 5 C 21744 2.51 5 N 6010 2.21 5 O 6660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34582 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "B" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "C" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "D" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "E" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "F" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "G" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3197 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "H" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3197 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "I" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 420 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 400 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' MN': 1} Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 8.58, per 1000 atoms: 0.25 Number of scatterers: 34582 At special positions: 0 Unit cell: (139.12, 149.648, 185.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 8 24.99 S 102 16.00 P 58 15.00 O 6660 8.00 N 6010 7.00 C 21744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 44 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 52 " 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: 3.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7724 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 23 sheets defined 49.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.616A pdb=" N GLN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 319 through 341 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.568A pdb=" N ALA A 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 402 Processing helix chain 'A' and resid 410 through 428 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.788A pdb=" N GLU A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.729A pdb=" N PHE A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 466 through 469 removed outlier: 3.536A pdb=" N GLY A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 466 through 469' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 500 through 509 removed outlier: 3.656A pdb=" N ARG A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 561 through 578 Processing helix chain 'B' and resid 50 through 55 removed outlier: 4.179A pdb=" N TRP B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 55' Processing helix chain 'B' and resid 84 through 96 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 190 through 207 Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.820A pdb=" N ALA B 243 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 281 through 297 removed outlier: 3.886A pdb=" N ALA B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 341 removed outlier: 3.554A pdb=" N GLU B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 367 through 403 Processing helix chain 'B' and resid 406 through 409 removed outlier: 3.834A pdb=" N ALA B 409 " --> pdb=" O ASN B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 409' Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.644A pdb=" N ALA B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.168A pdb=" N PHE B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 465 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.785A pdb=" N MET B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 523 " --> pdb=" O MET B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 561 through 578 Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.715A pdb=" N ARG C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 49 through 54' Processing helix chain 'C' and resid 84 through 95 removed outlier: 3.520A pdb=" N TYR C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 101 removed outlier: 3.578A pdb=" N ILE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 190 through 207 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 259 through 278 Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.825A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 300 " --> pdb=" O TRP C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 367 through 401 Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.664A pdb=" N GLU C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.807A pdb=" N PHE C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.547A pdb=" N ARG C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYS C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 548 through 552 removed outlier: 3.762A pdb=" N GLY C 552 " --> pdb=" O LYS C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 578 removed outlier: 3.506A pdb=" N GLU C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 95 through 101 removed outlier: 4.059A pdb=" N GLU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 190 through 206 removed outlier: 3.597A pdb=" N THR D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 259 through 278 Processing helix chain 'D' and resid 282 through 300 removed outlier: 3.769A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 345 removed outlier: 5.413A pdb=" N HIS D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 403 removed outlier: 3.629A pdb=" N LEU D 373 " --> pdb=" O GLY D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.761A pdb=" N GLU D 433 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.604A pdb=" N PHE D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.460A pdb=" N ILE D 457 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 519 removed outlier: 4.144A pdb=" N GLU D 517 " --> pdb=" O GLN D 513 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 561 through 578 Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.547A pdb=" N GLY E 55 " --> pdb=" O ASN E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 96 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 190 through 207 Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 245 through 253 Processing helix chain 'E' and resid 259 through 278 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.709A pdb=" N VAL E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 341 Processing helix chain 'E' and resid 348 through 353 removed outlier: 3.890A pdb=" N ILE E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 403 Processing helix chain 'E' and resid 406 through 428 removed outlier: 3.858A pdb=" N VAL E 410 " --> pdb=" O ASN E 406 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.783A pdb=" N GLU E 433 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.960A pdb=" N PHE E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 469 removed outlier: 5.616A pdb=" N ARG E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 488 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 513 through 521 removed outlier: 3.765A pdb=" N GLU E 517 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET E 519 " --> pdb=" O GLY E 516 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER E 520 " --> pdb=" O GLU E 517 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP E 521 " --> pdb=" O LEU E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 552 Processing helix chain 'E' and resid 561 through 577 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.502A pdb=" N TYR F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 102 Processing helix chain 'F' and resid 141 through 150 Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 245 through 253 Processing helix chain 'F' and resid 260 through 278 Processing helix chain 'F' and resid 282 through 300 removed outlier: 3.613A pdb=" N VAL F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 341 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.593A pdb=" N ILE F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 403 Processing helix chain 'F' and resid 404 through 407 removed outlier: 4.166A pdb=" N ILE F 407 " --> pdb=" O SER F 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 404 through 407' Processing helix chain 'F' and resid 410 through 428 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.567A pdb=" N ALA F 432 " --> pdb=" O PRO F 429 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU F 433 " --> pdb=" O ALA F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 441 through 446 removed outlier: 3.694A pdb=" N PHE F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 469 removed outlier: 4.555A pdb=" N ILE F 457 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ARG F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 Processing helix chain 'F' and resid 483 through 489 removed outlier: 3.700A pdb=" N GLN F 489 " --> pdb=" O ASP F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 511 Processing helix chain 'F' and resid 515 through 521 removed outlier: 4.206A pdb=" N ASP F 521 " --> pdb=" O GLU F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 551 removed outlier: 3.521A pdb=" N LEU F 551 " --> pdb=" O PHE F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 578 removed outlier: 3.968A pdb=" N ARG F 565 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 27 removed outlier: 3.749A pdb=" N LYS G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 114 removed outlier: 4.161A pdb=" N ALA G 111 " --> pdb=" O GLY G 107 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 131 Processing helix chain 'G' and resid 135 through 150 removed outlier: 4.206A pdb=" N VAL G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 179 removed outlier: 3.732A pdb=" N LEU G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS G 160 " --> pdb=" O GLU G 156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.684A pdb=" N GLU G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 203 removed outlier: 3.608A pdb=" N TYR G 200 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA G 202 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET G 203 " --> pdb=" O PHE G 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 196 through 203' Processing helix chain 'G' and resid 255 through 279 removed outlier: 4.188A pdb=" N VAL G 264 " --> pdb=" O ASN G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 removed outlier: 3.623A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 318 Processing helix chain 'G' and resid 339 through 344 removed outlier: 4.083A pdb=" N GLU G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 356 removed outlier: 3.548A pdb=" N GLU G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 388 Processing helix chain 'G' and resid 397 through 406 Processing helix chain 'G' and resid 409 through 428 Processing helix chain 'G' and resid 429 through 434 removed outlier: 4.151A pdb=" N VAL G 433 " --> pdb=" O GLU G 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 27 removed outlier: 3.564A pdb=" N GLY H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 90 through 114 removed outlier: 3.586A pdb=" N ALA H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 134 through 150 Processing helix chain 'H' and resid 153 through 179 Processing helix chain 'H' and resid 187 through 192 removed outlier: 3.610A pdb=" N GLU H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 196 through 205 removed outlier: 3.856A pdb=" N TYR H 200 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 279 removed outlier: 4.072A pdb=" N ALA H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 removed outlier: 4.452A pdb=" N LYS H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 318 removed outlier: 3.573A pdb=" N TYR H 308 " --> pdb=" O VAL H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 346 removed outlier: 3.906A pdb=" N GLU H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR H 345 " --> pdb=" O VAL H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 removed outlier: 3.841A pdb=" N GLU H 350 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 388 Processing helix chain 'H' and resid 396 through 407 Processing helix chain 'H' and resid 409 through 428 Processing helix chain 'H' and resid 429 through 435 removed outlier: 3.928A pdb=" N VAL H 433 " --> pdb=" O GLU H 430 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE H 434 " --> pdb=" O LEU H 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.868A pdb=" N ALA A 104 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN A 73 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 71 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 108 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 65 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A 114 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TRP A 63 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A 42 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 12 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN A 24 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU A 105 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 172 removed outlier: 6.965A pdb=" N VAL A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 209 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A 438 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 211 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU A 440 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 213 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN A 233 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP A 362 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 235 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 125 removed outlier: 6.768A pdb=" N GLU B 103 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 75 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 105 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN B 73 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 107 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 71 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 109 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG B 69 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL B 111 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR B 67 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TRP B 63 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG B 42 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG B 136 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 12 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN B 24 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU B 105 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.956A pdb=" N GLY B 159 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 171 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU B 157 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 182 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 437 " --> pdb=" O GLY B 473 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL B 475 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 439 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 211 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU B 440 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 213 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 210 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 361 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 212 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 15 removed outlier: 4.311A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU C 105 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 12 through 15 removed outlier: 4.311A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU C 105 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU C 103 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C 75 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C 105 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN C 73 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 107 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 71 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 109 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG C 69 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL C 111 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 67 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP C 63 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.988A pdb=" N GLY C 159 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 171 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLU C 157 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS C 180 " --> pdb=" O THR C 492 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE C 494 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA C 182 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 181 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY C 471 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 210 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE C 361 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 212 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 125 removed outlier: 6.811A pdb=" N ALA D 104 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN D 73 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 106 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU D 71 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR D 108 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE D 65 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS D 114 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TRP D 63 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 39 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG D 42 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D 24 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 105 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 168 through 172 removed outlier: 6.798A pdb=" N VAL D 169 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA D 182 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 474 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER D 476 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 209 " --> pdb=" O MET D 436 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 438 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 211 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 214 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN D 233 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 362 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 235 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 303 through 306 Processing sheet with id=AB5, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.696A pdb=" N GLU E 103 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN E 75 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU E 105 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN E 73 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL E 107 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU E 71 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL E 109 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG E 69 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL E 111 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR E 67 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TRP E 63 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG E 42 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARG E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 12 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.793A pdb=" N VAL E 169 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA E 182 " --> pdb=" O ILE E 494 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 181 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 209 " --> pdb=" O MET E 436 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE E 438 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE E 211 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL E 210 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE E 361 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E 212 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 302 through 306 removed outlier: 3.569A pdb=" N GLY E 302 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 121 through 125 removed outlier: 3.594A pdb=" N GLY F 70 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS F 110 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE F 68 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU F 112 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY F 66 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS F 114 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL F 64 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG F 42 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG F 136 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 12 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU F 105 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 168 through 172 removed outlier: 6.824A pdb=" N VAL F 169 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS F 180 " --> pdb=" O THR F 490 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE F 181 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N SER F 476 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE F 183 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU F 440 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 210 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE F 361 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 212 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 303 through 306 Processing sheet with id=AC2, first strand: chain 'G' and resid 181 through 183 removed outlier: 6.463A pdb=" N ARG G 77 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE G 61 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR G 46 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ASP G 122 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N VAL G 48 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL G 119 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL G 286 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET G 121 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER G 375 " --> pdb=" O PRO G 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 181 through 183 removed outlier: 6.463A pdb=" N ARG G 77 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE G 61 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR G 46 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N ASP G 122 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N VAL G 48 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL G 119 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL G 286 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET G 121 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER G 375 " --> pdb=" O PRO G 358 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 328 " --> pdb=" O MET G 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'H' and resid 181 through 183 removed outlier: 6.868A pdb=" N ARG H 77 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE H 61 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR H 46 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP H 122 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N VAL H 48 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL H 119 " --> pdb=" O VAL H 284 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL H 286 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N MET H 121 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N MET H 359 " --> pdb=" O ILE H 327 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE H 327 " --> pdb=" O MET H 359 " (cutoff:3.500A) 1741 hydrogen bonds defined for protein. 4995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 11609 1.36 - 1.51: 9069 1.51 - 1.66: 14398 1.66 - 1.80: 164 1.80 - 1.95: 22 Bond restraints: 35262 Sorted by residual: bond pdb=" O3B AGS E 601 " pdb=" PB AGS E 601 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" O3B AGS B 601 " pdb=" PB AGS B 601 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O3B AGS F 601 " pdb=" PB AGS F 601 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" O3B AGS D 601 " pdb=" PB AGS D 601 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3B AGS A 601 " pdb=" PB AGS A 601 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 35257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 47357 2.11 - 4.23: 401 4.23 - 6.34: 35 6.34 - 8.46: 29 8.46 - 10.57: 14 Bond angle restraints: 47836 Sorted by residual: angle pdb=" N ILE D 522 " pdb=" CA ILE D 522 " pdb=" C ILE D 522 " ideal model delta sigma weight residual 113.20 109.02 4.18 9.60e-01 1.09e+00 1.89e+01 angle pdb=" N3 DT J 20 " pdb=" C4 DT J 20 " pdb=" O4 DT J 20 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT J 16 " pdb=" C4 DT J 16 " pdb=" O4 DT J 16 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT J 3 " pdb=" C4 DT J 3 " pdb=" O4 DT J 3 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 47831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 21001 34.84 - 69.67: 316 69.67 - 104.51: 28 104.51 - 139.35: 8 139.35 - 174.18: 4 Dihedral angle restraints: 21357 sinusoidal: 9207 harmonic: 12150 Sorted by residual: dihedral pdb=" O1A AGS F 601 " pdb=" O3A AGS F 601 " pdb=" PA AGS F 601 " pdb=" PB AGS F 601 " ideal model delta sinusoidal sigma weight residual 82.37 -91.81 174.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS B 601 " pdb=" O3A AGS B 601 " pdb=" PA AGS B 601 " pdb=" PB AGS B 601 " ideal model delta sinusoidal sigma weight residual 82.37 -71.12 153.49 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" O1A AGS C 601 " pdb=" O3A AGS C 601 " pdb=" PA AGS C 601 " pdb=" PB AGS C 601 " ideal model delta sinusoidal sigma weight residual 82.37 -66.27 148.64 1 3.00e+01 1.11e-03 1.98e+01 ... (remaining 21354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4514 0.055 - 0.110: 690 0.110 - 0.164: 108 0.164 - 0.219: 0 0.219 - 0.274: 6 Chirality restraints: 5318 Sorted by residual: chirality pdb=" C3' AGS F 601 " pdb=" C2' AGS F 601 " pdb=" C4' AGS F 601 " pdb=" O3' AGS F 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' AGS A 601 " pdb=" C2' AGS A 601 " pdb=" C4' AGS A 601 " pdb=" O3' AGS A 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' AGS C 601 " pdb=" C2' AGS C 601 " pdb=" C4' AGS C 601 " pdb=" O3' AGS C 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 5315 not shown) Planarity restraints: 6018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 267 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLY G 267 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY G 267 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR G 268 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 214 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 215 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 215 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 215 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 287 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C LYS C 287 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS C 287 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU C 288 " 0.009 2.00e-02 2.50e+03 ... (remaining 6015 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 120 2.45 - 3.06: 22180 3.06 - 3.67: 49019 3.67 - 4.29: 74118 4.29 - 4.90: 128076 Nonbonded interactions: 273513 Sorted by model distance: nonbonded pdb=" OG SER C 192 " pdb="MN MN C 602 " model vdw 1.835 3.060 nonbonded pdb=" OG SER E 192 " pdb="MN MN E 602 " model vdw 1.845 3.060 nonbonded pdb=" O2B AGS E 601 " pdb="MN MN E 602 " model vdw 1.869 3.060 nonbonded pdb=" O2G AGS F 601 " pdb="MN MN F 602 " model vdw 1.880 3.060 nonbonded pdb=" O2B AGS D 601 " pdb="MN MN D 602 " model vdw 1.900 3.060 ... (remaining 273508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 34.590 Find NCS groups from input model: 0.780 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 35267 Z= 0.180 Angle : 0.527 10.569 47846 Z= 0.296 Chirality : 0.041 0.274 5318 Planarity : 0.003 0.039 6018 Dihedral : 12.421 174.181 13618 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.89 % Allowed : 3.38 % Favored : 95.73 % 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: 1.14 (0.13), residues: 4238 helix: 2.18 (0.13), residues: 1759 sheet: 0.38 (0.19), residues: 781 loop : -0.57 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.012 0.001 TYR F 95 PHE 0.012 0.001 PHE B 25 TRP 0.008 0.001 TRP G 389 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.18 (35262) covalent geometry : angle 0.52732 / 0.30 (47836) SS BOND : bond 0.00089 / 0.04 ( 5) SS BOND : angle 0.36773 / 0.18 ( 10) hydrogen bonds : bond 0.13381 / 8.95 ( 1706) hydrogen bonds : angle 5.97713 / 4.40 ( 4995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 599 time to evaluate : 1.482 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: A 214 ASP cc_start: 0.7698 (t0) cc_final: 0.7374 (p0) REVERT: B 395 ARG cc_start: 0.8072 (tpt90) cc_final: 0.7677 (tpt170) REVERT: B 441 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6827 (mt-10) REVERT: C 158 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9061 (mp) REVERT: C 251 ASP cc_start: 0.7908 (m-30) cc_final: 0.7634 (m-30) REVERT: C 256 GLN cc_start: 0.8343 (tt0) cc_final: 0.7921 (tt0) REVERT: C 373 LEU cc_start: 0.8922 (mt) cc_final: 0.8691 (tp) REVERT: G 16 LEU cc_start: 0.8692 (tp) cc_final: 0.8460 (tt) REVERT: G 41 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8481 (mmtt) REVERT: G 93 GLN cc_start: 0.8760 (mp10) cc_final: 0.8461 (mp10) REVERT: G 149 LEU cc_start: 0.9205 (tp) cc_final: 0.8962 (mm) REVERT: G 329 GLN cc_start: 0.8548 (mp10) cc_final: 0.7806 (mp10) REVERT: G 381 ASP cc_start: 0.8188 (p0) cc_final: 0.7271 (t0) REVERT: G 407 LYS cc_start: 0.8586 (tttt) cc_final: 0.8160 (tttp) REVERT: H 90 ILE cc_start: 0.8577 (mm) cc_final: 0.8242 (pt) REVERT: H 93 GLN cc_start: 0.8720 (mp10) cc_final: 0.7767 (mp10) REVERT: H 155 LYS cc_start: 0.8395 (mttt) cc_final: 0.8112 (mmtm) REVERT: H 281 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8128 (pp) outliers start: 32 outliers final: 11 residues processed: 627 average time/residue: 0.2762 time to fit residues: 261.7945 Evaluate side-chains 323 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 309 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 281 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 GLN A 513 GLN B 57 ASN C 50 GLN C 308 HIS C 489 GLN D 443 HIS D 477 GLN E 500 ASN H 147 ASN H 329 GLN H 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068402 restraints weight = 80217.412| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.08 r_work: 0.2883 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35267 Z= 0.161 Angle : 0.538 8.595 47846 Z= 0.289 Chirality : 0.042 0.151 5318 Planarity : 0.004 0.062 6018 Dihedral : 13.379 177.022 5433 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.28 % Allowed : 8.24 % Favored : 90.47 % 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: 1.23 (0.13), residues: 4238 helix: 2.34 (0.13), residues: 1780 sheet: 0.15 (0.19), residues: 755 loop : -0.50 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 313 TYR 0.029 0.001 TYR E 150 PHE 0.014 0.002 PHE B 25 TRP 0.006 0.001 TRP E 54 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (35262) covalent geometry : angle 0.53797 / 0.29 (47836) SS BOND : bond 0.00196 / 0.11 ( 5) SS BOND : angle 1.33535 / 0.50 ( 10) hydrogen bonds : bond 0.04229 / 2.84 ( 1706) hydrogen bonds : angle 4.83222 / 3.56 ( 4995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 336 time to evaluate : 1.395 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: A 17 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 490 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9105 (p) REVERT: A 503 ASP cc_start: 0.8250 (m-30) cc_final: 0.8042 (m-30) REVERT: B 72 LYS cc_start: 0.9211 (ptmt) cc_final: 0.8707 (ptmt) REVERT: B 395 ARG cc_start: 0.8308 (tpt90) cc_final: 0.8013 (tpt170) REVERT: B 397 ASP cc_start: 0.8700 (t0) cc_final: 0.8416 (m-30) REVERT: C 158 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9160 (mp) REVERT: C 251 ASP cc_start: 0.8545 (m-30) cc_final: 0.8251 (m-30) REVERT: C 395 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8311 (tpp80) REVERT: D 54 TRP cc_start: 0.8243 (m-10) cc_final: 0.7575 (m-90) REVERT: F 327 MET cc_start: 0.8752 (mmm) cc_final: 0.8437 (mmm) REVERT: F 484 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8441 (tp30) REVERT: G 93 GLN cc_start: 0.9240 (mp10) cc_final: 0.8955 (mp10) REVERT: G 260 ASN cc_start: 0.8806 (m-40) cc_final: 0.8563 (m-40) REVERT: G 340 LYS cc_start: 0.8909 (mttt) cc_final: 0.8676 (mmtt) REVERT: G 381 ASP cc_start: 0.8357 (p0) cc_final: 0.7763 (t70) REVERT: H 93 GLN cc_start: 0.8723 (mp10) cc_final: 0.8103 (mp10) outliers start: 46 outliers final: 27 residues processed: 369 average time/residue: 0.2245 time to fit residues: 133.0104 Evaluate side-chains 317 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 27 optimal weight: 10.0000 chunk 263 optimal weight: 0.7980 chunk 415 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 375 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 398 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 HIS D 57 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067468 restraints weight = 80352.352| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.10 r_work: 0.2849 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35267 Z= 0.212 Angle : 0.548 11.024 47846 Z= 0.291 Chirality : 0.043 0.150 5318 Planarity : 0.004 0.041 6018 Dihedral : 12.778 174.217 5424 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.62 % Allowed : 8.94 % Favored : 89.44 % 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: 1.17 (0.13), residues: 4238 helix: 2.32 (0.13), residues: 1789 sheet: 0.11 (0.19), residues: 738 loop : -0.58 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 53 TYR 0.019 0.001 TYR F 95 PHE 0.017 0.002 PHE A 25 TRP 0.007 0.001 TRP F 63 HIS 0.009 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (35262) covalent geometry : angle 0.54620 / 0.29 (47836) SS BOND : bond 0.01420 / 0.71 ( 5) SS BOND : angle 2.71952 / 1.20 ( 10) hydrogen bonds : bond 0.04191 / 2.83 ( 1706) hydrogen bonds : angle 4.63952 / 3.41 ( 4995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 1.384 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: A 490 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.9145 (p) REVERT: A 503 ASP cc_start: 0.8256 (m-30) cc_final: 0.8040 (m-30) REVERT: B 101 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: B 179 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.8050 (mtt-85) REVERT: B 216 HIS cc_start: 0.8432 (m170) cc_final: 0.8220 (m-70) REVERT: B 395 ARG cc_start: 0.8345 (tpt90) cc_final: 0.8012 (tpt170) REVERT: B 397 ASP cc_start: 0.8741 (t0) cc_final: 0.8530 (m-30) REVERT: C 158 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9167 (mp) REVERT: C 251 ASP cc_start: 0.8584 (m-30) cc_final: 0.8285 (m-30) REVERT: E 395 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8608 (tpt90) REVERT: F 327 MET cc_start: 0.8798 (mmm) cc_final: 0.8463 (mmm) REVERT: F 451 LYS cc_start: 0.8520 (tptt) cc_final: 0.8314 (tptt) REVERT: G 93 GLN cc_start: 0.9279 (mp10) cc_final: 0.8999 (mp10) REVERT: G 340 LYS cc_start: 0.9022 (mttt) cc_final: 0.8750 (mmtt) REVERT: G 381 ASP cc_start: 0.8396 (p0) cc_final: 0.7806 (t70) REVERT: H 93 GLN cc_start: 0.8856 (mp10) cc_final: 0.8209 (mp10) outliers start: 58 outliers final: 37 residues processed: 336 average time/residue: 0.2236 time to fit residues: 120.7810 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 456 ARG Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 313 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 286 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 308 HIS ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.067002 restraints weight = 79963.354| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.07 r_work: 0.2830 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35267 Z= 0.165 Angle : 0.510 10.308 47846 Z= 0.272 Chirality : 0.042 0.150 5318 Planarity : 0.003 0.046 6018 Dihedral : 12.387 171.939 5424 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.54 % Allowed : 9.33 % Favored : 89.13 % 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: 1.20 (0.13), residues: 4238 helix: 2.37 (0.13), residues: 1780 sheet: 0.13 (0.19), residues: 748 loop : -0.59 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 338 TYR 0.015 0.001 TYR F 95 PHE 0.014 0.001 PHE E 25 TRP 0.006 0.001 TRP F 63 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (35262) covalent geometry : angle 0.50983 / 0.27 (47836) SS BOND : bond 0.00165 / 0.09 ( 5) SS BOND : angle 1.85994 / 0.75 ( 10) hydrogen bonds : bond 0.03854 / 2.61 ( 1706) hydrogen bonds : angle 4.52570 / 3.33 ( 4995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 1.447 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: A 490 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9152 (p) REVERT: A 503 ASP cc_start: 0.8238 (m-30) cc_final: 0.8021 (m-30) REVERT: B 179 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8015 (mtt-85) REVERT: B 216 HIS cc_start: 0.8486 (m170) cc_final: 0.8272 (m-70) REVERT: B 395 ARG cc_start: 0.8354 (tpt90) cc_final: 0.7991 (tpt170) REVERT: B 397 ASP cc_start: 0.8738 (t0) cc_final: 0.8532 (m-30) REVERT: C 158 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9201 (mp) REVERT: C 251 ASP cc_start: 0.8570 (m-30) cc_final: 0.8258 (m-30) REVERT: C 422 ARG cc_start: 0.8624 (mtm110) cc_final: 0.8228 (mtm-85) REVERT: D 54 TRP cc_start: 0.8311 (m-10) cc_final: 0.7709 (m-90) REVERT: E 395 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8573 (tpt90) REVERT: E 496 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8429 (mtt) REVERT: F 327 MET cc_start: 0.8772 (mmm) cc_final: 0.8487 (mmm) REVERT: F 451 LYS cc_start: 0.8617 (tptt) cc_final: 0.8363 (tptt) REVERT: F 464 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: G 26 SER cc_start: 0.9485 (OUTLIER) cc_final: 0.9165 (p) REVERT: G 93 GLN cc_start: 0.9267 (mp10) cc_final: 0.8982 (mp10) REVERT: G 131 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7999 (mmm-85) REVERT: G 343 ARG cc_start: 0.8672 (mtp180) cc_final: 0.8395 (ttm-80) REVERT: G 381 ASP cc_start: 0.8380 (p0) cc_final: 0.7774 (t70) REVERT: H 93 GLN cc_start: 0.8869 (mp10) cc_final: 0.8255 (mp10) outliers start: 55 outliers final: 33 residues processed: 324 average time/residue: 0.2216 time to fit residues: 116.8945 Evaluate side-chains 298 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 39 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 417 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS C 308 HIS ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.067854 restraints weight = 80065.381| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.07 r_work: 0.2837 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35267 Z= 0.144 Angle : 0.490 10.175 47846 Z= 0.261 Chirality : 0.042 0.154 5318 Planarity : 0.003 0.043 6018 Dihedral : 12.187 171.362 5424 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 9.61 % Favored : 88.77 % 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: 1.22 (0.13), residues: 4238 helix: 2.38 (0.12), residues: 1783 sheet: 0.17 (0.19), residues: 748 loop : -0.58 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 456 TYR 0.013 0.001 TYR F 95 PHE 0.013 0.001 PHE E 25 TRP 0.006 0.001 TRP H 389 HIS 0.008 0.001 HIS A 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (35262) covalent geometry : angle 0.48982 / 0.26 (47836) SS BOND : bond 0.00109 / 0.06 ( 5) SS BOND : angle 1.07662 / 0.41 ( 10) hydrogen bonds : bond 0.03673 / 2.49 ( 1706) hydrogen bonds : angle 4.44423 / 3.27 ( 4995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 1.416 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: A 490 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9141 (p) REVERT: A 503 ASP cc_start: 0.8239 (m-30) cc_final: 0.8006 (m-30) REVERT: B 72 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8739 (pttt) REVERT: B 101 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: B 179 ARG cc_start: 0.8306 (mtt-85) cc_final: 0.8015 (mtt-85) REVERT: B 216 HIS cc_start: 0.8464 (m170) cc_final: 0.8238 (m-70) REVERT: B 395 ARG cc_start: 0.8340 (tpt90) cc_final: 0.7978 (tpt170) REVERT: B 397 ASP cc_start: 0.8735 (t0) cc_final: 0.8531 (m-30) REVERT: C 158 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9197 (mp) REVERT: C 251 ASP cc_start: 0.8563 (m-30) cc_final: 0.8249 (m-30) REVERT: C 422 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8254 (mtm-85) REVERT: D 1 MET cc_start: 0.7551 (ptm) cc_final: 0.7315 (ptt) REVERT: E 395 ARG cc_start: 0.8906 (tpp80) cc_final: 0.8572 (tpt90) REVERT: E 496 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8414 (mtt) REVERT: F 62 GLU cc_start: 0.8403 (pm20) cc_final: 0.8163 (mp0) REVERT: F 327 MET cc_start: 0.8793 (mmm) cc_final: 0.8522 (mmm) REVERT: F 464 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: G 26 SER cc_start: 0.9478 (OUTLIER) cc_final: 0.9159 (p) REVERT: G 93 GLN cc_start: 0.9284 (mp10) cc_final: 0.9018 (mp10) REVERT: G 131 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: G 171 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8576 (tm-30) REVERT: G 343 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8419 (ttm-80) REVERT: G 381 ASP cc_start: 0.8368 (p0) cc_final: 0.7787 (t70) REVERT: H 93 GLN cc_start: 0.8883 (mp10) cc_final: 0.8313 (mp10) outliers start: 58 outliers final: 40 residues processed: 321 average time/residue: 0.2166 time to fit residues: 112.8274 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 256 ASP Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 GLN C 216 HIS C 308 HIS ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067191 restraints weight = 78850.386| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.95 r_work: 0.2827 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35267 Z= 0.189 Angle : 0.513 8.977 47846 Z= 0.272 Chirality : 0.042 0.153 5318 Planarity : 0.003 0.041 6018 Dihedral : 12.126 172.414 5424 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.84 % Allowed : 10.08 % Favored : 88.07 % 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: 1.21 (0.13), residues: 4238 helix: 2.40 (0.13), residues: 1783 sheet: 0.15 (0.19), residues: 744 loop : -0.62 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 456 TYR 0.017 0.001 TYR F 95 PHE 0.022 0.002 PHE C 420 TRP 0.006 0.001 TRP B 305 HIS 0.008 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (35262) covalent geometry : angle 0.51272 / 0.27 (47836) SS BOND : bond 0.01107 / 0.55 ( 5) SS BOND : angle 0.75373 / 0.31 ( 10) hydrogen bonds : bond 0.03885 / 2.64 ( 1706) hydrogen bonds : angle 4.46126 / 3.27 ( 4995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 0.931 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: A 490 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9149 (p) REVERT: B 72 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8933 (pttt) REVERT: B 101 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: B 179 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8053 (mtt-85) REVERT: B 395 ARG cc_start: 0.8355 (tpt90) cc_final: 0.8034 (tpt170) REVERT: C 158 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9200 (mp) REVERT: C 251 ASP cc_start: 0.8563 (m-30) cc_final: 0.8246 (m-30) REVERT: C 372 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8696 (mtpt) REVERT: C 422 ARG cc_start: 0.8628 (mtm110) cc_final: 0.8226 (mtm-85) REVERT: E 69 ARG cc_start: 0.8706 (ttp-170) cc_final: 0.8436 (ttm170) REVERT: E 496 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8416 (mtt) REVERT: F 62 GLU cc_start: 0.8413 (pm20) cc_final: 0.8200 (mp0) REVERT: F 327 MET cc_start: 0.8800 (mmm) cc_final: 0.8594 (mmm) REVERT: F 456 ARG cc_start: 0.8593 (mtm-85) cc_final: 0.8354 (mpp80) REVERT: F 464 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: G 26 SER cc_start: 0.9467 (OUTLIER) cc_final: 0.9156 (p) REVERT: G 93 GLN cc_start: 0.9314 (mp10) cc_final: 0.9046 (mp10) REVERT: G 131 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8038 (mmm-85) REVERT: G 381 ASP cc_start: 0.8378 (p0) cc_final: 0.7812 (t70) REVERT: H 93 GLN cc_start: 0.8913 (mp10) cc_final: 0.8348 (mp10) outliers start: 66 outliers final: 42 residues processed: 316 average time/residue: 0.2009 time to fit residues: 104.5799 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 82 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS D 118 ASN F 57 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066663 restraints weight = 80126.100| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.11 r_work: 0.2819 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35267 Z= 0.135 Angle : 0.481 9.052 47846 Z= 0.257 Chirality : 0.041 0.190 5318 Planarity : 0.003 0.041 6018 Dihedral : 12.052 173.632 5424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.56 % Allowed : 10.59 % Favored : 87.85 % 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: 1.26 (0.13), residues: 4238 helix: 2.43 (0.12), residues: 1784 sheet: 0.18 (0.19), residues: 744 loop : -0.58 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 395 TYR 0.013 0.001 TYR H 200 PHE 0.014 0.001 PHE C 420 TRP 0.006 0.001 TRP H 389 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (35262) covalent geometry : angle 0.48090 / 0.26 (47836) SS BOND : bond 0.00309 / 0.16 ( 5) SS BOND : angle 0.98864 / 0.44 ( 10) hydrogen bonds : bond 0.03582 / 2.43 ( 1706) hydrogen bonds : angle 4.38525 / 3.22 ( 4995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.647 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: A 490 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9140 (p) REVERT: B 101 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: B 179 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8061 (mtt-85) REVERT: B 395 ARG cc_start: 0.8346 (tpt90) cc_final: 0.8027 (tpt170) REVERT: C 158 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9213 (mp) REVERT: C 251 ASP cc_start: 0.8566 (m-30) cc_final: 0.8248 (m-30) REVERT: C 422 ARG cc_start: 0.8676 (mtm110) cc_final: 0.8274 (mtm-85) REVERT: E 69 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8453 (ttm170) REVERT: E 395 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8542 (tpt90) REVERT: E 496 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: E 519 MET cc_start: 0.8668 (mtm) cc_final: 0.8427 (mtm) REVERT: F 62 GLU cc_start: 0.8463 (pm20) cc_final: 0.8238 (mp0) REVERT: F 327 MET cc_start: 0.8761 (mmm) cc_final: 0.8510 (mmm) REVERT: F 456 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8411 (mpp80) REVERT: F 464 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: G 26 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9148 (p) REVERT: G 93 GLN cc_start: 0.9311 (mp10) cc_final: 0.9044 (mp10) REVERT: G 171 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8607 (tm-30) REVERT: G 381 ASP cc_start: 0.8401 (p0) cc_final: 0.7817 (t70) REVERT: H 93 GLN cc_start: 0.8898 (mp10) cc_final: 0.8343 (mp10) outliers start: 56 outliers final: 44 residues processed: 311 average time/residue: 0.2089 time to fit residues: 105.4601 Evaluate side-chains 307 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 311 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 338 optimal weight: 0.0030 chunk 115 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 396 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066457 restraints weight = 80133.792| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.09 r_work: 0.2811 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35267 Z= 0.158 Angle : 0.501 12.588 47846 Z= 0.265 Chirality : 0.042 0.282 5318 Planarity : 0.003 0.040 6018 Dihedral : 12.036 174.382 5424 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.70 % Allowed : 10.70 % Favored : 87.60 % 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: 1.24 (0.13), residues: 4238 helix: 2.42 (0.13), residues: 1783 sheet: 0.17 (0.19), residues: 744 loop : -0.59 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 395 TYR 0.014 0.001 TYR F 95 PHE 0.014 0.001 PHE E 25 TRP 0.006 0.001 TRP H 389 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (35262) covalent geometry : angle 0.50077 / 0.26 (47836) SS BOND : bond 0.00100 / 0.06 ( 5) SS BOND : angle 1.10357 / 0.50 ( 10) hydrogen bonds : bond 0.03656 / 2.48 ( 1706) hydrogen bonds : angle 4.38372 / 3.22 ( 4995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 1.295 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: A 490 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9135 (p) REVERT: A 497 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8504 (ttp80) REVERT: B 101 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: B 179 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8054 (mtt-85) REVERT: B 248 GLU cc_start: 0.8267 (mp0) cc_final: 0.7853 (pm20) REVERT: B 395 ARG cc_start: 0.8333 (tpt90) cc_final: 0.8013 (tpt170) REVERT: C 158 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9222 (mp) REVERT: C 251 ASP cc_start: 0.8574 (m-30) cc_final: 0.8252 (m-30) REVERT: E 69 ARG cc_start: 0.8762 (ttp-170) cc_final: 0.8465 (ttm170) REVERT: E 496 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8381 (mtt) REVERT: F 62 GLU cc_start: 0.8497 (pm20) cc_final: 0.8259 (mp0) REVERT: F 327 MET cc_start: 0.8766 (mmm) cc_final: 0.8566 (mmm) REVERT: F 456 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.8416 (mpp80) REVERT: F 464 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: G 26 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.9137 (p) REVERT: G 93 GLN cc_start: 0.9301 (mp10) cc_final: 0.9029 (mp10) REVERT: G 131 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7994 (mmm-85) REVERT: G 171 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8587 (tm-30) REVERT: G 381 ASP cc_start: 0.8413 (p0) cc_final: 0.7810 (t70) REVERT: H 93 GLN cc_start: 0.8904 (mp10) cc_final: 0.8350 (mp10) outliers start: 61 outliers final: 44 residues processed: 310 average time/residue: 0.2145 time to fit residues: 108.9496 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 255 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 258 ASN Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 256 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 323 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 366 optimal weight: 0.5980 chunk 393 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS H 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.065946 restraints weight = 78766.375| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.01 r_work: 0.2801 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35267 Z= 0.195 Angle : 0.524 13.462 47846 Z= 0.278 Chirality : 0.043 0.253 5318 Planarity : 0.003 0.040 6018 Dihedral : 12.057 175.280 5424 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.56 % Allowed : 11.09 % Favored : 87.35 % 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: 1.18 (0.13), residues: 4238 helix: 2.37 (0.13), residues: 1783 sheet: 0.13 (0.19), residues: 754 loop : -0.63 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 395 TYR 0.017 0.001 TYR F 95 PHE 0.016 0.002 PHE E 25 TRP 0.007 0.001 TRP B 305 HIS 0.008 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (35262) covalent geometry : angle 0.52435 / 0.28 (47836) SS BOND : bond 0.00316 / 0.16 ( 5) SS BOND : angle 0.98523 / 0.43 ( 10) hydrogen bonds : bond 0.03911 / 2.66 ( 1706) hydrogen bonds : angle 4.43149 / 3.25 ( 4995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 259 time to evaluate : 1.388 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: A 490 THR cc_start: 0.9410 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 101 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: B 179 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8058 (mtt-85) REVERT: B 248 GLU cc_start: 0.8166 (mp0) cc_final: 0.7813 (pm20) REVERT: B 395 ARG cc_start: 0.8357 (tpt90) cc_final: 0.8041 (tpt170) REVERT: C 251 ASP cc_start: 0.8576 (m-30) cc_final: 0.8257 (m-30) REVERT: E 69 ARG cc_start: 0.8737 (ttp-170) cc_final: 0.8455 (ttm170) REVERT: E 395 ARG cc_start: 0.8931 (tpp80) cc_final: 0.8268 (tpt90) REVERT: E 496 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: F 456 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8429 (mtm-85) REVERT: F 464 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: G 26 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9125 (p) REVERT: G 93 GLN cc_start: 0.9310 (mp10) cc_final: 0.9035 (mp10) REVERT: G 131 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8073 (mmm-85) REVERT: G 381 ASP cc_start: 0.8443 (p0) cc_final: 0.7825 (t70) REVERT: H 156 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8140 (tm-30) REVERT: H 391 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8616 (tm-30) outliers start: 56 outliers final: 45 residues processed: 300 average time/residue: 0.2190 time to fit residues: 107.4267 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 496 MET Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 496 MET Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 321 ILE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 276 GLU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 391 GLU Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 122 optimal weight: 0.9990 chunk 390 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 314 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 117 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 375 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS C 256 GLN H 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067692 restraints weight = 79812.565| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.10 r_work: 0.2842 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35267 Z= 0.099 Angle : 0.492 11.908 47846 Z= 0.261 Chirality : 0.041 0.272 5318 Planarity : 0.003 0.037 6018 Dihedral : 11.916 179.252 5421 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.12 % Allowed : 11.68 % Favored : 87.21 % 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: 1.28 (0.13), residues: 4238 helix: 2.42 (0.13), residues: 1782 sheet: 0.25 (0.19), residues: 756 loop : -0.57 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.013 0.001 TYR H 200 PHE 0.014 0.001 PHE C 420 TRP 0.008 0.001 TRP B 270 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (35262) covalent geometry : angle 0.49226 / 0.26 (47836) SS BOND : bond 0.00188 / 0.10 ( 5) SS BOND : angle 0.78487 / 0.34 ( 10) hydrogen bonds : bond 0.03220 / 2.18 ( 1706) hydrogen bonds : angle 4.30002 / 3.16 ( 4995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 1.258 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: A 490 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9123 (p) REVERT: A 497 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8433 (ttp80) REVERT: B 101 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: B 179 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.8063 (mtt-85) REVERT: B 216 HIS cc_start: 0.8197 (m-70) cc_final: 0.7875 (m170) REVERT: B 248 GLU cc_start: 0.8129 (mp0) cc_final: 0.7768 (pm20) REVERT: B 395 ARG cc_start: 0.8330 (tpt90) cc_final: 0.7974 (tpt170) REVERT: C 251 ASP cc_start: 0.8529 (m-30) cc_final: 0.8208 (m-30) REVERT: C 422 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8241 (mtm110) REVERT: E 69 ARG cc_start: 0.8692 (ttp-170) cc_final: 0.8468 (ttm170) REVERT: E 395 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8269 (tpt90) REVERT: E 450 GLU cc_start: 0.8440 (tp30) cc_final: 0.8186 (tp30) REVERT: E 519 MET cc_start: 0.8654 (mtm) cc_final: 0.8290 (mtm) REVERT: F 450 GLU cc_start: 0.8071 (mp0) cc_final: 0.7776 (mp0) REVERT: F 456 ARG cc_start: 0.8684 (mtm-85) cc_final: 0.8439 (mpp80) REVERT: F 464 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: G 26 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9115 (p) REVERT: G 93 GLN cc_start: 0.9307 (mp10) cc_final: 0.9042 (mp10) REVERT: G 131 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: G 149 LEU cc_start: 0.9173 (mm) cc_final: 0.8880 (mm) REVERT: G 171 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8595 (tm-30) REVERT: G 381 ASP cc_start: 0.8393 (p0) cc_final: 0.7838 (t70) REVERT: H 93 GLN cc_start: 0.8901 (mp10) cc_final: 0.8362 (mp10) outliers start: 40 outliers final: 30 residues processed: 315 average time/residue: 0.2213 time to fit residues: 113.3529 Evaluate side-chains 295 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 573 GLU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 315 LYS Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 240 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 270 optimal weight: 0.4980 chunk 370 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 415 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 419 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS H 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066313 restraints weight = 78805.222| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.00 r_work: 0.2810 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35267 Z= 0.194 Angle : 0.524 11.861 47846 Z= 0.277 Chirality : 0.042 0.245 5318 Planarity : 0.003 0.038 6018 Dihedral : 11.940 177.611 5419 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 11.62 % Favored : 87.15 % 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: 1.21 (0.13), residues: 4238 helix: 2.38 (0.13), residues: 1784 sheet: 0.18 (0.19), residues: 751 loop : -0.61 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 395 TYR 0.016 0.001 TYR F 95 PHE 0.029 0.002 PHE C 420 TRP 0.007 0.001 TRP F 63 HIS 0.008 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (35262) covalent geometry : angle 0.52421 / 0.28 (47836) SS BOND : bond 0.00261 / 0.14 ( 5) SS BOND : angle 0.88783 / 0.38 ( 10) hydrogen bonds : bond 0.03711 / 2.52 ( 1706) hydrogen bonds : angle 4.37394 / 3.22 ( 4995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7864.89 seconds wall clock time: 135 minutes 35.03 seconds (8135.03 seconds total)