Starting phenix.real_space_refine on Fri Mar 6 23:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1n_66464/03_2026/9x1n_66464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1n_66464/03_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_66464/03_2026/9x1n_66464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1n_66464/03_2026/9x1n_66464.map" model { file = "/net/cci-nas-00/data/ceres_data/9x1n_66464/03_2026/9x1n_66464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1n_66464/03_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.93, per 1000 atoms: 0.23 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 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: 1.29 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: 7.31 Time building geometry restraints manager: 3.62 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=" C TYR H 135 " pdb=" N PRO H 136 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.03e+00 bond pdb=" CB PRO F 215 " pdb=" CG PRO F 215 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.26e-01 bond pdb=" C TYR G 135 " pdb=" N PRO G 136 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.95e-01 bond pdb=" C3' DA I 14 " pdb=" O3' DA I 14 " ideal model delta sigma weight residual 1.422 1.449 -0.027 3.00e-02 1.11e+03 7.83e-01 bond pdb=" C4' DA I 4 " pdb=" O4' DA I 4 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.53e-01 ... (remaining 35257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 47355 1.62 - 3.25: 437 3.25 - 4.87: 36 4.87 - 6.49: 7 6.49 - 8.12: 1 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=" N VAL D 350 " pdb=" CA VAL D 350 " pdb=" C VAL D 350 " ideal model delta sigma weight residual 111.91 109.06 2.85 8.90e-01 1.26e+00 1.02e+01 angle pdb=" N VAL A 499 " pdb=" CA VAL A 499 " pdb=" C VAL A 499 " ideal model delta sigma weight residual 113.53 110.47 3.06 9.80e-01 1.04e+00 9.73e+00 angle pdb=" N GLY B 159 " pdb=" CA GLY B 159 " pdb=" C GLY B 159 " ideal model delta sigma weight residual 110.56 114.69 -4.13 1.36e+00 5.41e-01 9.22e+00 angle pdb=" N ILE B 407 " pdb=" CA ILE B 407 " pdb=" C ILE B 407 " ideal model delta sigma weight residual 112.98 110.00 2.98 1.25e+00 6.40e-01 5.68e+00 ... (remaining 47831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 20936 34.81 - 69.62: 306 69.62 - 104.44: 3 104.44 - 139.25: 1 139.25 - 174.06: 3 Dihedral angle restraints: 21249 sinusoidal: 9099 harmonic: 12150 Sorted by residual: dihedral pdb=" O1A AGS E 601 " pdb=" O3A AGS E 601 " pdb=" PA AGS E 601 " pdb=" PB AGS E 601 " ideal model delta sinusoidal sigma weight residual 292.27 118.21 174.06 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS A 601 " pdb=" O3A AGS A 601 " pdb=" PA AGS A 601 " pdb=" PB AGS A 601 " ideal model delta sinusoidal sigma weight residual -67.73 79.57 -147.30 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4' DT J 18 " pdb=" C3' DT J 18 " pdb=" O3' DT J 18 " pdb=" P DT J 19 " ideal model delta sinusoidal sigma weight residual 220.00 79.04 140.96 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 21246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3540 0.030 - 0.060: 1158 0.060 - 0.089: 290 0.089 - 0.119: 301 0.119 - 0.149: 41 Chirality restraints: 5330 Sorted by residual: chirality pdb=" CA ILE C 211 " pdb=" N ILE C 211 " pdb=" C ILE C 211 " pdb=" CB ILE C 211 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE G 61 " pdb=" N ILE G 61 " pdb=" C ILE G 61 " pdb=" CB ILE G 61 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE E 494 " pdb=" N ILE E 494 " pdb=" C ILE E 494 " pdb=" CB ILE E 494 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 5327 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 2.320 nonbonded pdb=" OG SER E 192 " pdb="MN MN E 602 " model vdw 1.845 2.320 nonbonded pdb=" O2B AGS E 601 " pdb="MN MN E 602 " model vdw 1.869 2.320 nonbonded pdb=" O2G AGS F 601 " pdb="MN MN F 602 " model vdw 1.880 2.320 nonbonded pdb=" O2B AGS D 601 " pdb="MN MN D 602 " model vdw 1.900 2.320 ... (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: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.470 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.002 0.045 35267 Z= 0.094 Angle : 0.421 8.115 47846 Z= 0.237 Chirality : 0.040 0.149 5330 Planarity : 0.003 0.039 6018 Dihedral : 11.393 174.062 13510 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 covalent geometry : bond 0.00186 (35262) covalent geometry : angle 0.42142 (47836) SS BOND : bond 0.00089 ( 5) SS BOND : angle 0.36773 ( 10) hydrogen bonds : bond 0.13381 ( 1706) hydrogen bonds : angle 5.97713 ( 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 : 1.322 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 191 LYS cc_start: 0.6837 (pttt) cc_final: 0.6107 (pttp) REVERT: A 214 ASP cc_start: 0.7698 (t0) cc_final: 0.7377 (p0) REVERT: A 440 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7443 (mm-30) 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: 0.2618 time to fit residues: 247.7677 Evaluate side-chains 327 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 313 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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: 8.9990 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: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3464 r_free = 0.3464 target = 0.092458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068700 restraints weight = 78953.419| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.98 r_work: 0.2876 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35267 Z= 0.174 Angle : 0.536 8.844 47846 Z= 0.286 Chirality : 0.042 0.169 5330 Planarity : 0.004 0.051 6018 Dihedral : 11.609 172.659 5325 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 7.91 % Favored : 90.59 % 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: 2.35 (0.13), residues: 1783 sheet: 0.12 (0.19), residues: 740 loop : -0.52 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 313 TYR 0.029 0.001 TYR E 150 PHE 0.016 0.002 PHE C 420 TRP 0.005 0.001 TRP B 63 HIS 0.007 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00408 (35262) covalent geometry : angle 0.53563 (47836) SS BOND : bond 0.00160 ( 5) SS BOND : angle 1.06000 ( 10) hydrogen bonds : bond 0.04068 ( 1706) hydrogen bonds : angle 4.73604 ( 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 387 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 333 time to evaluate : 1.310 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: 0.8568 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 490 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 72 LYS cc_start: 0.9212 (ptmt) cc_final: 0.8723 (ptmt) REVERT: B 395 ARG cc_start: 0.8311 (tpt90) cc_final: 0.8063 (tpt170) REVERT: B 397 ASP cc_start: 0.8736 (t0) cc_final: 0.8471 (m-30) REVERT: C 158 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9159 (mp) REVERT: C 251 ASP cc_start: 0.8563 (m-30) cc_final: 0.8261 (m-30) REVERT: D 319 LYS cc_start: 0.8295 (mttt) cc_final: 0.8056 (mmtp) REVERT: D 504 GLN cc_start: 0.8610 (mt0) cc_final: 0.8384 (mt0) REVERT: E 245 ASP cc_start: 0.8515 (p0) cc_final: 0.8253 (p0) REVERT: F 327 MET cc_start: 0.8738 (mmm) cc_final: 0.8412 (mmm) REVERT: G 93 GLN cc_start: 0.9242 (mp10) cc_final: 0.8927 (mp10) REVERT: G 340 LYS cc_start: 0.8930 (mttt) cc_final: 0.8695 (mmtt) REVERT: G 381 ASP cc_start: 0.8351 (p0) cc_final: 0.7787 (t70) REVERT: H 93 GLN cc_start: 0.8694 (mp10) cc_final: 0.8038 (mp10) REVERT: H 281 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8380 (pp) outliers start: 54 outliers final: 31 residues processed: 373 average time/residue: 0.2271 time to fit residues: 136.0394 Evaluate side-chains 308 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 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 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 H residue 79 VAL 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 357 VAL 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: 4.9990 chunk 415 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 375 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 HIS E 118 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 = 0.3429 r_free = 0.3429 target = 0.090849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.066195 restraints weight = 80444.005| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.06 r_work: 0.2832 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35267 Z= 0.245 Angle : 0.558 11.360 47846 Z= 0.295 Chirality : 0.043 0.148 5330 Planarity : 0.004 0.045 6018 Dihedral : 11.638 172.112 5318 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 8.72 % Favored : 89.64 % 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: 1.10 (0.13), residues: 4238 helix: 2.29 (0.13), residues: 1789 sheet: 0.03 (0.19), residues: 746 loop : -0.62 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 338 TYR 0.020 0.001 TYR F 95 PHE 0.017 0.002 PHE E 25 TRP 0.007 0.001 TRP B 305 HIS 0.009 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00581 (35262) covalent geometry : angle 0.55734 (47836) SS BOND : bond 0.00186 ( 5) SS BOND : angle 1.48883 ( 10) hydrogen bonds : bond 0.04371 ( 1706) hydrogen bonds : angle 4.65245 ( 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 333 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 1.255 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: 0.8565 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 440 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8564 (mm-30) REVERT: A 490 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9162 (p) REVERT: B 72 LYS cc_start: 0.9281 (ptmt) cc_final: 0.8632 (ptmt) REVERT: B 101 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8605 (mp0) REVERT: B 179 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.8069 (mtt-85) REVERT: B 395 ARG cc_start: 0.8368 (tpt90) cc_final: 0.8018 (tpt170) REVERT: B 436 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8648 (ttm) REVERT: C 158 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9168 (mp) REVERT: C 251 ASP cc_start: 0.8599 (m-30) cc_final: 0.8297 (m-30) REVERT: E 245 ASP cc_start: 0.8509 (p0) cc_final: 0.8264 (p0) REVERT: E 395 ARG cc_start: 0.8946 (tpp80) cc_final: 0.8593 (tpt90) REVERT: F 327 MET cc_start: 0.8800 (mmm) cc_final: 0.8572 (mmm) REVERT: G 93 GLN cc_start: 0.9295 (mp10) cc_final: 0.8995 (mp10) REVERT: G 343 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8442 (ttm-80) REVERT: G 381 ASP cc_start: 0.8418 (p0) cc_final: 0.7807 (t70) REVERT: H 93 GLN cc_start: 0.8919 (mp10) cc_final: 0.8366 (mp10) REVERT: H 281 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8339 (pp) outliers start: 59 outliers final: 37 residues processed: 317 average time/residue: 0.2153 time to fit residues: 110.2661 Evaluate side-chains 297 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 44 CYS 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 B residue 436 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 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 531 VAL 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 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 14 LYS Chi-restraints excluded: chain G residue 121 MET 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 313 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 286 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 262 GLN C 308 HIS D 57 ASN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067330 restraints weight = 79441.930| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.07 r_work: 0.2832 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35267 Z= 0.146 Angle : 0.490 9.408 47846 Z= 0.261 Chirality : 0.041 0.146 5330 Planarity : 0.003 0.043 6018 Dihedral : 11.542 173.374 5318 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.84 % Allowed : 9.16 % Favored : 88.99 % 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: 1.19 (0.13), residues: 4238 helix: 2.37 (0.13), residues: 1782 sheet: 0.14 (0.19), residues: 738 loop : -0.60 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 456 TYR 0.014 0.001 TYR H 200 PHE 0.013 0.001 PHE E 25 TRP 0.006 0.001 TRP H 389 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00340 (35262) covalent geometry : angle 0.49024 (47836) SS BOND : bond 0.00526 ( 5) SS BOND : angle 0.84609 ( 10) hydrogen bonds : bond 0.03737 ( 1706) hydrogen bonds : angle 4.47956 ( 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 350 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 284 time to evaluate : 1.364 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: 0.8613 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 440 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 490 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9151 (p) REVERT: A 496 MET cc_start: 0.8912 (mtt) cc_final: 0.8574 (mtt) REVERT: B 72 LYS cc_start: 0.9239 (ptmt) cc_final: 0.8653 (ptmt) REVERT: B 101 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: B 179 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8074 (mtt-85) REVERT: B 395 ARG cc_start: 0.8337 (tpt90) cc_final: 0.7983 (tpt170) REVERT: B 436 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: C 158 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9182 (mp) REVERT: C 251 ASP cc_start: 0.8570 (m-30) cc_final: 0.8255 (m-30) REVERT: E 245 ASP cc_start: 0.8502 (p0) cc_final: 0.8291 (p0) REVERT: F 327 MET cc_start: 0.8781 (mmm) cc_final: 0.8577 (mmm) REVERT: F 451 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8313 (tptp) REVERT: G 26 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9159 (p) REVERT: G 93 GLN cc_start: 0.9284 (mp10) cc_final: 0.8986 (mp10) REVERT: G 131 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: G 343 ARG cc_start: 0.8704 (mtp180) cc_final: 0.8449 (ttm-80) REVERT: G 381 ASP cc_start: 0.8383 (p0) cc_final: 0.7806 (t70) REVERT: H 281 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8332 (pp) outliers start: 66 outliers final: 44 residues processed: 334 average time/residue: 0.2108 time to fit residues: 113.9482 Evaluate side-chains 309 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 7 ILE Chi-restraints excluded: chain B residue 44 CYS 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 B residue 436 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 82 LYS 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 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 531 VAL Chi-restraints excluded: chain E residue 162 ILE 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 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 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 121 MET 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 276 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 364 optimal weight: 2.9990 chunk 417 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3467 r_free = 0.3467 target = 0.092903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.068398 restraints weight = 79619.134| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.08 r_work: 0.2859 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35267 Z= 0.104 Angle : 0.461 8.847 47846 Z= 0.245 Chirality : 0.041 0.149 5330 Planarity : 0.003 0.038 6018 Dihedral : 11.428 175.727 5318 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.54 % Allowed : 9.78 % Favored : 88.69 % 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: 1.27 (0.13), residues: 4238 helix: 2.44 (0.12), residues: 1782 sheet: 0.19 (0.19), residues: 740 loop : -0.57 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 456 TYR 0.013 0.001 TYR H 200 PHE 0.019 0.001 PHE C 420 TRP 0.006 0.001 TRP E 270 HIS 0.009 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00233 (35262) covalent geometry : angle 0.46093 (47836) SS BOND : bond 0.00105 ( 5) SS BOND : angle 0.61748 ( 10) hydrogen bonds : bond 0.03291 ( 1706) hydrogen bonds : angle 4.34818 ( 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 347 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 1.045 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 17 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 490 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.9127 (p) REVERT: A 496 MET cc_start: 0.8836 (mtt) cc_final: 0.8332 (mtt) REVERT: B 72 LYS cc_start: 0.9177 (ptmt) cc_final: 0.8647 (ptmt) REVERT: B 179 ARG cc_start: 0.8306 (mtt-85) cc_final: 0.8047 (mtt-85) REVERT: B 248 GLU cc_start: 0.8237 (mp0) cc_final: 0.7877 (pm20) REVERT: B 395 ARG cc_start: 0.8323 (tpt90) cc_final: 0.7983 (tpt170) REVERT: C 158 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9191 (mp) REVERT: C 251 ASP cc_start: 0.8534 (m-30) cc_final: 0.8212 (m-30) REVERT: C 519 MET cc_start: 0.8560 (ttp) cc_final: 0.8155 (tpp) REVERT: E 54 TRP cc_start: 0.8009 (m100) cc_final: 0.7779 (m100) REVERT: E 69 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8467 (ttm170) REVERT: E 245 ASP cc_start: 0.8480 (p0) cc_final: 0.8269 (p0) REVERT: E 395 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8247 (tpt90) REVERT: E 496 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: F 327 MET cc_start: 0.8770 (mmm) cc_final: 0.8528 (mmm) REVERT: F 484 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8457 (tp30) REVERT: G 26 SER cc_start: 0.9452 (OUTLIER) cc_final: 0.9151 (p) REVERT: G 93 GLN cc_start: 0.9279 (mp10) cc_final: 0.8992 (mp10) REVERT: G 131 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: G 171 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8560 (tm-30) REVERT: G 340 LYS cc_start: 0.9081 (mttt) cc_final: 0.8803 (mmtt) REVERT: G 381 ASP cc_start: 0.8364 (p0) cc_final: 0.7851 (t70) REVERT: H 87 ASN cc_start: 0.8721 (t0) cc_final: 0.8514 (t0) REVERT: H 156 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8191 (tm-30) outliers start: 55 outliers final: 37 residues processed: 332 average time/residue: 0.2167 time to fit residues: 116.1521 Evaluate side-chains 308 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 44 CYS Chi-restraints excluded: chain B residue 52 CYS 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 82 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C 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 242 GLU Chi-restraints excluded: chain E residue 403 TYR 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 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 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 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: 4.9990 chunk 131 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 124 optimal weight: 0.0050 chunk 2 optimal weight: 6.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3442 r_free = 0.3442 target = 0.091270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.067577 restraints weight = 78790.732| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.96 r_work: 0.2853 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2446 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= 0.179 Angle : 0.506 12.322 47846 Z= 0.267 Chirality : 0.042 0.274 5330 Planarity : 0.003 0.037 6018 Dihedral : 11.434 176.207 5314 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 10.56 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4238 helix: 2.43 (0.12), residues: 1785 sheet: 0.21 (0.19), residues: 734 loop : -0.60 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 395 TYR 0.016 0.001 TYR F 95 PHE 0.016 0.002 PHE E 468 TRP 0.006 0.001 TRP B 305 HIS 0.008 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00424 (35262) covalent geometry : angle 0.50560 (47836) SS BOND : bond 0.00166 ( 5) SS BOND : angle 0.55660 ( 10) hydrogen bonds : bond 0.03724 ( 1706) hydrogen bonds : angle 4.40071 ( 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 331 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 269 time to evaluate : 1.334 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 17 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 490 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9133 (p) REVERT: A 496 MET cc_start: 0.8922 (mtt) cc_final: 0.8707 (mtt) REVERT: A 497 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8550 (ttp80) REVERT: B 72 LYS cc_start: 0.9244 (ptmt) cc_final: 0.8602 (ptmt) REVERT: B 179 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.8040 (mtt-85) REVERT: B 248 GLU cc_start: 0.8194 (mp0) cc_final: 0.7878 (pm20) REVERT: B 395 ARG cc_start: 0.8348 (tpt90) cc_final: 0.8050 (tpt170) REVERT: B 436 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8621 (ttm) REVERT: C 158 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9202 (mp) REVERT: C 251 ASP cc_start: 0.8545 (m-30) cc_final: 0.8240 (m-30) REVERT: C 422 ARG cc_start: 0.8825 (mtm180) cc_final: 0.8386 (mtm110) REVERT: E 69 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.8460 (ttm170) REVERT: E 245 ASP cc_start: 0.8474 (p0) cc_final: 0.8255 (p0) REVERT: E 496 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: G 26 SER cc_start: 0.9445 (OUTLIER) cc_final: 0.9143 (p) REVERT: G 93 GLN cc_start: 0.9329 (mp10) cc_final: 0.9043 (mp10) REVERT: G 131 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.8056 (mmm-85) REVERT: G 340 LYS cc_start: 0.9099 (mttt) cc_final: 0.8831 (mmtt) REVERT: G 381 ASP cc_start: 0.8371 (p0) cc_final: 0.7839 (t70) REVERT: H 87 ASN cc_start: 0.8686 (t0) cc_final: 0.8459 (t0) outliers start: 62 outliers final: 40 residues processed: 315 average time/residue: 0.2054 time to fit residues: 105.1439 Evaluate side-chains 304 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 7 ILE Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 82 LYS 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 198 MET Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 531 VAL Chi-restraints excluded: chain E residue 162 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 82 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 306 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 234 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS D 118 ASN H 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.068119 restraints weight = 79581.537| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.08 r_work: 0.2852 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35267 Z= 0.112 Angle : 0.467 9.907 47846 Z= 0.248 Chirality : 0.041 0.149 5330 Planarity : 0.003 0.036 6018 Dihedral : 11.342 179.655 5314 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.48 % Allowed : 10.87 % Favored : 87.65 % 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: 1.30 (0.13), residues: 4238 helix: 2.46 (0.12), residues: 1783 sheet: 0.26 (0.19), residues: 744 loop : -0.58 (0.15), residues: 1711 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 0.012 0.001 PHE C 25 TRP 0.006 0.001 TRP E 270 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00257 (35262) covalent geometry : angle 0.46614 (47836) SS BOND : bond 0.00102 ( 5) SS BOND : angle 1.69875 ( 10) hydrogen bonds : bond 0.03284 ( 1706) hydrogen bonds : angle 4.30570 ( 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 336 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 1.417 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: A 17 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8249 (mt-10) REVERT: A 490 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9120 (p) REVERT: A 496 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8500 (mtt) REVERT: B 72 LYS cc_start: 0.9202 (ptmt) cc_final: 0.8669 (ptmt) REVERT: B 216 HIS cc_start: 0.8303 (m-70) cc_final: 0.8096 (m170) REVERT: B 248 GLU cc_start: 0.8224 (mp0) cc_final: 0.7847 (pm20) REVERT: B 395 ARG cc_start: 0.8322 (tpt90) cc_final: 0.7968 (tpt170) REVERT: B 436 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8701 (ttm) REVERT: C 251 ASP cc_start: 0.8528 (m-30) cc_final: 0.8201 (m-30) REVERT: C 422 ARG cc_start: 0.8847 (mtm180) cc_final: 0.8394 (mtm110) REVERT: C 519 MET cc_start: 0.8552 (ttp) cc_final: 0.8159 (tpp) REVERT: D 484 GLU cc_start: 0.8728 (tp30) cc_final: 0.8308 (mm-30) REVERT: E 69 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8464 (ttm170) REVERT: E 245 ASP cc_start: 0.8474 (p0) cc_final: 0.8266 (p0) REVERT: E 496 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: E 519 MET cc_start: 0.8664 (mtm) cc_final: 0.8386 (mtm) REVERT: F 327 MET cc_start: 0.8745 (mmm) cc_final: 0.8537 (mmm) REVERT: F 484 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8493 (tp30) REVERT: G 26 SER cc_start: 0.9426 (OUTLIER) cc_final: 0.9123 (p) REVERT: G 93 GLN cc_start: 0.9313 (mp10) cc_final: 0.9028 (mp10) REVERT: G 131 ARG cc_start: 0.8299 (mmm-85) cc_final: 0.8045 (mmm-85) REVERT: G 171 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8613 (tm-30) REVERT: G 340 LYS cc_start: 0.9091 (mttt) cc_final: 0.8800 (mmtt) REVERT: G 381 ASP cc_start: 0.8371 (p0) cc_final: 0.7846 (t70) REVERT: H 87 ASN cc_start: 0.8674 (t0) cc_final: 0.8469 (t0) REVERT: H 391 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8586 (tm-30) outliers start: 53 outliers final: 39 residues processed: 321 average time/residue: 0.2152 time to fit residues: 112.9855 Evaluate side-chains 307 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 496 MET Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 424 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 403 TYR 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 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 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 391 GLU 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: 9.9990 chunk 96 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 364 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 396 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3458 r_free = 0.3458 target = 0.092121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068529 restraints weight = 78517.066| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.96 r_work: 0.2854 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35267 Z= 0.131 Angle : 0.482 9.789 47846 Z= 0.255 Chirality : 0.041 0.147 5330 Planarity : 0.003 0.037 6018 Dihedral : 11.290 177.268 5312 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.42 % Allowed : 11.17 % Favored : 87.40 % 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: 1.31 (0.13), residues: 4238 helix: 2.46 (0.12), residues: 1784 sheet: 0.23 (0.19), residues: 758 loop : -0.56 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 395 TYR 0.012 0.001 TYR D 506 PHE 0.013 0.001 PHE C 25 TRP 0.005 0.001 TRP E 270 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00307 (35262) covalent geometry : angle 0.48018 (47836) SS BOND : bond 0.00167 ( 5) SS BOND : angle 2.77698 ( 10) hydrogen bonds : bond 0.03346 ( 1706) hydrogen bonds : angle 4.30246 ( 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 318 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 1.134 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 17 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 490 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9116 (p) REVERT: A 496 MET cc_start: 0.8874 (mtt) cc_final: 0.8539 (mtt) REVERT: B 72 LYS cc_start: 0.9207 (ptmt) cc_final: 0.8661 (ptmt) REVERT: B 248 GLU cc_start: 0.8221 (mp0) cc_final: 0.7855 (pm20) REVERT: B 395 ARG cc_start: 0.8343 (tpt90) cc_final: 0.8044 (tpt170) REVERT: B 436 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8684 (ttm) REVERT: C 158 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9192 (mp) REVERT: C 251 ASP cc_start: 0.8531 (m-30) cc_final: 0.8202 (m-30) REVERT: C 422 ARG cc_start: 0.8811 (mtm180) cc_final: 0.8361 (mtm110) REVERT: D 484 GLU cc_start: 0.8748 (tp30) cc_final: 0.8318 (mm-30) REVERT: E 69 ARG cc_start: 0.8702 (ttp-170) cc_final: 0.8484 (ttm170) REVERT: E 245 ASP cc_start: 0.8449 (p0) cc_final: 0.8235 (p0) REVERT: E 496 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8360 (mtt) REVERT: F 327 MET cc_start: 0.8772 (mmm) cc_final: 0.8527 (mmm) REVERT: F 450 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: F 484 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8477 (tp30) REVERT: G 26 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9111 (p) REVERT: G 93 GLN cc_start: 0.9325 (mp10) cc_final: 0.9041 (mp10) REVERT: G 131 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.8074 (mmm-85) REVERT: G 171 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8551 (tm-30) REVERT: G 381 ASP cc_start: 0.8397 (p0) cc_final: 0.7898 (t70) REVERT: H 87 ASN cc_start: 0.8670 (t0) cc_final: 0.8276 (t0) REVERT: H 391 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8567 (tm-30) outliers start: 51 outliers final: 39 residues processed: 302 average time/residue: 0.2055 time to fit residues: 101.9105 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 : 1.423 ------------------------------------------------------------------------------- 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 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 82 LYS 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 11 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 502 ASN 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 403 TYR 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 450 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 256 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 323 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 366 optimal weight: 0.2980 chunk 393 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 301 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3425 r_free = 0.3425 target = 0.090312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066606 restraints weight = 78789.215| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.95 r_work: 0.2832 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35267 Z= 0.225 Angle : 0.542 10.047 47846 Z= 0.287 Chirality : 0.043 0.154 5330 Planarity : 0.004 0.040 6018 Dihedral : 11.414 174.102 5312 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 11.23 % 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: 2.39 (0.13), residues: 1784 sheet: 0.16 (0.19), residues: 746 loop : -0.67 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 395 TYR 0.019 0.001 TYR F 95 PHE 0.017 0.002 PHE A 25 TRP 0.011 0.001 TRP F 63 HIS 0.008 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00531 (35262) covalent geometry : angle 0.54193 (47836) SS BOND : bond 0.00270 ( 5) SS BOND : angle 1.48354 ( 10) hydrogen bonds : bond 0.04103 ( 1706) hydrogen bonds : angle 4.46767 ( 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 303 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.9155 (p) REVERT: B 248 GLU cc_start: 0.8254 (mp0) cc_final: 0.7869 (pm20) REVERT: B 395 ARG cc_start: 0.8385 (tpt90) cc_final: 0.8076 (tpt170) REVERT: B 436 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8650 (ttm) REVERT: C 251 ASP cc_start: 0.8571 (m-30) cc_final: 0.8239 (m-30) REVERT: D 484 GLU cc_start: 0.8776 (tp30) cc_final: 0.8358 (mm-30) REVERT: E 245 ASP cc_start: 0.8434 (p0) cc_final: 0.8202 (p0) REVERT: E 395 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8545 (tpt90) REVERT: E 496 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8403 (mtt) REVERT: F 327 MET cc_start: 0.8796 (mmm) cc_final: 0.8533 (mmm) REVERT: F 450 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: G 26 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9112 (p) REVERT: G 93 GLN cc_start: 0.9342 (mp10) cc_final: 0.9086 (mp10) REVERT: G 131 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8093 (mmm-85) REVERT: G 203 MET cc_start: 0.7894 (mmm) cc_final: 0.7536 (mpp) REVERT: G 340 LYS cc_start: 0.9093 (mttt) cc_final: 0.8844 (mmtt) REVERT: G 343 ARG cc_start: 0.8705 (mtp180) cc_final: 0.8502 (ttm-80) REVERT: G 381 ASP cc_start: 0.8421 (p0) cc_final: 0.7848 (t70) REVERT: H 92 ASP cc_start: 0.9125 (p0) cc_final: 0.8906 (p0) REVERT: H 93 GLN cc_start: 0.8959 (mp10) cc_final: 0.8370 (mp10) outliers start: 51 outliers final: 34 residues processed: 290 average time/residue: 0.2119 time to fit residues: 101.0656 Evaluate side-chains 285 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 246 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 A residue 513 GLN 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 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 436 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 198 MET 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 82 LYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 450 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 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 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 122 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 306 optimal weight: 1.9990 chunk 375 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS C 256 GLN F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068035 restraints weight = 79835.075| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.07 r_work: 0.2838 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35267 Z= 0.128 Angle : 0.490 10.365 47846 Z= 0.260 Chirality : 0.041 0.182 5330 Planarity : 0.003 0.038 6018 Dihedral : 11.258 166.262 5311 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.06 % Allowed : 11.65 % Favored : 87.29 % 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: 2.43 (0.12), residues: 1783 sheet: 0.20 (0.19), residues: 744 loop : -0.65 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 422 TYR 0.012 0.001 TYR H 200 PHE 0.013 0.001 PHE C 25 TRP 0.007 0.001 TRP E 270 HIS 0.006 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00298 (35262) covalent geometry : angle 0.48950 (47836) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.28614 ( 10) hydrogen bonds : bond 0.03438 ( 1706) hydrogen bonds : angle 4.33902 ( 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 307 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9128 (p) REVERT: A 497 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8479 (ttp80) REVERT: B 248 GLU cc_start: 0.8270 (mp0) cc_final: 0.7884 (pm20) REVERT: B 395 ARG cc_start: 0.8333 (tpt90) cc_final: 0.8024 (tpt170) REVERT: B 436 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8714 (ttm) REVERT: C 251 ASP cc_start: 0.8535 (m-30) cc_final: 0.8205 (m-30) REVERT: C 422 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8150 (mtm110) REVERT: D 1 MET cc_start: 0.7386 (ptt) cc_final: 0.7183 (ptt) REVERT: D 484 GLU cc_start: 0.8761 (tp30) cc_final: 0.8312 (mm-30) REVERT: E 395 ARG cc_start: 0.8910 (tpp80) cc_final: 0.8525 (tpt90) REVERT: E 496 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8385 (mtt) REVERT: E 519 MET cc_start: 0.8725 (mtm) cc_final: 0.8394 (mtm) REVERT: F 327 MET cc_start: 0.8786 (mmm) cc_final: 0.8520 (mmm) REVERT: F 450 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: F 484 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8470 (tp30) REVERT: G 26 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.9091 (p) REVERT: G 93 GLN cc_start: 0.9322 (mp10) cc_final: 0.9077 (mp10) REVERT: G 131 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.8060 (mmm-85) REVERT: G 171 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8695 (tm-30) REVERT: G 203 MET cc_start: 0.7870 (mmm) cc_final: 0.7470 (mpp) REVERT: G 340 LYS cc_start: 0.9086 (mttt) cc_final: 0.8807 (mmtt) REVERT: G 343 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8441 (ttm-80) REVERT: G 381 ASP cc_start: 0.8423 (p0) cc_final: 0.7858 (t70) REVERT: G 443 GLU cc_start: 0.8810 (tp30) cc_final: 0.8326 (tp30) REVERT: H 92 ASP cc_start: 0.9141 (p0) cc_final: 0.8917 (p0) REVERT: H 93 GLN cc_start: 0.8937 (mp10) cc_final: 0.8318 (mp10) outliers start: 38 outliers final: 30 residues processed: 296 average time/residue: 0.2122 time to fit residues: 102.5728 Evaluate side-chains 293 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 A residue 513 GLN Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 436 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 198 MET 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 82 LYS Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 450 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 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 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: 0.5980 chunk 103 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 370 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 chunk 332 optimal weight: 0.0270 chunk 401 optimal weight: 6.9990 chunk 419 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS C 443 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.092780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069198 restraints weight = 78107.557| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.97 r_work: 0.2869 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35267 Z= 0.100 Angle : 0.471 10.578 47846 Z= 0.250 Chirality : 0.041 0.162 5330 Planarity : 0.003 0.048 6018 Dihedral : 11.126 158.877 5311 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.06 % Allowed : 11.65 % Favored : 87.29 % 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: 1.29 (0.13), residues: 4238 helix: 2.49 (0.12), residues: 1781 sheet: 0.22 (0.19), residues: 746 loop : -0.61 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 422 TYR 0.014 0.001 TYR H 135 PHE 0.013 0.001 PHE C 25 TRP 0.006 0.001 TRP B 270 HIS 0.008 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00225 (35262) covalent geometry : angle 0.47024 (47836) SS BOND : bond 0.00651 ( 5) SS BOND : angle 1.33885 ( 10) hydrogen bonds : bond 0.03116 ( 1706) hydrogen bonds : angle 4.25369 ( 4995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7652.81 seconds wall clock time: 131 minutes 38.44 seconds (7898.44 seconds total)