Starting phenix.real_space_refine on Sat Mar 7 00:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1o_66465/03_2026/9x1o_66465.map" } resolution = 3.0 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 5 7.51 5 P 75 5.49 5 S 99 5.16 5 C 21944 2.51 5 N 6080 2.21 5 O 6774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 34977 Number of models: 1 Model: "" Number of chains: 16 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: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 630 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "J" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 600 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MN': 1, 'ADP': 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} Time building chain proxies: 8.64, per 1000 atoms: 0.25 Number of scatterers: 34977 At special positions: 0 Unit cell: (136.864, 148.144, 186.496, 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 5 24.99 S 99 16.00 P 75 15.00 O 6774 8.00 N 6080 7.00 C 21944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 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: 160 helices and 21 sheets defined 47.8% alpha, 18.2% beta 14 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 4.23 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 190 through 205 Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.612A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 341 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 403 Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.745A pdb=" N PHE A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.145A pdb=" N ILE A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) 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 510 Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.502A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 577 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 205 removed outlier: 3.619A pdb=" N GLU B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 319 through 341 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 367 through 403 Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.678A pdb=" N ALA B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 433' Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.772A pdb=" N PHE B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.187A pdb=" N ILE B 457 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 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 524 removed outlier: 3.525A pdb=" N MET B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 578 Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.529A pdb=" N ARG C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 96 Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.490A pdb=" N GLY C 100 " --> pdb=" O GLY C 96 " (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 260 through 278 Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.606A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 341 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 367 through 403 Processing helix chain 'C' and resid 408 through 428 Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.566A pdb=" N ALA C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.028A pdb=" N PHE C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 469 removed outlier: 5.527A pdb=" N ARG C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS C 467 " --> pdb=" O ARG C 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 489 removed outlier: 3.502A pdb=" N GLN C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.565A pdb=" N ASP C 521 " --> pdb=" O GLU C 517 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 523 " --> pdb=" O MET C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 578 Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.762A pdb=" N GLU D 80 " --> pdb=" O TRP D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 76 through 80' Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 95 through 100 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 205 removed outlier: 3.738A pdb=" N GLU D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 259 through 277 Processing helix chain 'D' and resid 282 through 300 removed outlier: 3.688A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 341 Processing helix chain 'D' and resid 348 through 353 removed outlier: 3.598A pdb=" N ILE D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 400 Processing helix chain 'D' and resid 414 through 428 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.550A pdb=" N ALA D 432 " --> pdb=" O PRO D 429 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 433 " --> pdb=" O ALA D 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 429 through 433' Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.690A pdb=" N PHE D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 469 removed outlier: 5.325A pdb=" N ARG D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS D 467 " --> pdb=" O ARG D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 489 removed outlier: 3.882A pdb=" N GLN D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.604A pdb=" N ALA D 523 " --> pdb=" O MET D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 578 Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.831A pdb=" N GLU E 80 " --> pdb=" O TRP E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 80' 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 179 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 215 through 218 removed outlier: 3.674A pdb=" N ASP E 218 " --> pdb=" O PRO E 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 218' Processing helix chain 'E' and resid 240 through 244 removed outlier: 3.830A pdb=" N ALA E 243 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 253 Processing helix chain 'E' and resid 259 through 277 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.853A pdb=" N VAL E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 341 Processing helix chain 'E' and resid 367 through 403 Processing helix chain 'E' and resid 406 through 428 removed outlier: 4.143A pdb=" N VAL E 410 " --> pdb=" O ASN E 406 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 416 " --> pdb=" O ASP E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.554A pdb=" N GLU E 433 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.817A pdb=" N PHE E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 469 removed outlier: 5.705A pdb=" N ARG E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 468 " --> pdb=" O GLU E 464 " (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 517 through 522 removed outlier: 4.081A pdb=" N ASP E 521 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 522 " --> pdb=" O MET E 519 " (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 54 Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.783A pdb=" N GLU F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 102' Processing helix chain 'F' and resid 141 through 149 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 190 through 207 removed outlier: 3.518A pdb=" N LEU F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 253 Processing helix chain 'F' and resid 259 through 277 Processing helix chain 'F' and resid 282 through 300 removed outlier: 3.673A 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 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 348 through 353 removed outlier: 3.587A pdb=" N ILE F 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 403 removed outlier: 3.661A pdb=" N LYS F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 373 " --> pdb=" O GLY F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 428 removed outlier: 4.095A pdb=" N ASP F 412 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.563A pdb=" N ALA F 432 " --> pdb=" O PRO F 429 " (cutoff:3.500A) removed outlier: 3.820A 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: 4.086A pdb=" N PHE F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 469 removed outlier: 3.514A pdb=" N ARG F 456 " --> pdb=" O GLY F 452 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ARG F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYS F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 500 through 510 Processing helix chain 'F' and resid 512 through 516 Processing helix chain 'F' and resid 517 through 522 removed outlier: 3.736A pdb=" N ASP F 521 " --> pdb=" O LEU F 518 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE F 522 " --> pdb=" O MET F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 576 Processing helix chain 'G' and resid 6 through 27 removed outlier: 4.000A pdb=" N LYS G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 130 Processing helix chain 'G' and resid 134 through 148 Processing helix chain 'G' and resid 151 through 179 removed outlier: 3.715A pdb=" N LYS G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 171 " --> pdb=" O GLU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 removed outlier: 4.056A pdb=" N GLU G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 3.910A pdb=" N PHE G 196 " --> pdb=" O LYS G 192 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 197 " --> pdb=" O LEU G 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 192 through 197' Processing helix chain 'G' and resid 255 through 279 Processing helix chain 'G' and resid 295 through 300 removed outlier: 3.638A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 318 removed outlier: 3.557A pdb=" N TYR G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 344 removed outlier: 4.406A pdb=" N GLU G 344 " --> pdb=" O LYS G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 356 removed outlier: 3.594A 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 407 Processing helix chain 'G' and resid 409 through 428 Processing helix chain 'G' and resid 429 through 435 removed outlier: 3.928A pdb=" N VAL G 433 " --> pdb=" O GLU G 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 26 removed outlier: 3.898A pdb=" N GLU H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 25 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 114 removed outlier: 3.597A pdb=" N GLY H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 134 through 148 removed outlier: 3.526A pdb=" N LYS H 140 " --> pdb=" O PRO H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 179 Processing helix chain 'H' and resid 187 through 192 removed outlier: 3.592A pdb=" N GLU H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 205 removed outlier: 3.929A pdb=" N PHE H 196 " --> pdb=" O LYS H 192 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU H 198 " --> pdb=" O GLU H 194 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA H 202 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N MET H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS H 204 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY H 205 " --> pdb=" O LYS H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 279 Processing helix chain 'H' and resid 304 through 318 Processing helix chain 'H' and resid 339 through 346 removed outlier: 3.879A pdb=" N GLU H 344 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR H 345 " --> pdb=" O VAL H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 removed outlier: 3.786A 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 397 through 407 Processing helix chain 'H' and resid 409 through 428 Processing helix chain 'H' and resid 429 through 434 removed outlier: 4.208A pdb=" N VAL H 433 " --> pdb=" O GLU H 430 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 removed outlier: 6.800A pdb=" N ALA A 104 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN A 73 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU A 71 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A 108 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 65 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS A 114 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TRP A 63 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 42 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 136 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN A 24 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 5.118A 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: 3.719A pdb=" N GLY A 159 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 171 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU A 157 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 182 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 181 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 435 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY A 473 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 437 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL A 475 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL A 439 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU A 440 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 210 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 361 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 212 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASN A 233 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP A 362 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 7.300A 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 306 Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 125 removed outlier: 6.761A pdb=" N GLU B 103 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN B 75 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 105 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 73 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 107 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 71 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 109 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG B 69 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 111 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR B 67 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG B 42 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG B 136 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLN B 24 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 5.145A 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: 6.802A pdb=" N VAL B 169 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 182 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B 181 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU B 440 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 210 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE B 361 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 212 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASN B 233 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ASP B 362 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE B 235 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 125 removed outlier: 6.822A pdb=" N ALA C 104 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN C 73 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 106 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 71 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 108 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 65 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 12 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU C 105 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.746A pdb=" N GLY C 159 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 171 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU C 157 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA C 182 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 474 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLY C 473 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL C 437 " --> pdb=" O GLY C 473 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL C 475 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL C 439 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 209 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE C 438 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 211 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU C 440 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 213 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 210 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE C 361 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 212 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AA9, first strand: chain 'D' and resid 121 through 125 removed outlier: 6.727A pdb=" N ALA D 104 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN D 73 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 106 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU D 71 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N THR D 108 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE D 65 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS D 114 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TRP D 63 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG D 42 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY D 12 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN D 24 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU D 105 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 168 through 172 removed outlier: 6.887A pdb=" N VAL D 169 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA D 182 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 211 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU D 440 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 213 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 210 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE D 361 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 212 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AB3, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.578A pdb=" N GLY E 70 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS E 110 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE E 68 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU E 112 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY E 66 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS E 114 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 64 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG E 42 " --> pdb=" O ARG E 136 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG E 136 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN E 24 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.720A pdb=" N VAL E 169 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS E 180 " --> pdb=" O THR E 490 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 492 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 210 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE E 361 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL E 212 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 303 through 306 removed outlier: 4.478A pdb=" N GLN E 311 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.848A pdb=" N ALA F 104 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN F 73 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 106 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU F 71 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR F 108 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE F 65 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS F 114 " --> pdb=" O TRP F 63 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TRP F 63 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG F 42 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG F 136 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN F 24 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU F 105 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 168 through 172 removed outlier: 6.900A pdb=" N VAL F 169 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS F 180 " --> pdb=" O THR F 490 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR F 492 " --> pdb=" O HIS F 180 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP F 214 " --> pdb=" O ILE F 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 302 through 305 Processing sheet with id=AB9, first strand: chain 'G' and resid 181 through 182 removed outlier: 6.301A pdb=" N TYR G 46 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASP G 122 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL G 48 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL G 119 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL G 286 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N MET G 121 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET G 359 " --> pdb=" O ILE G 327 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 391 through 392 Processing sheet with id=AC2, first strand: chain 'H' and resid 181 through 183 removed outlier: 3.578A pdb=" N ILE H 61 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR H 46 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ASP H 122 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL H 48 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL H 119 " --> pdb=" O VAL H 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL H 286 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET H 121 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET H 359 " --> pdb=" O ILE H 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 391 through 392 1713 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 8.33 Time building geometry restraints manager: 3.88 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: 11706 1.36 - 1.51: 9294 1.51 - 1.66: 14527 1.66 - 1.80: 153 1.80 - 1.95: 30 Bond restraints: 35710 Sorted by residual: bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C3' DA I 2 " pdb=" O3' DA I 2 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C3' DT J 1 " pdb=" O3' DT J 1 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.08e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 35705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 47407 1.17 - 2.34: 860 2.34 - 3.51: 208 3.51 - 4.68: 26 4.68 - 5.85: 24 Bond angle restraints: 48525 Sorted by residual: angle pdb=" N VAL A 11 " pdb=" CA VAL A 11 " pdb=" C VAL A 11 " ideal model delta sigma weight residual 111.81 109.52 2.29 8.60e-01 1.35e+00 7.08e+00 angle pdb=" N VAL A 439 " pdb=" CA VAL A 439 " pdb=" C VAL A 439 " ideal model delta sigma weight residual 106.85 109.95 -3.10 1.42e+00 4.96e-01 4.75e+00 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 113.07 110.12 2.95 1.36e+00 5.41e-01 4.70e+00 angle pdb=" N GLU C 46 " pdb=" CA GLU C 46 " pdb=" CB GLU C 46 " ideal model delta sigma weight residual 113.65 110.63 3.02 1.47e+00 4.63e-01 4.23e+00 angle pdb=" CA GLY C 208 " pdb=" C GLY C 208 " pdb=" O GLY C 208 " ideal model delta sigma weight residual 122.39 120.56 1.83 9.30e-01 1.16e+00 3.86e+00 ... (remaining 48520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 21063 35.50 - 71.00: 377 71.00 - 106.49: 13 106.49 - 141.99: 2 141.99 - 177.49: 4 Dihedral angle restraints: 21459 sinusoidal: 9309 harmonic: 12150 Sorted by residual: dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 10.50 -70.50 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" C4' DA I 2 " pdb=" C3' DA I 2 " pdb=" O3' DA I 2 " pdb=" P DA I 3 " ideal model delta sinusoidal sigma weight residual -140.00 37.49 -177.49 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 1 " pdb=" C3' DT J 1 " pdb=" O3' DT J 1 " pdb=" P DT J 2 " ideal model delta sinusoidal sigma weight residual -140.00 37.21 -177.21 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 21456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3673 0.031 - 0.061: 1110 0.061 - 0.092: 289 0.092 - 0.123: 304 0.123 - 0.153: 28 Chirality restraints: 5404 Sorted by residual: chirality pdb=" CA ILE E 318 " pdb=" N ILE E 318 " pdb=" C ILE E 318 " pdb=" CB ILE E 318 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-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 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 494 " pdb=" N ILE A 494 " pdb=" C ILE A 494 " pdb=" CB ILE A 494 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 5401 not shown) Planarity restraints: 6038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 105 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LYS H 105 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS H 105 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU H 106 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 103 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C GLU H 103 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU H 103 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN H 104 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 101 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C THR H 101 " -0.026 2.00e-02 2.50e+03 pdb=" O THR H 101 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU H 102 " 0.009 2.00e-02 2.50e+03 ... (remaining 6035 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 138 2.47 - 3.07: 23343 3.07 - 3.68: 51258 3.68 - 4.29: 75825 4.29 - 4.90: 129800 Nonbonded interactions: 280364 Sorted by model distance: nonbonded pdb=" O2B ADP D 601 " pdb="MN MN D 602 " model vdw 1.857 2.320 nonbonded pdb=" OG SER E 192 " pdb="MN MN E 602 " model vdw 1.872 2.320 nonbonded pdb=" O1B AGS E 601 " pdb="MN MN E 602 " model vdw 1.881 2.320 nonbonded pdb=" O3G AGS F 601 " pdb="MN MN F 602 " model vdw 1.886 2.320 nonbonded pdb=" O3B ADP C 601 " pdb="MN MN C 602 " model vdw 1.897 2.320 ... (remaining 280359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) selection = (chain 'D' and resid 1 through 578) selection = (chain 'E' and resid 1 through 578) selection = (chain 'F' and resid 1 through 578) } 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.810 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.034 35714 Z= 0.094 Angle : 0.440 5.845 48533 Z= 0.239 Chirality : 0.040 0.153 5404 Planarity : 0.003 0.032 6038 Dihedral : 12.467 177.491 13723 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.53 % Allowed : 3.49 % Favored : 95.98 % 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: 2.48 (0.13), residues: 1768 sheet: 0.31 (0.19), residues: 753 loop : -0.76 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.008 0.001 TYR H 361 PHE 0.014 0.001 PHE C 25 TRP 0.013 0.001 TRP B 54 HIS 0.003 0.001 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00187 (35710) covalent geometry : angle 0.43971 (48525) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.31946 ( 8) hydrogen bonds : bond 0.13493 ( 1741) hydrogen bonds : angle 5.93133 ( 5006) *********************** 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 601 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 582 time to evaluate : 1.451 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: A 54 TRP cc_start: 0.8114 (m-90) cc_final: 0.7771 (m-90) REVERT: A 394 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8205 (tppt) REVERT: A 464 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 219 TYR cc_start: 0.8898 (m-80) cc_final: 0.8607 (m-80) REVERT: B 271 ASP cc_start: 0.8783 (m-30) cc_final: 0.8429 (m-30) REVERT: B 362 ASP cc_start: 0.8463 (t70) cc_final: 0.7944 (p0) REVERT: C 254 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7910 (tm-30) REVERT: C 261 ILE cc_start: 0.8586 (mt) cc_final: 0.8004 (mp) REVERT: C 327 MET cc_start: 0.8384 (tpt) cc_final: 0.7874 (tpp) REVERT: C 331 MET cc_start: 0.9118 (ttm) cc_final: 0.8786 (mtp) REVERT: C 558 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7765 (mm-30) REVERT: D 54 TRP cc_start: 0.8846 (m100) cc_final: 0.8412 (m100) REVERT: D 324 GLU cc_start: 0.9026 (tt0) cc_final: 0.8587 (tp30) REVERT: D 380 GLU cc_start: 0.8934 (tp30) cc_final: 0.8354 (tm-30) REVERT: D 575 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8338 (tm-30) REVERT: E 519 MET cc_start: 0.9022 (mtm) cc_final: 0.8679 (mtm) REVERT: F 52 CYS cc_start: 0.8897 (m) cc_final: 0.8196 (t) REVERT: F 74 ILE cc_start: 0.8865 (tt) cc_final: 0.8651 (pt) REVERT: F 413 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8091 (mp0) REVERT: F 441 GLU cc_start: 0.7862 (tp30) cc_final: 0.7620 (tp30) REVERT: F 513 GLN cc_start: 0.8614 (tp40) cc_final: 0.8177 (tp-100) REVERT: G 256 ASP cc_start: 0.7612 (p0) cc_final: 0.7355 (p0) REVERT: H 174 ASP cc_start: 0.8508 (t0) cc_final: 0.8218 (t0) REVERT: H 256 ASP cc_start: 0.8522 (m-30) cc_final: 0.7942 (t70) outliers start: 19 outliers final: 8 residues processed: 595 average time/residue: 0.9741 time to fit residues: 662.8174 Evaluate side-chains 305 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 297 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 257 ASP Chi-restraints excluded: chain H residue 304 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS B 116 GLN C 50 GLN C 256 GLN C 448 HIS D 50 GLN D 118 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN E 504 GLN F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.103203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.074290 restraints weight = 74754.846| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.85 r_work: 0.2802 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 35714 Z= 0.255 Angle : 0.625 7.807 48533 Z= 0.330 Chirality : 0.044 0.162 5404 Planarity : 0.004 0.042 6038 Dihedral : 13.634 177.813 5525 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.35 % Allowed : 10.73 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4238 helix: 2.56 (0.13), residues: 1772 sheet: 0.24 (0.19), residues: 762 loop : -0.73 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 571 TYR 0.018 0.001 TYR G 68 PHE 0.021 0.002 PHE B 420 TRP 0.010 0.001 TRP B 54 HIS 0.009 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00606 (35710) covalent geometry : angle 0.62525 (48525) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.66265 ( 8) hydrogen bonds : bond 0.04802 ( 1741) hydrogen bonds : angle 4.72561 ( 5006) *********************** 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 392 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 308 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8477 (tppt) REVERT: A 464 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 271 ASP cc_start: 0.8848 (m-30) cc_final: 0.8496 (m-30) REVERT: B 362 ASP cc_start: 0.8665 (t70) cc_final: 0.8142 (p0) REVERT: C 254 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8058 (tm-30) REVERT: C 327 MET cc_start: 0.8540 (tpt) cc_final: 0.8004 (tpp) REVERT: C 331 MET cc_start: 0.9196 (ttm) cc_final: 0.8971 (mtp) REVERT: C 422 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8201 (mmt-90) REVERT: C 436 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8722 (ttm) REVERT: D 48 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8568 (mtmm) REVERT: D 324 GLU cc_start: 0.9349 (tt0) cc_final: 0.8841 (tp30) REVERT: D 380 GLU cc_start: 0.9186 (tp30) cc_final: 0.8653 (tp30) REVERT: D 436 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8812 (ttm) REVERT: D 575 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8433 (tm-30) REVERT: E 238 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8870 (mttp) REVERT: E 254 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8740 (tt0) REVERT: E 258 ASN cc_start: 0.8480 (m110) cc_final: 0.8096 (p0) REVERT: E 478 ARG cc_start: 0.8504 (mmm160) cc_final: 0.7901 (mmp-170) REVERT: E 505 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8600 (tp40) REVERT: E 519 MET cc_start: 0.9081 (mtm) cc_final: 0.8813 (mtm) REVERT: F 52 CYS cc_start: 0.8945 (m) cc_final: 0.8420 (t) REVERT: F 244 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8936 (mtt) REVERT: F 413 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8222 (mp0) REVERT: G 121 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8628 (mtt) REVERT: G 203 MET cc_start: 0.8495 (ttm) cc_final: 0.7851 (mtp) REVERT: H 174 ASP cc_start: 0.8820 (t0) cc_final: 0.8504 (t0) REVERT: H 257 ASP cc_start: 0.8788 (m-30) cc_final: 0.8350 (m-30) REVERT: H 386 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8694 (mt-10) outliers start: 84 outliers final: 19 residues processed: 367 average time/residue: 0.8926 time to fit residues: 380.4843 Evaluate side-chains 293 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 48 LYS Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 121 MET Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 97 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS B 57 ASN C 448 HIS D 73 ASN D 216 HIS D 502 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 183 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.073836 restraints weight = 75618.701| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.92 r_work: 0.2805 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35714 Z= 0.175 Angle : 0.557 8.526 48533 Z= 0.295 Chirality : 0.043 0.160 5404 Planarity : 0.003 0.035 6038 Dihedral : 13.626 178.858 5516 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.82 % Allowed : 12.01 % Favored : 86.17 % 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: 2.54 (0.13), residues: 1779 sheet: 0.13 (0.19), residues: 760 loop : -0.75 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 456 TYR 0.037 0.001 TYR F 150 PHE 0.024 0.002 PHE B 420 TRP 0.009 0.001 TRP B 54 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00409 (35710) covalent geometry : angle 0.55661 (48525) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.47385 ( 8) hydrogen bonds : bond 0.04262 ( 1741) hydrogen bonds : angle 4.50280 ( 5006) *********************** 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 358 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 1.361 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 54 TRP cc_start: 0.8326 (m-90) cc_final: 0.8116 (m-90) REVERT: A 394 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8504 (tppt) REVERT: A 464 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8527 (mt-10) REVERT: A 506 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 271 ASP cc_start: 0.8823 (m-30) cc_final: 0.8467 (m-30) REVERT: B 327 MET cc_start: 0.8843 (tpp) cc_final: 0.8633 (mmm) REVERT: B 362 ASP cc_start: 0.8666 (t70) cc_final: 0.8143 (p0) REVERT: B 448 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7907 (t-90) REVERT: C 254 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8092 (tm-30) REVERT: C 261 ILE cc_start: 0.8680 (mp) cc_final: 0.7728 (OUTLIER) REVERT: C 265 TYR cc_start: 0.9137 (m-80) cc_final: 0.8443 (m-80) REVERT: C 331 MET cc_start: 0.9197 (ttm) cc_final: 0.8976 (mtp) REVERT: C 422 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8212 (mmt-90) REVERT: C 436 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8647 (ttm) REVERT: D 92 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9194 (mp) REVERT: D 313 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8191 (mpt-90) REVERT: D 324 GLU cc_start: 0.9372 (tt0) cc_final: 0.8854 (tp30) REVERT: D 380 GLU cc_start: 0.9195 (tp30) cc_final: 0.8651 (tp30) REVERT: D 436 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8808 (ttm) REVERT: E 258 ASN cc_start: 0.8543 (m110) cc_final: 0.8128 (p0) REVERT: E 478 ARG cc_start: 0.8494 (mmm160) cc_final: 0.7871 (mmp-170) REVERT: E 509 ARG cc_start: 0.8643 (ttp-170) cc_final: 0.8319 (ttm110) REVERT: E 519 MET cc_start: 0.8989 (mtm) cc_final: 0.8742 (mtm) REVERT: F 52 CYS cc_start: 0.8935 (m) cc_final: 0.8415 (t) REVERT: F 413 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8198 (mp0) REVERT: F 481 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8590 (mtp85) REVERT: G 93 GLN cc_start: 0.9343 (mp10) cc_final: 0.8933 (mp-120) REVERT: G 203 MET cc_start: 0.8555 (ttm) cc_final: 0.8058 (mtm) REVERT: H 174 ASP cc_start: 0.8815 (t0) cc_final: 0.8519 (t0) REVERT: H 386 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (mt-10) outliers start: 65 outliers final: 25 residues processed: 339 average time/residue: 0.8768 time to fit residues: 345.6410 Evaluate side-chains 298 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 448 HIS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 153 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 328 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 404 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 217 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS B 57 ASN B 448 HIS C 57 ASN C 448 HIS D 216 HIS E 50 GLN E 73 ASN F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 351 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.110790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082005 restraints weight = 74944.847| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.82 r_work: 0.2857 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35714 Z= 0.160 Angle : 0.543 8.508 48533 Z= 0.287 Chirality : 0.042 0.162 5404 Planarity : 0.003 0.050 6038 Dihedral : 13.707 179.305 5516 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.18 % Allowed : 12.35 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4238 helix: 2.56 (0.13), residues: 1778 sheet: 0.15 (0.19), residues: 754 loop : -0.75 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 456 TYR 0.016 0.001 TYR E 506 PHE 0.016 0.002 PHE D 25 TRP 0.009 0.001 TRP B 54 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00375 (35710) covalent geometry : angle 0.54349 (48525) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.44213 ( 8) hydrogen bonds : bond 0.04057 ( 1741) hydrogen bonds : angle 4.42312 ( 5006) *********************** 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 371 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 293 time to evaluate : 0.929 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 54 TRP cc_start: 0.8339 (m-90) cc_final: 0.8118 (m-90) REVERT: A 394 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8511 (tppt) REVERT: A 464 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 506 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 271 ASP cc_start: 0.8838 (m-30) cc_final: 0.8512 (m-30) REVERT: B 362 ASP cc_start: 0.8653 (t70) cc_final: 0.8126 (p0) REVERT: C 254 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8074 (tm-30) REVERT: C 261 ILE cc_start: 0.8617 (mp) cc_final: 0.7684 (OUTLIER) REVERT: C 265 TYR cc_start: 0.9097 (m-80) cc_final: 0.8464 (m-80) REVERT: C 327 MET cc_start: 0.8878 (ttt) cc_final: 0.8293 (tpp) REVERT: C 394 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8177 (ttmm) REVERT: C 422 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8243 (mmt-90) REVERT: D 92 ILE cc_start: 0.9543 (OUTLIER) cc_final: 0.9198 (mp) REVERT: D 324 GLU cc_start: 0.9396 (tt0) cc_final: 0.8873 (tp30) REVERT: D 380 GLU cc_start: 0.9165 (tp30) cc_final: 0.8623 (tp30) REVERT: D 436 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8846 (ttm) REVERT: D 575 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8392 (tm-30) REVERT: E 238 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8799 (mttp) REVERT: E 258 ASN cc_start: 0.8529 (m110) cc_final: 0.8089 (p0) REVERT: E 436 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8715 (ttm) REVERT: E 505 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8196 (tp40) REVERT: E 509 ARG cc_start: 0.8626 (ttp-170) cc_final: 0.8114 (ttm170) REVERT: E 519 MET cc_start: 0.8954 (mtm) cc_final: 0.8693 (mtm) REVERT: F 52 CYS cc_start: 0.8953 (m) cc_final: 0.8449 (t) REVERT: F 413 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8186 (mp0) REVERT: F 481 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8592 (mtp85) REVERT: H 155 LYS cc_start: 0.8142 (mmpt) cc_final: 0.7825 (tmmm) REVERT: H 174 ASP cc_start: 0.8795 (t0) cc_final: 0.8494 (t0) REVERT: H 386 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (mt-10) outliers start: 78 outliers final: 29 residues processed: 349 average time/residue: 0.8354 time to fit residues: 339.7194 Evaluate side-chains 300 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 365 MET Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 118 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 397 optimal weight: 4.9990 chunk 422 optimal weight: 20.0000 chunk 372 optimal weight: 3.9990 chunk 419 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 369 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 216 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 133 ASN F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.080911 restraints weight = 75752.912| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.81 r_work: 0.2831 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35714 Z= 0.229 Angle : 0.586 9.375 48533 Z= 0.308 Chirality : 0.044 0.174 5404 Planarity : 0.004 0.041 6038 Dihedral : 13.833 179.978 5516 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.23 % Allowed : 13.24 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.13), residues: 4238 helix: 2.55 (0.13), residues: 1764 sheet: 0.12 (0.19), residues: 766 loop : -0.79 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 456 TYR 0.014 0.001 TYR G 352 PHE 0.025 0.002 PHE B 420 TRP 0.009 0.001 TRP B 54 HIS 0.008 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00542 (35710) covalent geometry : angle 0.58616 (48525) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.47192 ( 8) hydrogen bonds : bond 0.04445 ( 1741) hydrogen bonds : angle 4.48136 ( 5006) *********************** 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 354 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 274 time to evaluate : 1.356 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 54 TRP cc_start: 0.8348 (m-90) cc_final: 0.8121 (m-90) REVERT: A 394 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8466 (tppt) REVERT: A 464 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 506 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 271 ASP cc_start: 0.8878 (m-30) cc_final: 0.8538 (m-30) REVERT: B 362 ASP cc_start: 0.8695 (t70) cc_final: 0.8135 (p0) REVERT: B 512 GLU cc_start: 0.6925 (pm20) cc_final: 0.6587 (tt0) REVERT: C 254 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8089 (tm-30) REVERT: C 261 ILE cc_start: 0.8628 (mp) cc_final: 0.7676 (OUTLIER) REVERT: C 265 TYR cc_start: 0.9113 (m-80) cc_final: 0.8544 (m-80) REVERT: C 327 MET cc_start: 0.8860 (ttt) cc_final: 0.8334 (tpp) REVERT: C 394 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8187 (ttmm) REVERT: C 422 ARG cc_start: 0.8641 (tpp80) cc_final: 0.8270 (mmt-90) REVERT: C 436 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: C 496 MET cc_start: 0.9167 (mtt) cc_final: 0.8840 (mtt) REVERT: D 1 MET cc_start: 0.8305 (tmm) cc_final: 0.8054 (tmm) REVERT: D 92 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9181 (mp) REVERT: D 324 GLU cc_start: 0.9380 (tt0) cc_final: 0.8866 (tp30) REVERT: D 380 GLU cc_start: 0.9203 (tp30) cc_final: 0.8670 (tp30) REVERT: D 436 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8834 (ttm) REVERT: E 238 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8829 (mttp) REVERT: E 258 ASN cc_start: 0.8519 (m110) cc_final: 0.8068 (p0) REVERT: E 505 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8245 (tp40) REVERT: E 509 ARG cc_start: 0.8645 (ttp-170) cc_final: 0.8137 (ttm170) REVERT: E 519 MET cc_start: 0.8956 (mtm) cc_final: 0.8690 (mtm) REVERT: F 52 CYS cc_start: 0.8896 (m) cc_final: 0.8422 (t) REVERT: F 150 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7689 (p90) REVERT: F 413 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8210 (mp0) REVERT: F 450 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8087 (tm-30) REVERT: F 481 ARG cc_start: 0.8868 (mmm160) cc_final: 0.8627 (mtp85) REVERT: G 203 MET cc_start: 0.8401 (ttm) cc_final: 0.7986 (mtm) REVERT: H 155 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7880 (tmmm) REVERT: H 174 ASP cc_start: 0.8801 (t0) cc_final: 0.8501 (t0) REVERT: H 382 ASP cc_start: 0.8951 (m-30) cc_final: 0.8531 (t0) REVERT: H 386 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8622 (mt-10) outliers start: 80 outliers final: 30 residues processed: 333 average time/residue: 0.7983 time to fit residues: 311.5691 Evaluate side-chains 298 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 150 TYR Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 365 MET Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 260 optimal weight: 2.9990 chunk 342 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 411 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 73 ASN D 216 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 133 ASN F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080888 restraints weight = 75146.351| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.80 r_work: 0.2830 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35714 Z= 0.217 Angle : 0.581 8.693 48533 Z= 0.305 Chirality : 0.043 0.172 5404 Planarity : 0.004 0.052 6038 Dihedral : 13.897 179.898 5516 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 13.74 % Favored : 84.16 % 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: 2.54 (0.13), residues: 1764 sheet: 0.11 (0.19), residues: 765 loop : -0.80 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 456 TYR 0.017 0.001 TYR E 506 PHE 0.018 0.002 PHE D 25 TRP 0.009 0.001 TRP B 54 HIS 0.007 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00515 (35710) covalent geometry : angle 0.58139 (48525) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.43882 ( 8) hydrogen bonds : bond 0.04383 ( 1741) hydrogen bonds : angle 4.46701 ( 5006) *********************** 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 346 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.8349 (m-90) cc_final: 0.8140 (m-90) REVERT: A 394 LYS cc_start: 0.8680 (ttmt) cc_final: 0.8468 (tppt) REVERT: A 464 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8543 (mt-10) REVERT: A 506 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8175 (t80) REVERT: B 271 ASP cc_start: 0.8878 (m-30) cc_final: 0.8534 (m-30) REVERT: B 362 ASP cc_start: 0.8710 (t70) cc_final: 0.8145 (p0) REVERT: B 512 GLU cc_start: 0.6963 (pm20) cc_final: 0.6680 (tt0) REVERT: C 254 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8103 (tm-30) REVERT: C 261 ILE cc_start: 0.8646 (mp) cc_final: 0.7753 (mp) REVERT: C 265 TYR cc_start: 0.9057 (m-80) cc_final: 0.8525 (m-80) REVERT: C 327 MET cc_start: 0.8822 (ttt) cc_final: 0.8326 (tpp) REVERT: C 394 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8201 (ttmm) REVERT: C 422 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8268 (mmt-90) REVERT: C 436 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8675 (ttm) REVERT: C 496 MET cc_start: 0.9156 (mtt) cc_final: 0.8840 (mtt) REVERT: D 1 MET cc_start: 0.8335 (tmm) cc_final: 0.8104 (tmm) REVERT: D 92 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9181 (mp) REVERT: D 324 GLU cc_start: 0.9377 (tt0) cc_final: 0.8865 (tp30) REVERT: D 380 GLU cc_start: 0.9203 (tp30) cc_final: 0.8632 (tp30) REVERT: D 436 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8853 (ttm) REVERT: E 238 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8821 (mttp) REVERT: E 258 ASN cc_start: 0.8503 (m110) cc_final: 0.8064 (p0) REVERT: E 478 ARG cc_start: 0.8294 (mmp-170) cc_final: 0.7987 (mtp-110) REVERT: E 505 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8248 (tp40) REVERT: E 509 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8134 (ttm170) REVERT: E 519 MET cc_start: 0.8959 (mtm) cc_final: 0.8668 (mtm) REVERT: F 52 CYS cc_start: 0.8879 (m) cc_final: 0.8380 (t) REVERT: F 244 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.8757 (mtt) REVERT: F 413 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8197 (mp0) REVERT: F 451 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8676 (mmmt) REVERT: F 481 ARG cc_start: 0.8860 (mmm160) cc_final: 0.8631 (mtp85) REVERT: G 203 MET cc_start: 0.8438 (ttm) cc_final: 0.8024 (mtm) REVERT: H 131 ARG cc_start: 0.8421 (mmm160) cc_final: 0.7604 (tpt170) REVERT: H 174 ASP cc_start: 0.8813 (t0) cc_final: 0.8512 (t0) REVERT: H 382 ASP cc_start: 0.8952 (m-30) cc_final: 0.8523 (t0) REVERT: H 386 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8627 (mt-10) outliers start: 75 outliers final: 40 residues processed: 327 average time/residue: 0.7837 time to fit residues: 302.0324 Evaluate side-chains 303 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 365 MET Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 418 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 392 optimal weight: 8.9990 chunk 225 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 216 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.072405 restraints weight = 75352.108| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.92 r_work: 0.2755 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 35714 Z= 0.252 Angle : 0.604 9.423 48533 Z= 0.317 Chirality : 0.044 0.171 5404 Planarity : 0.004 0.040 6038 Dihedral : 13.978 179.750 5516 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 14.11 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.13), residues: 4238 helix: 2.47 (0.13), residues: 1773 sheet: 0.07 (0.19), residues: 770 loop : -0.81 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 456 TYR 0.031 0.001 TYR F 150 PHE 0.027 0.002 PHE B 420 TRP 0.008 0.001 TRP B 54 HIS 0.008 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00598 (35710) covalent geometry : angle 0.60378 (48525) SS BOND : bond 0.00239 ( 4) SS BOND : angle 0.45100 ( 8) hydrogen bonds : bond 0.04552 ( 1741) hydrogen bonds : angle 4.50081 ( 5006) *********************** 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 344 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 271 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.8348 (m-90) cc_final: 0.8127 (m-90) REVERT: A 394 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8435 (tppt) REVERT: A 464 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 506 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 271 ASP cc_start: 0.8886 (m-30) cc_final: 0.8543 (m-30) REVERT: B 362 ASP cc_start: 0.8706 (t70) cc_final: 0.8148 (p0) REVERT: C 261 ILE cc_start: 0.8639 (mp) cc_final: 0.7750 (mp) REVERT: C 265 TYR cc_start: 0.9065 (m-80) cc_final: 0.8544 (m-80) REVERT: C 327 MET cc_start: 0.8818 (ttt) cc_final: 0.8347 (tpp) REVERT: C 394 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8174 (ttmm) REVERT: C 422 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8262 (mmt-90) REVERT: C 436 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8705 (ttm) REVERT: D 1 MET cc_start: 0.8354 (tmm) cc_final: 0.8124 (tmm) REVERT: D 92 ILE cc_start: 0.9537 (OUTLIER) cc_final: 0.9185 (mp) REVERT: D 324 GLU cc_start: 0.9387 (tt0) cc_final: 0.8884 (tp30) REVERT: D 380 GLU cc_start: 0.9253 (tp30) cc_final: 0.8706 (tp30) REVERT: D 436 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8793 (ttm) REVERT: E 238 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8806 (mttp) REVERT: E 258 ASN cc_start: 0.8528 (m110) cc_final: 0.8100 (p0) REVERT: E 478 ARG cc_start: 0.8351 (mmp-170) cc_final: 0.8015 (mtp-110) REVERT: E 505 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8339 (tp40) REVERT: E 509 ARG cc_start: 0.8681 (ttp-170) cc_final: 0.8181 (ttm170) REVERT: E 519 MET cc_start: 0.8975 (mtm) cc_final: 0.8679 (mtm) REVERT: F 52 CYS cc_start: 0.8871 (m) cc_final: 0.8381 (t) REVERT: F 244 MET cc_start: 0.9485 (OUTLIER) cc_final: 0.8778 (mtt) REVERT: F 413 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8212 (mp0) REVERT: F 481 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8642 (mtp85) REVERT: G 131 ARG cc_start: 0.8652 (mmp80) cc_final: 0.8223 (tpm170) REVERT: G 203 MET cc_start: 0.8477 (ttm) cc_final: 0.8208 (mtm) REVERT: H 155 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7778 (ttpp) REVERT: H 174 ASP cc_start: 0.8813 (t0) cc_final: 0.8512 (t0) REVERT: H 386 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8733 (mt-10) outliers start: 73 outliers final: 37 residues processed: 322 average time/residue: 0.8108 time to fit residues: 306.6307 Evaluate side-chains 299 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 244 MET Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 327 MET Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 269 LEU Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 365 MET Chi-restraints excluded: chain H residue 386 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 189 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 113 optimal weight: 0.3980 chunk 224 optimal weight: 4.9990 chunk 370 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 280 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 216 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.103858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073844 restraints weight = 74123.299| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.94 r_work: 0.2800 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35714 Z= 0.155 Angle : 0.571 10.270 48533 Z= 0.299 Chirality : 0.042 0.181 5404 Planarity : 0.003 0.045 6038 Dihedral : 14.006 179.549 5516 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.51 % Allowed : 15.03 % Favored : 83.46 % 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: 2.52 (0.13), residues: 1778 sheet: 0.07 (0.19), residues: 742 loop : -0.77 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 131 TYR 0.020 0.001 TYR E 506 PHE 0.029 0.002 PHE B 420 TRP 0.006 0.001 TRP C 270 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00364 (35710) covalent geometry : angle 0.57069 (48525) SS BOND : bond 0.00216 ( 4) SS BOND : angle 0.38385 ( 8) hydrogen bonds : bond 0.03965 ( 1741) hydrogen bonds : angle 4.38831 ( 5006) *********************** 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 326 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.8317 (m-90) cc_final: 0.8097 (m-90) REVERT: A 384 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: A 394 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8459 (tppt) REVERT: A 464 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8491 (mt-10) REVERT: A 506 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 271 ASP cc_start: 0.8874 (m-30) cc_final: 0.8526 (m-30) REVERT: B 362 ASP cc_start: 0.8668 (t70) cc_final: 0.8137 (p0) REVERT: B 512 GLU cc_start: 0.6896 (pm20) cc_final: 0.6607 (tt0) REVERT: C 261 ILE cc_start: 0.8614 (mp) cc_final: 0.7717 (mp) REVERT: C 265 TYR cc_start: 0.9044 (m-80) cc_final: 0.8554 (m-80) REVERT: C 327 MET cc_start: 0.8845 (ttt) cc_final: 0.8310 (tpp) REVERT: C 394 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: C 422 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8326 (mmt-90) REVERT: C 436 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8703 (ttm) REVERT: D 1 MET cc_start: 0.8336 (tmm) cc_final: 0.8101 (tmm) REVERT: D 92 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9173 (mp) REVERT: D 324 GLU cc_start: 0.9400 (tt0) cc_final: 0.8885 (tp30) REVERT: D 380 GLU cc_start: 0.9213 (tp30) cc_final: 0.8637 (tp30) REVERT: D 436 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8783 (ttm) REVERT: E 258 ASN cc_start: 0.8534 (m110) cc_final: 0.8127 (p0) REVERT: E 478 ARG cc_start: 0.8307 (mmp-170) cc_final: 0.7955 (mtp-110) REVERT: E 505 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8233 (tp40) REVERT: E 509 ARG cc_start: 0.8696 (ttp-170) cc_final: 0.8155 (ttm170) REVERT: E 519 MET cc_start: 0.8949 (mtm) cc_final: 0.8654 (mtm) REVERT: F 52 CYS cc_start: 0.8900 (m) cc_final: 0.8412 (t) REVERT: F 413 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8169 (mp0) REVERT: F 450 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8062 (tm-30) REVERT: F 481 ARG cc_start: 0.8832 (mmm160) cc_final: 0.8608 (mtp85) REVERT: G 131 ARG cc_start: 0.8644 (mmp80) cc_final: 0.8217 (tpm170) REVERT: G 190 ASP cc_start: 0.8567 (m-30) cc_final: 0.8366 (m-30) REVERT: G 203 MET cc_start: 0.8503 (ttm) cc_final: 0.8220 (mtm) REVERT: H 131 ARG cc_start: 0.8478 (mmm160) cc_final: 0.7826 (tpt170) REVERT: H 155 LYS cc_start: 0.8234 (mmpt) cc_final: 0.7785 (ttpp) REVERT: H 174 ASP cc_start: 0.8801 (t0) cc_final: 0.8498 (t0) REVERT: H 382 ASP cc_start: 0.8949 (m-30) cc_final: 0.8538 (t0) REVERT: H 386 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: H 421 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8832 (mp) outliers start: 54 outliers final: 24 residues processed: 314 average time/residue: 0.8250 time to fit residues: 303.5774 Evaluate side-chains 289 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 394 LYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 365 MET Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 404 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 311 optimal weight: 1.9990 chunk 405 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 308 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 276 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 216 HIS E 50 GLN E 258 ASN F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.075141 restraints weight = 73802.942| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.93 r_work: 0.2815 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35714 Z= 0.130 Angle : 0.561 12.065 48533 Z= 0.293 Chirality : 0.042 0.286 5404 Planarity : 0.003 0.053 6038 Dihedral : 14.024 179.329 5516 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.34 % Allowed : 15.20 % Favored : 83.46 % 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: 2.56 (0.13), residues: 1778 sheet: 0.10 (0.19), residues: 743 loop : -0.74 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 456 TYR 0.013 0.001 TYR F 150 PHE 0.029 0.001 PHE B 420 TRP 0.007 0.001 TRP D 54 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00302 (35710) covalent geometry : angle 0.56123 (48525) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.39113 ( 8) hydrogen bonds : bond 0.03769 ( 1741) hydrogen bonds : angle 4.33462 ( 5006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.8312 (m-90) cc_final: 0.8096 (m-90) REVERT: A 384 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: A 394 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8482 (tppt) REVERT: A 464 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8448 (mt-10) REVERT: A 506 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 271 ASP cc_start: 0.8831 (m-30) cc_final: 0.8496 (m-30) REVERT: B 362 ASP cc_start: 0.8635 (t70) cc_final: 0.8140 (p0) REVERT: C 261 ILE cc_start: 0.8605 (mp) cc_final: 0.7714 (mp) REVERT: C 265 TYR cc_start: 0.9055 (m-80) cc_final: 0.8572 (m-80) REVERT: C 394 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8159 (ttmm) REVERT: C 422 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8344 (mmt-90) REVERT: C 436 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8676 (ttm) REVERT: C 496 MET cc_start: 0.9023 (mtt) cc_final: 0.8522 (mtt) REVERT: D 92 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9167 (mp) REVERT: D 245 ASP cc_start: 0.8817 (t0) cc_final: 0.8617 (t0) REVERT: D 324 GLU cc_start: 0.9396 (tt0) cc_final: 0.8877 (tp30) REVERT: D 380 GLU cc_start: 0.9180 (tp30) cc_final: 0.8610 (tp30) REVERT: E 258 ASN cc_start: 0.8528 (m-40) cc_final: 0.8127 (p0) REVERT: E 478 ARG cc_start: 0.8241 (mmp-170) cc_final: 0.7923 (mtp-110) REVERT: E 505 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8238 (tp40) REVERT: E 509 ARG cc_start: 0.8697 (ttp-170) cc_final: 0.8166 (ttm170) REVERT: E 519 MET cc_start: 0.8920 (mtm) cc_final: 0.8641 (mtm) REVERT: F 52 CYS cc_start: 0.8893 (m) cc_final: 0.8419 (t) REVERT: F 413 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8165 (mp0) REVERT: F 450 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8054 (tm-30) REVERT: F 481 ARG cc_start: 0.8793 (mmm160) cc_final: 0.8576 (mtp85) REVERT: G 131 ARG cc_start: 0.8650 (mmp80) cc_final: 0.8239 (tpm170) REVERT: G 203 MET cc_start: 0.8519 (ttm) cc_final: 0.8244 (mtm) REVERT: H 131 ARG cc_start: 0.8473 (mmm160) cc_final: 0.7767 (tpt170) REVERT: H 155 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7755 (ttpp) REVERT: H 174 ASP cc_start: 0.8788 (t0) cc_final: 0.8483 (t0) REVERT: H 386 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: H 421 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8827 (mp) outliers start: 48 outliers final: 23 residues processed: 307 average time/residue: 0.7888 time to fit residues: 284.0322 Evaluate side-chains 283 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 366 optimal weight: 0.1980 chunk 295 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 120 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 229 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 271 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 425 optimal weight: 10.0000 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 73 ASN D 216 HIS E 102 ASN E 504 GLN F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN G 183 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075976 restraints weight = 73834.991| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.95 r_work: 0.2844 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35714 Z= 0.110 Angle : 0.558 15.019 48533 Z= 0.290 Chirality : 0.042 0.421 5404 Planarity : 0.003 0.057 6038 Dihedral : 13.997 178.862 5516 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.89 % Allowed : 15.75 % Favored : 83.35 % 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: 1.26 (0.13), residues: 4238 helix: 2.53 (0.13), residues: 1787 sheet: 0.17 (0.20), residues: 721 loop : -0.70 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 456 TYR 0.010 0.001 TYR G 352 PHE 0.030 0.001 PHE B 420 TRP 0.008 0.001 TRP D 54 HIS 0.006 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00250 (35710) covalent geometry : angle 0.55804 (48525) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.41648 ( 8) hydrogen bonds : bond 0.03412 ( 1741) hydrogen bonds : angle 4.24405 ( 5006) ********************** 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 317 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TRP cc_start: 0.8344 (m-90) cc_final: 0.8104 (m-90) REVERT: A 384 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: A 394 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8468 (tppt) REVERT: A 464 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 506 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8085 (t80) REVERT: B 271 ASP cc_start: 0.8842 (m-30) cc_final: 0.8513 (m-30) REVERT: B 362 ASP cc_start: 0.8580 (t70) cc_final: 0.8185 (p0) REVERT: B 512 GLU cc_start: 0.6900 (pm20) cc_final: 0.6657 (tt0) REVERT: C 1 MET cc_start: 0.8774 (tpp) cc_final: 0.8426 (ttp) REVERT: C 261 ILE cc_start: 0.8616 (mp) cc_final: 0.7810 (mp) REVERT: C 265 TYR cc_start: 0.9000 (m-80) cc_final: 0.8614 (m-80) REVERT: C 394 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8187 (ttmm) REVERT: C 422 ARG cc_start: 0.8644 (tpp80) cc_final: 0.8342 (mmt-90) REVERT: D 92 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9208 (mp) REVERT: D 324 GLU cc_start: 0.9393 (tt0) cc_final: 0.8928 (tp30) REVERT: D 380 GLU cc_start: 0.9163 (tp30) cc_final: 0.8588 (tm-30) REVERT: E 258 ASN cc_start: 0.8543 (m-40) cc_final: 0.8194 (p0) REVERT: E 478 ARG cc_start: 0.8231 (mmp-170) cc_final: 0.7873 (mtp-110) REVERT: E 505 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8481 (tp40) REVERT: E 519 MET cc_start: 0.8898 (mtm) cc_final: 0.8636 (mtm) REVERT: F 52 CYS cc_start: 0.8854 (m) cc_final: 0.8406 (t) REVERT: F 413 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8163 (mp0) REVERT: F 451 LYS cc_start: 0.8948 (mmmm) cc_final: 0.8688 (mmpt) REVERT: G 100 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8780 (mp0) REVERT: G 131 ARG cc_start: 0.8634 (mmp80) cc_final: 0.8220 (tpm170) REVERT: H 131 ARG cc_start: 0.8462 (mmm160) cc_final: 0.7658 (tpt170) REVERT: H 174 ASP cc_start: 0.8777 (t0) cc_final: 0.8466 (t0) REVERT: H 382 ASP cc_start: 0.8951 (m-30) cc_final: 0.8577 (t0) REVERT: H 386 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: H 421 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8816 (mp) outliers start: 32 outliers final: 20 residues processed: 313 average time/residue: 0.8159 time to fit residues: 299.8627 Evaluate side-chains 283 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 398 TYR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 495 ILE Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 281 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 386 GLU Chi-restraints excluded: chain H residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 272 optimal weight: 0.9980 chunk 278 optimal weight: 4.9990 chunk 414 optimal weight: 8.9990 chunk 296 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 448 HIS D 73 ASN D 216 HIS D 502 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS F 216 HIS F 415 ASN ** F 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN ** H 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.074444 restraints weight = 73715.723| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.93 r_work: 0.2815 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 35714 Z= 0.169 Angle : 0.586 13.805 48533 Z= 0.305 Chirality : 0.043 0.312 5404 Planarity : 0.004 0.060 6038 Dihedral : 14.042 179.315 5516 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.89 % Allowed : 16.09 % Favored : 83.02 % 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: 1.25 (0.13), residues: 4238 helix: 2.51 (0.13), residues: 1795 sheet: 0.19 (0.20), residues: 734 loop : -0.73 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 481 TYR 0.012 0.001 TYR G 352 PHE 0.030 0.002 PHE B 420 TRP 0.010 0.001 TRP D 54 HIS 0.007 0.001 HIS E 180 Details of bonding type rmsd covalent geometry : bond 0.00404 (35710) covalent geometry : angle 0.58569 (48525) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.44828 ( 8) hydrogen bonds : bond 0.03741 ( 1741) hydrogen bonds : angle 4.28805 ( 5006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11027.89 seconds wall clock time: 188 minutes 45.34 seconds (11325.34 seconds total)