Starting phenix.real_space_refine on Fri Aug 7 10:42:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.map" model { file = "/net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9f_72696/08_2026/9y9f_72696.cif" } resolution = 3.69 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= 0.000 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 P 12 5.49 5 Mg 16 5.21 5 S 116 5.16 5 C 13112 2.51 5 N 3394 2.21 5 O 3866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5092 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 21, 'TRANS': 616} Chain breaks: 2 Chain: "B" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5096 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 21, 'TRANS': 617} Chain breaks: 2 Chain: "C" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5092 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 21, 'TRANS': 616} Chain breaks: 2 Chain: "D" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5096 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 21, 'TRANS': 617} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 4, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.75, per 1000 atoms: 0.18 Number of scatterers: 20516 At special positions: 0 Unit cell: (101.673, 136.433, 231.154, 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) S 116 16.00 P 12 15.00 Mg 16 11.99 O 3866 8.00 N 3394 7.00 C 13112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS B 262 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS D 262 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 151 " 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: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 47.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 98 through 105 Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 222 through 239 Proline residue: A 234 - end of helix removed outlier: 3.937A pdb=" N LYS A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 265 Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 302 through 329 removed outlier: 3.544A pdb=" N THR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.580A pdb=" N GLY A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 428 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.823A pdb=" N ILE A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.725A pdb=" N GLY A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 547 through 561 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 641 through 646 removed outlier: 4.547A pdb=" N THR A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 181 through 209 removed outlier: 3.828A pdb=" N MET B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 222 through 238 Proline residue: B 234 - end of helix removed outlier: 4.101A pdb=" N LYS B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 313 through 329 Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.536A pdb=" N GLY B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.818A pdb=" N ALA B 428 " --> pdb=" O LYS B 425 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 429 " --> pdb=" O ASP B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.751A pdb=" N GLY B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 547 through 561 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.529A pdb=" N TYR B 601 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 4.184A pdb=" N THR B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 728 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 181 through 209 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 222 through 239 Proline residue: C 234 - end of helix removed outlier: 4.019A pdb=" N LYS C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'C' and resid 268 through 284 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 302 through 329 removed outlier: 3.557A pdb=" N THR C 306 " --> pdb=" O THR C 302 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 355 through 368 Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.577A pdb=" N GLY C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 428 Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 437 through 446 removed outlier: 3.824A pdb=" N ILE C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.722A pdb=" N GLY C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 547 through 561 Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 641 through 646 removed outlier: 4.545A pdb=" N THR C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 728 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 181 through 209 removed outlier: 3.811A pdb=" N MET D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 238 Proline residue: D 234 - end of helix removed outlier: 4.100A pdb=" N LYS D 238 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 265 Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 313 through 329 Proline residue: D 319 - end of helix Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 355 through 368 Processing helix chain 'D' and resid 372 through 376 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.536A pdb=" N GLY D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.825A pdb=" N ALA D 428 " --> pdb=" O LYS D 425 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE D 429 " --> pdb=" O ASP D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.781A pdb=" N GLY D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.531A pdb=" N TYR D 601 " --> pdb=" O ALA D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 646 removed outlier: 4.184A pdb=" N THR D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 728 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 54 removed outlier: 6.278A pdb=" N TYR A 79 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A 77 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU A 51 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 75 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 53 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR A 73 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER A 129 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 122 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL A 131 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU A 120 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 133 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.274A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.274A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.822A pdb=" N PHE A 487 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 475 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 493 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA A 473 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS A 450 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN A 476 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 452 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL A 478 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.574A pdb=" N GLN A 707 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 637 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 607 through 608 removed outlier: 3.862A pdb=" N LYS A 607 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 629 through 633 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 54 removed outlier: 6.846A pdb=" N TYR B 79 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N MET B 49 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG B 77 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU B 51 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN B 75 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER B 53 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 73 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER B 129 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 123 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 119 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 135 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 117 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.016A pdb=" N TYR B 488 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASN B 479 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL B 490 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 477 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 492 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS B 450 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN B 476 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL B 452 " --> pdb=" O GLN B 476 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL B 478 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 386 through 387 removed outlier: 6.032A pdb=" N ILE B 386 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 408 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 410 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 391 through 392 removed outlier: 4.154A pdb=" N THR B 436 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 515 through 517 removed outlier: 7.751A pdb=" N LYS B 522 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.485A pdb=" N GLN B 707 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 607 through 609 removed outlier: 3.706A pdb=" N LYS B 607 " --> pdb=" O SER B 696 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B 694 " --> pdb=" O ALA B 609 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 629 through 633 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 54 removed outlier: 6.277A pdb=" N TYR C 79 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N MET C 49 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG C 77 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU C 51 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASN C 75 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER C 53 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C 73 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER C 129 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN C 122 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL C 131 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 120 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 133 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.276A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.276A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 378 through 379 removed outlier: 3.822A pdb=" N PHE C 487 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 475 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 493 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 473 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS C 450 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN C 476 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 452 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL C 478 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC6, first strand: chain 'C' and resid 585 through 588 removed outlier: 6.572A pdb=" N GLN C 707 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 637 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 607 through 608 removed outlier: 3.856A pdb=" N LYS C 607 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 629 through 633 Processing sheet with id=AC9, first strand: chain 'D' and resid 45 through 54 removed outlier: 6.846A pdb=" N TYR D 79 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N MET D 49 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG D 77 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LEU D 51 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASN D 75 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER D 53 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR D 73 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER D 129 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL D 123 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN D 119 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU D 135 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL D 117 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AD2, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AD3, first strand: chain 'D' and resid 378 through 379 removed outlier: 6.020A pdb=" N TYR D 488 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN D 479 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL D 490 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS D 477 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 492 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N HIS D 450 " --> pdb=" O ILE D 474 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLN D 476 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 452 " --> pdb=" O GLN D 476 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL D 478 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 386 through 387 removed outlier: 6.032A pdb=" N ILE D 386 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 408 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE D 421 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL D 410 " --> pdb=" O VAL D 419 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 391 through 392 removed outlier: 4.154A pdb=" N THR D 436 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 515 through 517 removed outlier: 7.748A pdb=" N LYS D 522 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 585 through 588 removed outlier: 6.486A pdb=" N GLN D 707 " --> pdb=" O LEU D 616 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 607 through 609 removed outlier: 3.701A pdb=" N LYS D 607 " --> pdb=" O SER D 696 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR D 694 " --> pdb=" O ALA D 609 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 629 through 633 1028 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6594 1.35 - 1.47: 4789 1.47 - 1.60: 9285 1.60 - 1.73: 0 1.73 - 1.85: 192 Bond restraints: 20860 Sorted by residual: bond pdb=" CB VAL B 280 " pdb=" CG2 VAL B 280 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB VAL A 280 " pdb=" CG2 VAL A 280 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" C GLY C 283 " pdb=" N GLU C 284 " ideal model delta sigma weight residual 1.332 1.313 0.020 1.40e-02 5.10e+03 1.99e+00 bond pdb=" CB CYS A 262 " pdb=" SG CYS A 262 " ideal model delta sigma weight residual 1.808 1.853 -0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" C LEU A 261 " pdb=" N CYS A 262 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.33e-02 5.65e+03 1.84e+00 ... (remaining 20855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 27852 1.69 - 3.37: 316 3.37 - 5.06: 46 5.06 - 6.74: 3 6.74 - 8.43: 1 Bond angle restraints: 28218 Sorted by residual: angle pdb=" N ARG D 178 " pdb=" CA ARG D 178 " pdb=" C ARG D 178 " ideal model delta sigma weight residual 112.97 108.22 4.75 1.06e+00 8.90e-01 2.01e+01 angle pdb=" N ARG B 178 " pdb=" CA ARG B 178 " pdb=" C ARG B 178 " ideal model delta sigma weight residual 112.97 108.48 4.49 1.06e+00 8.90e-01 1.79e+01 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 124.73 -8.43 3.50e+00 8.16e-02 5.80e+00 angle pdb=" N MET A 270 " pdb=" CA MET A 270 " pdb=" C MET A 270 " ideal model delta sigma weight residual 111.02 113.78 -2.76 1.22e+00 6.72e-01 5.12e+00 angle pdb=" C LEU B 269 " pdb=" N MET B 270 " pdb=" CA MET B 270 " ideal model delta sigma weight residual 121.54 125.65 -4.11 1.91e+00 2.74e-01 4.64e+00 ... (remaining 28213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 12252 17.68 - 35.37: 441 35.37 - 53.05: 89 53.05 - 70.73: 18 70.73 - 88.41: 4 Dihedral angle restraints: 12804 sinusoidal: 5330 harmonic: 7474 Sorted by residual: dihedral pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" N SER A 292 " pdb=" CA SER A 292 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" N ILE A 265 " pdb=" CA ILE A 265 " pdb=" CB ILE A 265 " pdb=" CG1 ILE A 265 " ideal model delta sinusoidal sigma weight residual 60.00 0.40 59.60 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET D 270 " pdb=" CA MET D 270 " pdb=" CB MET D 270 " pdb=" CG MET D 270 " ideal model delta sinusoidal sigma weight residual -60.00 -117.67 57.67 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 12801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1996 0.030 - 0.060: 855 0.060 - 0.089: 246 0.089 - 0.119: 174 0.119 - 0.149: 25 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CA ILE C 709 " pdb=" N ILE C 709 " pdb=" C ILE C 709 " pdb=" CB ILE C 709 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE A 709 " pdb=" N ILE A 709 " pdb=" C ILE A 709 " pdb=" CB ILE A 709 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE B 709 " pdb=" N ILE B 709 " pdb=" C ILE B 709 " pdb=" CB ILE B 709 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 3293 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 175 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO C 176 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 175 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 176 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 431 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C 432 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 432 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 432 " 0.018 5.00e-02 4.00e+02 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5183 2.81 - 3.33: 19609 3.33 - 3.85: 32503 3.85 - 4.38: 38503 4.38 - 4.90: 66183 Nonbonded interactions: 161981 Sorted by model distance: nonbonded pdb=" OE2 GLU B 501 " pdb="MG MG B 903 " model vdw 2.286 2.170 nonbonded pdb=" OE2 GLU D 501 " pdb="MG MG D 903 " model vdw 2.300 2.170 nonbonded pdb=" OD1 ASP B 510 " pdb="MG MG B 902 " model vdw 2.345 2.170 nonbonded pdb=" OD1 ASP D 510 " pdb="MG MG D 902 " model vdw 2.346 2.170 nonbonded pdb=" O ILE A 508 " pdb="MG MG A 903 " model vdw 2.427 2.170 ... (remaining 161976 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 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 : 0.004 0.055 20870 Z= 0.163 Angle : 0.495 8.429 28238 Z= 0.265 Chirality : 0.041 0.149 3296 Planarity : 0.003 0.033 3538 Dihedral : 9.918 88.414 7934 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.13 % Allowed : 5.33 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2530 helix: 1.68 (0.17), residues: 1056 sheet: -0.50 (0.28), residues: 342 loop : -0.15 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.012 0.001 TYR C 611 PHE 0.018 0.001 PHE A 612 TRP 0.011 0.001 TRP D 183 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (20860) covalent geometry : angle 0.49414 / 0.26 (28218) SS BOND : bond 0.00343 / 0.20 ( 10) SS BOND : angle 1.20692 / 0.81 ( 20) hydrogen bonds : bond 0.12130 / 8.28 ( 996) hydrogen bonds : angle 6.35511 / 4.64 ( 2910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 389 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5932 (m-80) REVERT: C 171 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6190 (m-80) outliers start: 26 outliers final: 7 residues processed: 409 average time/residue: 0.1454 time to fit residues: 90.1662 Evaluate side-chains 237 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 228 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.0870 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN A 250 ASN A 352 ASN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 GLN B 103 HIS B 254 ASN C 240 ASN C 352 ASN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.078289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.059265 restraints weight = 87402.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.058784 restraints weight = 50836.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059467 restraints weight = 44319.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059750 restraints weight = 35038.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060018 restraints weight = 33216.992| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 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 : 0.003 0.040 20870 Z= 0.120 Angle : 0.579 11.195 28238 Z= 0.287 Chirality : 0.042 0.209 3296 Planarity : 0.003 0.044 3538 Dihedral : 6.385 88.336 2908 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.78 % Allowed : 12.00 % Favored : 86.22 % 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: 1.05 (0.17), residues: 2530 helix: 1.80 (0.16), residues: 1068 sheet: -0.23 (0.28), residues: 328 loop : 0.01 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 333 TYR 0.012 0.001 TYR B 597 PHE 0.011 0.001 PHE A 612 TRP 0.014 0.001 TRP D 183 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (20860) covalent geometry : angle 0.57831 / 0.29 (28218) SS BOND : bond 0.00650 / 0.45 ( 10) SS BOND : angle 1.45326 / 1.00 ( 20) hydrogen bonds : bond 0.03804 / 2.63 ( 996) hydrogen bonds : angle 5.11591 / 3.71 ( 2910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.7055 (pmm) cc_final: 0.6478 (tmm) REVERT: A 296 LEU cc_start: 0.8993 (pt) cc_final: 0.8742 (pp) REVERT: A 309 PHE cc_start: 0.8624 (m-80) cc_final: 0.8285 (m-80) REVERT: A 389 ASP cc_start: 0.8295 (p0) cc_final: 0.8069 (p0) REVERT: C 138 PHE cc_start: 0.8459 (m-10) cc_final: 0.8214 (m-80) REVERT: C 171 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: C 296 LEU cc_start: 0.8942 (pt) cc_final: 0.8680 (pp) REVERT: C 308 PHE cc_start: 0.9087 (t80) cc_final: 0.8851 (t80) REVERT: C 309 PHE cc_start: 0.8621 (m-80) cc_final: 0.8198 (m-80) REVERT: C 389 ASP cc_start: 0.8284 (p0) cc_final: 0.8058 (p0) REVERT: D 284 GLU cc_start: 0.7938 (tp30) cc_final: 0.7386 (tp30) outliers start: 41 outliers final: 18 residues processed: 279 average time/residue: 0.1273 time to fit residues: 55.8792 Evaluate side-chains 227 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 391 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 154 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN C 381 GLN D 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.076882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058184 restraints weight = 86532.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057746 restraints weight = 48754.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.058546 restraints weight = 45023.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058590 restraints weight = 34445.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059890 restraints weight = 32308.181| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20870 Z= 0.138 Angle : 0.557 8.922 28238 Z= 0.276 Chirality : 0.041 0.175 3296 Planarity : 0.003 0.052 3538 Dihedral : 6.159 85.519 2903 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.21 % Allowed : 12.69 % Favored : 85.10 % 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: 1.09 (0.17), residues: 2530 helix: 1.81 (0.16), residues: 1070 sheet: -0.13 (0.28), residues: 340 loop : 0.02 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.022 0.001 TYR B 241 PHE 0.013 0.001 PHE A 612 TRP 0.012 0.001 TRP B 183 HIS 0.007 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (20860) covalent geometry : angle 0.55652 / 0.28 (28218) SS BOND : bond 0.00320 / 0.21 ( 10) SS BOND : angle 1.10910 / 0.76 ( 20) hydrogen bonds : bond 0.03602 / 2.46 ( 996) hydrogen bonds : angle 4.78526 / 3.47 ( 2910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8557 (m-80) cc_final: 0.7892 (m-80) REVERT: A 202 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 270 MET cc_start: 0.6900 (pmm) cc_final: 0.6440 (tmm) REVERT: A 282 PHE cc_start: 0.8398 (m-10) cc_final: 0.8165 (m-10) REVERT: A 296 LEU cc_start: 0.8989 (pt) cc_final: 0.8719 (pp) REVERT: A 309 PHE cc_start: 0.8501 (m-80) cc_final: 0.8252 (m-80) REVERT: A 389 ASP cc_start: 0.8186 (p0) cc_final: 0.7945 (p0) REVERT: B 220 CYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8096 (p) REVERT: B 284 GLU cc_start: 0.7857 (tp30) cc_final: 0.7632 (tp30) REVERT: C 171 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: C 296 LEU cc_start: 0.8969 (pt) cc_final: 0.8685 (pp) REVERT: C 309 PHE cc_start: 0.8578 (m-80) cc_final: 0.8218 (m-80) REVERT: C 389 ASP cc_start: 0.8138 (p0) cc_final: 0.7857 (p0) REVERT: D 204 LEU cc_start: 0.8747 (tp) cc_final: 0.8500 (tt) REVERT: D 220 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8100 (p) REVERT: D 284 GLU cc_start: 0.7927 (tp30) cc_final: 0.7427 (tp30) outliers start: 51 outliers final: 29 residues processed: 259 average time/residue: 0.1215 time to fit residues: 50.3070 Evaluate side-chains 231 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 517 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 391 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 16 optimal weight: 0.4980 chunk 123 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.075121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.056320 restraints weight = 85069.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055752 restraints weight = 50868.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056219 restraints weight = 47728.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056352 restraints weight = 35603.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057462 restraints weight = 32205.270| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20870 Z= 0.116 Angle : 0.544 8.516 28238 Z= 0.264 Chirality : 0.041 0.176 3296 Planarity : 0.003 0.052 3538 Dihedral : 6.086 78.620 2903 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.82 % Allowed : 14.25 % Favored : 83.93 % 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: 1.13 (0.17), residues: 2530 helix: 1.89 (0.16), residues: 1072 sheet: -0.25 (0.26), residues: 370 loop : 0.06 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 577 TYR 0.018 0.001 TYR B 241 PHE 0.011 0.001 PHE A 612 TRP 0.011 0.001 TRP B 183 HIS 0.004 0.000 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (20860) covalent geometry : angle 0.54374 / 0.26 (28218) SS BOND : bond 0.00437 / 0.27 ( 10) SS BOND : angle 0.72743 / 0.50 ( 20) hydrogen bonds : bond 0.03365 / 2.30 ( 996) hydrogen bonds : angle 4.61790 / 3.35 ( 2910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 270 MET cc_start: 0.6850 (pmm) cc_final: 0.5535 (mmm) REVERT: A 282 PHE cc_start: 0.8464 (m-10) cc_final: 0.8227 (m-10) REVERT: A 284 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (mm-30) REVERT: A 296 LEU cc_start: 0.9007 (pt) cc_final: 0.8724 (pp) REVERT: A 309 PHE cc_start: 0.8653 (m-80) cc_final: 0.8394 (m-80) REVERT: A 389 ASP cc_start: 0.8402 (p0) cc_final: 0.8146 (p0) REVERT: B 258 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6467 (p) REVERT: B 581 TYR cc_start: 0.8620 (t80) cc_final: 0.8411 (t80) REVERT: C 171 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: C 202 LEU cc_start: 0.9062 (tp) cc_final: 0.8779 (tt) REVERT: C 270 MET cc_start: 0.6500 (pmm) cc_final: 0.4848 (tpt) REVERT: C 296 LEU cc_start: 0.8913 (pt) cc_final: 0.8605 (pp) REVERT: C 309 PHE cc_start: 0.8658 (m-80) cc_final: 0.8351 (m-80) REVERT: C 389 ASP cc_start: 0.8417 (p0) cc_final: 0.8149 (p0) REVERT: D 284 GLU cc_start: 0.8008 (tp30) cc_final: 0.7134 (tp30) REVERT: D 306 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8593 (m) outliers start: 42 outliers final: 24 residues processed: 244 average time/residue: 0.1161 time to fit residues: 46.7829 Evaluate side-chains 229 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 0.0870 chunk 63 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.073083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.053733 restraints weight = 85340.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054746 restraints weight = 49250.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054485 restraints weight = 42966.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054751 restraints weight = 33427.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055044 restraints weight = 29968.708| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20870 Z= 0.178 Angle : 0.573 9.891 28238 Z= 0.283 Chirality : 0.042 0.182 3296 Planarity : 0.003 0.054 3538 Dihedral : 6.206 68.501 2902 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.69 % Allowed : 12.82 % Favored : 84.49 % 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: 1.07 (0.17), residues: 2530 helix: 1.85 (0.16), residues: 1066 sheet: -0.39 (0.27), residues: 364 loop : 0.08 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 577 TYR 0.016 0.001 TYR D 581 PHE 0.016 0.001 PHE A 612 TRP 0.010 0.001 TRP B 183 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (20860) covalent geometry : angle 0.57259 / 0.28 (28218) SS BOND : bond 0.00529 / 0.34 ( 10) SS BOND : angle 1.31430 / 0.91 ( 20) hydrogen bonds : bond 0.03678 / 2.49 ( 996) hydrogen bonds : angle 4.67655 / 3.39 ( 2910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.805 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 138 PHE cc_start: 0.8396 (m-80) cc_final: 0.7958 (m-10) REVERT: A 202 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 270 MET cc_start: 0.6930 (pmm) cc_final: 0.5665 (mmm) REVERT: A 284 GLU cc_start: 0.8257 (tp30) cc_final: 0.7931 (mm-30) REVERT: A 296 LEU cc_start: 0.9007 (pt) cc_final: 0.8705 (pp) REVERT: A 389 ASP cc_start: 0.8496 (p0) cc_final: 0.8258 (p0) REVERT: C 49 MET cc_start: 0.8783 (ptm) cc_final: 0.8288 (ppp) REVERT: C 171 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: C 202 LEU cc_start: 0.9101 (tp) cc_final: 0.8851 (tt) REVERT: C 296 LEU cc_start: 0.8987 (pt) cc_final: 0.8685 (pp) REVERT: C 389 ASP cc_start: 0.8454 (p0) cc_final: 0.8201 (p0) REVERT: D 284 GLU cc_start: 0.8044 (tp30) cc_final: 0.7692 (mt-10) REVERT: D 306 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8634 (m) outliers start: 62 outliers final: 41 residues processed: 254 average time/residue: 0.1133 time to fit residues: 48.0367 Evaluate side-chains 244 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 517 ASP Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 517 ASP Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 220 CYS Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 156 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN ** B 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.074312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055366 restraints weight = 84078.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055004 restraints weight = 48539.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055615 restraints weight = 41213.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055947 restraints weight = 31641.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056200 restraints weight = 29795.947| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20870 Z= 0.110 Angle : 0.549 11.747 28238 Z= 0.265 Chirality : 0.041 0.206 3296 Planarity : 0.003 0.054 3538 Dihedral : 6.097 65.208 2902 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 14.47 % Favored : 83.67 % 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: 1.12 (0.17), residues: 2530 helix: 1.92 (0.16), residues: 1068 sheet: -0.47 (0.26), residues: 382 loop : 0.11 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 521 TYR 0.017 0.001 TYR B 581 PHE 0.012 0.001 PHE B 309 TRP 0.012 0.001 TRP B 183 HIS 0.004 0.000 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20860) covalent geometry : angle 0.54792 / 0.26 (28218) SS BOND : bond 0.00264 / 0.20 ( 10) SS BOND : angle 1.21752 / 0.84 ( 20) hydrogen bonds : bond 0.03293 / 2.23 ( 996) hydrogen bonds : angle 4.52011 / 3.29 ( 2910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8703 (tt) REVERT: A 270 MET cc_start: 0.6831 (pmm) cc_final: 0.5618 (mmm) REVERT: A 284 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: A 296 LEU cc_start: 0.9018 (pt) cc_final: 0.8736 (pp) REVERT: A 389 ASP cc_start: 0.8485 (p0) cc_final: 0.8240 (p0) REVERT: A 513 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8242 (t0) REVERT: C 49 MET cc_start: 0.8735 (ptm) cc_final: 0.8327 (ppp) REVERT: C 202 LEU cc_start: 0.9071 (tp) cc_final: 0.8836 (tt) REVERT: C 270 MET cc_start: 0.6451 (pmm) cc_final: 0.4969 (tpt) REVERT: C 296 LEU cc_start: 0.8951 (pt) cc_final: 0.8649 (pp) REVERT: C 389 ASP cc_start: 0.8469 (p0) cc_final: 0.8206 (p0) REVERT: C 513 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8232 (t0) REVERT: D 284 GLU cc_start: 0.7976 (tp30) cc_final: 0.7676 (mt-10) outliers start: 43 outliers final: 29 residues processed: 237 average time/residue: 0.1104 time to fit residues: 44.2029 Evaluate side-chains 236 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 11 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.073591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054309 restraints weight = 84559.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054126 restraints weight = 50994.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054609 restraints weight = 46613.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054878 restraints weight = 35064.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055330 restraints weight = 31953.119| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20870 Z= 0.135 Angle : 0.560 8.152 28238 Z= 0.273 Chirality : 0.041 0.199 3296 Planarity : 0.003 0.056 3538 Dihedral : 6.140 66.375 2902 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.82 % Allowed : 14.86 % Favored : 83.32 % 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: 1.04 (0.17), residues: 2530 helix: 1.84 (0.16), residues: 1068 sheet: -0.55 (0.26), residues: 386 loop : 0.10 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.018 0.001 TYR D 581 PHE 0.017 0.001 PHE D 171 TRP 0.011 0.001 TRP B 183 HIS 0.003 0.000 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (20860) covalent geometry : angle 0.55924 / 0.27 (28218) SS BOND : bond 0.00333 / 0.23 ( 10) SS BOND : angle 1.16645 / 0.81 ( 20) hydrogen bonds : bond 0.03409 / 2.31 ( 996) hydrogen bonds : angle 4.53804 / 3.31 ( 2910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.8225 (m-80) cc_final: 0.7936 (m-10) REVERT: A 202 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8695 (tt) REVERT: A 270 MET cc_start: 0.6806 (pmm) cc_final: 0.5608 (mmm) REVERT: A 284 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: A 296 LEU cc_start: 0.9021 (pt) cc_final: 0.8736 (pp) REVERT: A 389 ASP cc_start: 0.8507 (p0) cc_final: 0.8259 (p0) REVERT: A 513 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 258 THR cc_start: 0.6686 (OUTLIER) cc_final: 0.6301 (t) REVERT: C 202 LEU cc_start: 0.9081 (tp) cc_final: 0.8816 (tt) REVERT: C 270 MET cc_start: 0.6440 (pmm) cc_final: 0.5048 (tpt) REVERT: C 296 LEU cc_start: 0.8965 (pt) cc_final: 0.8668 (pp) REVERT: C 389 ASP cc_start: 0.8479 (p0) cc_final: 0.8209 (p0) REVERT: C 513 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8280 (t0) REVERT: D 284 GLU cc_start: 0.7957 (tp30) cc_final: 0.7688 (mt-10) outliers start: 42 outliers final: 32 residues processed: 232 average time/residue: 0.1199 time to fit residues: 45.9283 Evaluate side-chains 239 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.073489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.054349 restraints weight = 84819.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054529 restraints weight = 50662.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054864 restraints weight = 46076.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054975 restraints weight = 34557.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055604 restraints weight = 31180.519| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20870 Z= 0.128 Angle : 0.560 10.581 28238 Z= 0.273 Chirality : 0.041 0.209 3296 Planarity : 0.003 0.057 3538 Dihedral : 6.177 69.192 2902 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.99 % Allowed : 14.86 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2530 helix: 1.86 (0.16), residues: 1068 sheet: -0.44 (0.26), residues: 394 loop : 0.10 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 521 TYR 0.023 0.001 TYR B 597 PHE 0.013 0.001 PHE C 612 TRP 0.011 0.001 TRP B 183 HIS 0.002 0.000 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (20860) covalent geometry : angle 0.55920 / 0.27 (28218) SS BOND : bond 0.00481 / 0.35 ( 10) SS BOND : angle 0.91138 / 0.62 ( 20) hydrogen bonds : bond 0.03373 / 2.28 ( 996) hydrogen bonds : angle 4.52262 / 3.29 ( 2910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.8174 (m-80) cc_final: 0.7915 (m-10) REVERT: A 202 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8719 (tt) REVERT: A 270 MET cc_start: 0.6760 (pmm) cc_final: 0.5617 (mmm) REVERT: A 284 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: A 296 LEU cc_start: 0.9013 (pt) cc_final: 0.8725 (pp) REVERT: A 389 ASP cc_start: 0.8491 (p0) cc_final: 0.8252 (p0) REVERT: A 513 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 258 THR cc_start: 0.6673 (OUTLIER) cc_final: 0.6210 (t) REVERT: C 202 LEU cc_start: 0.9046 (tp) cc_final: 0.8771 (tt) REVERT: C 270 MET cc_start: 0.6433 (pmm) cc_final: 0.5077 (tpt) REVERT: C 296 LEU cc_start: 0.8963 (pt) cc_final: 0.8664 (pp) REVERT: C 389 ASP cc_start: 0.8488 (p0) cc_final: 0.8208 (p0) REVERT: C 513 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8290 (t0) REVERT: D 284 GLU cc_start: 0.7904 (tp30) cc_final: 0.7440 (tp30) outliers start: 46 outliers final: 35 residues processed: 236 average time/residue: 0.1160 time to fit residues: 45.5384 Evaluate side-chains 239 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 309 PHE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 211 optimal weight: 0.1980 chunk 200 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.073150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054000 restraints weight = 84882.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054342 restraints weight = 50276.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054594 restraints weight = 45820.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054724 restraints weight = 34129.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055124 restraints weight = 30808.890| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20870 Z= 0.133 Angle : 0.585 10.812 28238 Z= 0.282 Chirality : 0.041 0.192 3296 Planarity : 0.003 0.056 3538 Dihedral : 6.210 69.780 2902 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.34 % Allowed : 15.25 % Favored : 82.41 % 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: 1.09 (0.17), residues: 2530 helix: 1.88 (0.16), residues: 1060 sheet: -0.45 (0.26), residues: 394 loop : 0.12 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 521 TYR 0.020 0.001 TYR D 581 PHE 0.014 0.001 PHE B 309 TRP 0.011 0.001 TRP B 183 HIS 0.003 0.000 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (20860) covalent geometry : angle 0.58515 / 0.28 (28218) SS BOND : bond 0.00383 / 0.26 ( 10) SS BOND : angle 0.47051 / 0.31 ( 20) hydrogen bonds : bond 0.03403 / 2.30 ( 996) hydrogen bonds : angle 4.57571 / 3.34 ( 2910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 PHE cc_start: 0.8216 (m-80) cc_final: 0.7964 (m-10) REVERT: A 202 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8727 (tt) REVERT: A 261 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 270 MET cc_start: 0.6793 (pmm) cc_final: 0.5573 (mmm) REVERT: A 284 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: A 296 LEU cc_start: 0.9015 (pt) cc_final: 0.8725 (pp) REVERT: A 389 ASP cc_start: 0.8505 (p0) cc_final: 0.8249 (p0) REVERT: A 413 ASP cc_start: 0.8354 (p0) cc_final: 0.7956 (p0) REVERT: B 258 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6337 (t) REVERT: C 179 PHE cc_start: 0.5972 (t80) cc_final: 0.5745 (t80) REVERT: C 202 LEU cc_start: 0.9079 (tp) cc_final: 0.8807 (tt) REVERT: C 270 MET cc_start: 0.6418 (pmm) cc_final: 0.4796 (tpp) REVERT: C 296 LEU cc_start: 0.8961 (pt) cc_final: 0.8664 (pp) REVERT: C 389 ASP cc_start: 0.8484 (p0) cc_final: 0.8208 (p0) REVERT: D 284 GLU cc_start: 0.7965 (tp30) cc_final: 0.7682 (tp30) outliers start: 54 outliers final: 39 residues processed: 239 average time/residue: 0.1095 time to fit residues: 43.9974 Evaluate side-chains 240 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 561 GLU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 262 CYS Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 309 PHE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 0.0870 chunk 218 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 219 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 139 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055416 restraints weight = 84214.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.057011 restraints weight = 48914.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056621 restraints weight = 42430.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056680 restraints weight = 31312.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056943 restraints weight = 28008.439| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20870 Z= 0.100 Angle : 0.591 11.066 28238 Z= 0.282 Chirality : 0.041 0.182 3296 Planarity : 0.003 0.050 3538 Dihedral : 6.157 69.538 2902 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.43 % Allowed : 16.42 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2530 helix: 1.92 (0.16), residues: 1060 sheet: -0.31 (0.26), residues: 388 loop : 0.11 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.020 0.001 TYR B 581 PHE 0.015 0.001 PHE B 171 TRP 0.013 0.001 TRP B 183 HIS 0.015 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (20860) covalent geometry : angle 0.59066 / 0.28 (28218) SS BOND : bond 0.00292 / 0.21 ( 10) SS BOND : angle 0.85789 / 0.58 ( 20) hydrogen bonds : bond 0.03171 / 2.14 ( 996) hydrogen bonds : angle 4.49292 / 3.28 ( 2910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 270 MET cc_start: 0.6622 (pmm) cc_final: 0.5448 (mmm) REVERT: A 284 GLU cc_start: 0.8295 (tp30) cc_final: 0.8020 (mm-30) REVERT: A 389 ASP cc_start: 0.8483 (p0) cc_final: 0.8241 (p0) REVERT: A 413 ASP cc_start: 0.8260 (p0) cc_final: 0.7873 (p0) REVERT: B 258 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6628 (p) REVERT: B 310 MET cc_start: 0.8891 (tpp) cc_final: 0.8663 (tpp) REVERT: C 179 PHE cc_start: 0.5935 (t80) cc_final: 0.5733 (t80) REVERT: C 202 LEU cc_start: 0.9046 (tp) cc_final: 0.8787 (tt) REVERT: C 270 MET cc_start: 0.6400 (pmm) cc_final: 0.5029 (tpt) REVERT: C 296 LEU cc_start: 0.8923 (pt) cc_final: 0.8616 (pp) REVERT: C 389 ASP cc_start: 0.8455 (p0) cc_final: 0.8194 (p0) REVERT: C 642 MET cc_start: 0.8115 (mmm) cc_final: 0.7788 (mmt) REVERT: D 284 GLU cc_start: 0.7899 (tp30) cc_final: 0.7696 (mt-10) outliers start: 33 outliers final: 23 residues processed: 225 average time/residue: 0.1137 time to fit residues: 43.1520 Evaluate side-chains 220 residues out of total 2308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 309 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 309 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 113 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 190 optimal weight: 0.6980 chunk 183 optimal weight: 0.0670 chunk 63 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 447 HIS C 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.074202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055266 restraints weight = 84380.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056074 restraints weight = 49331.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056108 restraints weight = 46601.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056623 restraints weight = 31953.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056858 restraints weight = 28041.614| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20870 Z= 0.103 Angle : 0.595 11.347 28238 Z= 0.283 Chirality : 0.041 0.180 3296 Planarity : 0.003 0.050 3538 Dihedral : 6.177 68.863 2902 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.39 % Allowed : 16.64 % Favored : 81.98 % 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: 1.15 (0.17), residues: 2530 helix: 1.79 (0.16), residues: 1082 sheet: -0.21 (0.26), residues: 386 loop : 0.18 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 237 TYR 0.019 0.001 TYR D 581 PHE 0.022 0.001 PHE C 326 TRP 0.012 0.001 TRP B 183 HIS 0.015 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20860) covalent geometry : angle 0.59364 / 0.28 (28218) SS BOND : bond 0.00303 / 0.18 ( 10) SS BOND : angle 1.51404 / 1.05 ( 20) hydrogen bonds : bond 0.03183 / 2.15 ( 996) hydrogen bonds : angle 4.50731 / 3.30 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.25 seconds wall clock time: 55 minutes 34.66 seconds (3334.66 seconds total)