Starting phenix.real_space_refine on Sat Feb 17 23:08:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xem_33156/02_2024/7xem_33156_updated.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13172 2.51 5 N 3372 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4995 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.43, per 1000 atoms: 0.52 Number of scatterers: 20096 At special positions: 0 Unit cell: (153.114, 153.114, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3444 8.00 N 3372 7.00 C 13172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 7.77 Conformation dependent library (CDL) restraints added in 3.7 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 54.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.555A pdb=" N ARG A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.506A pdb=" N ARG A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.516A pdb=" N LEU A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.638A pdb=" N LEU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 256 through 276 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 371 through 407 removed outlier: 3.535A pdb=" N GLN A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 453 Processing helix chain 'A' and resid 457 through 460 No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 468 through 487 removed outlier: 3.986A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.992A pdb=" N LEU A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 530 removed outlier: 3.855A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.934A pdb=" N VAL A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 632 through 667 removed outlier: 5.317A pdb=" N THR A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.555A pdb=" N ARG B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.506A pdb=" N ARG B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.516A pdb=" N LEU B 134 " --> pdb=" O CYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.638A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 371 through 407 removed outlier: 3.535A pdb=" N GLN B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 453 Processing helix chain 'B' and resid 457 through 460 No H-bonds generated for 'chain 'B' and resid 457 through 460' Processing helix chain 'B' and resid 468 through 487 removed outlier: 3.986A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.992A pdb=" N LEU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N TYR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 530 removed outlier: 3.856A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 removed outlier: 3.934A pdb=" N VAL B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 600 Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 632 through 667 removed outlier: 5.317A pdb=" N THR B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 713 No H-bonds generated for 'chain 'B' and resid 711 through 713' Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.555A pdb=" N ARG C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 96 removed outlier: 3.507A pdb=" N ARG C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.516A pdb=" N LEU C 134 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.639A pdb=" N LEU C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 256 through 276 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 371 through 407 removed outlier: 3.536A pdb=" N GLN C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 453 Processing helix chain 'C' and resid 457 through 460 No H-bonds generated for 'chain 'C' and resid 457 through 460' Processing helix chain 'C' and resid 468 through 487 removed outlier: 3.986A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.992A pdb=" N LEU C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU C 508 " --> pdb=" O TRP C 504 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TYR C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 530 removed outlier: 3.855A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.934A pdb=" N VAL C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 632 through 667 removed outlier: 5.316A pdb=" N THR C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 713 No H-bonds generated for 'chain 'C' and resid 711 through 713' Processing helix chain 'D' and resid 72 through 81 removed outlier: 3.554A pdb=" N ARG D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.507A pdb=" N ARG D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.517A pdb=" N LEU D 134 " --> pdb=" O CYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 172 through 180 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.638A pdb=" N LEU D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 256 through 276 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 371 through 407 removed outlier: 3.535A pdb=" N GLN D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 453 Processing helix chain 'D' and resid 457 through 460 No H-bonds generated for 'chain 'D' and resid 457 through 460' Processing helix chain 'D' and resid 468 through 487 removed outlier: 3.987A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 511 removed outlier: 3.991A pdb=" N LEU D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N TYR D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 510 " --> pdb=" O ASN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 530 removed outlier: 3.855A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.933A pdb=" N VAL D 548 " --> pdb=" O PHE D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 632 through 667 removed outlier: 5.316A pdb=" N THR D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASP D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 713 No H-bonds generated for 'chain 'D' and resid 711 through 713' Processing sheet with id= A, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.254A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.254A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.253A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 324 through 326 removed outlier: 4.254A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2628 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: 5.42 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6166 1.34 - 1.46: 3301 1.46 - 1.57: 10981 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 20608 Sorted by residual: bond pdb=" C13 CLR B1001 " pdb=" C17 CLR B1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C13 CLR D1001 " pdb=" C17 CLR D1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C13 CLR C1001 " pdb=" C17 CLR C1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C13 CLR A1001 " pdb=" C17 CLR A1001 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" CG1 ILE D 436 " pdb=" CD1 ILE D 436 " ideal model delta sigma weight residual 1.513 1.449 0.064 3.90e-02 6.57e+02 2.66e+00 ... (remaining 20603 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.24: 484 106.24 - 113.20: 11246 113.20 - 120.16: 7469 120.16 - 127.12: 8512 127.12 - 134.08: 277 Bond angle restraints: 27988 Sorted by residual: angle pdb=" N PHE C 467 " pdb=" CA PHE C 467 " pdb=" C PHE C 467 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.76e+01 angle pdb=" N PHE B 467 " pdb=" CA PHE B 467 " pdb=" C PHE B 467 " ideal model delta sigma weight residual 114.75 107.03 7.72 1.26e+00 6.30e-01 3.75e+01 angle pdb=" N PHE D 467 " pdb=" CA PHE D 467 " pdb=" C PHE D 467 " ideal model delta sigma weight residual 114.75 107.05 7.70 1.26e+00 6.30e-01 3.74e+01 angle pdb=" N PHE A 467 " pdb=" CA PHE A 467 " pdb=" C PHE A 467 " ideal model delta sigma weight residual 114.75 107.08 7.67 1.26e+00 6.30e-01 3.71e+01 angle pdb=" N ASN A 143 " pdb=" CA ASN A 143 " pdb=" C ASN A 143 " ideal model delta sigma weight residual 110.24 102.34 7.90 1.46e+00 4.69e-01 2.93e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 11246 21.94 - 43.88: 886 43.88 - 65.82: 112 65.82 - 87.76: 24 87.76 - 109.70: 16 Dihedral angle restraints: 12284 sinusoidal: 5116 harmonic: 7168 Sorted by residual: dihedral pdb=" CA LEU B 631 " pdb=" C LEU B 631 " pdb=" N LEU B 632 " pdb=" CA LEU B 632 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU A 631 " pdb=" C LEU A 631 " pdb=" N LEU A 632 " pdb=" CA LEU A 632 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LEU C 631 " pdb=" C LEU C 631 " pdb=" N LEU C 632 " pdb=" CA LEU C 632 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 12281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2829 0.067 - 0.134: 296 0.134 - 0.201: 27 0.201 - 0.269: 8 0.269 - 0.336: 12 Chirality restraints: 3172 Sorted by residual: chirality pdb=" CA TYR C 466 " pdb=" N TYR C 466 " pdb=" C TYR C 466 " pdb=" CB TYR C 466 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA TYR D 466 " pdb=" N TYR D 466 " pdb=" C TYR D 466 " pdb=" CB TYR D 466 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA TYR A 466 " pdb=" N TYR A 466 " pdb=" C TYR A 466 " pdb=" CB TYR A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3169 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 465 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C SER B 465 " -0.034 2.00e-02 2.50e+03 pdb=" O SER B 465 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR B 466 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 465 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C SER D 465 " 0.034 2.00e-02 2.50e+03 pdb=" O SER D 465 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR D 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C SER A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O SER A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR A 466 " -0.011 2.00e-02 2.50e+03 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6475 2.84 - 3.35: 19597 3.35 - 3.87: 32823 3.87 - 4.38: 36299 4.38 - 4.90: 62776 Nonbonded interactions: 157970 Sorted by model distance: nonbonded pdb=" NZ LYS B 299 " pdb=" OE2 GLU B 300 " model vdw 2.324 2.520 nonbonded pdb=" NZ LYS A 299 " pdb=" OE2 GLU A 300 " model vdw 2.325 2.520 nonbonded pdb=" NZ LYS D 299 " pdb=" OE2 GLU D 300 " model vdw 2.325 2.520 nonbonded pdb=" NZ LYS C 299 " pdb=" OE2 GLU C 300 " model vdw 2.325 2.520 nonbonded pdb=" O PHE C 76 " pdb=" OG SER C 80 " model vdw 2.325 2.440 ... (remaining 157965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.190 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 51.620 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.064 20608 Z= 0.252 Angle : 0.733 10.055 27988 Z= 0.391 Chirality : 0.046 0.336 3172 Planarity : 0.004 0.048 3432 Dihedral : 15.956 109.698 7660 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.59 % Favored : 94.08 % Rotamer: Outliers : 0.74 % Allowed : 0.74 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2432 helix: 1.07 (0.14), residues: 1432 sheet: -1.75 (0.47), residues: 76 loop : -2.34 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 655 HIS 0.003 0.001 HIS D 433 PHE 0.016 0.001 PHE D 462 TYR 0.010 0.001 TYR D 510 ARG 0.007 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 274 time to evaluate : 2.199 Fit side-chains REVERT: B 263 ILE cc_start: 0.8684 (mp) cc_final: 0.8088 (mp) REVERT: B 272 MET cc_start: 0.8022 (tpp) cc_final: 0.7632 (tpp) REVERT: B 684 LEU cc_start: 0.7750 (mm) cc_final: 0.7445 (mm) REVERT: C 272 MET cc_start: 0.8059 (tpp) cc_final: 0.7859 (tpt) REVERT: C 619 LEU cc_start: 0.8785 (mm) cc_final: 0.8577 (mm) REVERT: D 684 LEU cc_start: 0.7778 (mm) cc_final: 0.7469 (mm) outliers start: 16 outliers final: 12 residues processed: 286 average time/residue: 0.3286 time to fit residues: 142.3756 Evaluate side-chains 239 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 6.9990 chunk 184 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 0.2980 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN A 658 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN B 658 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 525 GLN C 658 GLN ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 525 GLN D 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20608 Z= 0.257 Angle : 0.609 7.897 27988 Z= 0.296 Chirality : 0.040 0.192 3172 Planarity : 0.004 0.048 3432 Dihedral : 5.882 49.687 2980 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 2.21 % Allowed : 10.62 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2432 helix: 1.17 (0.14), residues: 1444 sheet: -1.52 (0.47), residues: 76 loop : -2.25 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 328 HIS 0.003 0.001 HIS B 433 PHE 0.010 0.001 PHE C 596 TYR 0.023 0.001 TYR B 466 ARG 0.005 0.000 ARG C 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8234 (mm) REVERT: C 435 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7616 (mp) REVERT: C 619 LEU cc_start: 0.8677 (mm) cc_final: 0.8274 (mm) REVERT: D 619 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (mm) outliers start: 48 outliers final: 37 residues processed: 261 average time/residue: 0.3250 time to fit residues: 129.7607 Evaluate side-chains 264 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 184 optimal weight: 40.0000 chunk 150 optimal weight: 20.0000 chunk 61 optimal weight: 40.0000 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 20608 Z= 0.403 Angle : 0.674 8.399 27988 Z= 0.334 Chirality : 0.043 0.245 3172 Planarity : 0.005 0.049 3432 Dihedral : 5.586 50.070 2960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.33 % Rotamer: Outliers : 3.91 % Allowed : 12.82 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2432 helix: 1.04 (0.14), residues: 1436 sheet: -1.54 (0.48), residues: 76 loop : -2.22 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 655 HIS 0.005 0.001 HIS D 433 PHE 0.014 0.002 PHE D 596 TYR 0.014 0.002 TYR C 407 ARG 0.006 0.001 ARG C 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 226 time to evaluate : 2.178 Fit side-chains REVERT: A 433 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6432 (t70) REVERT: A 619 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 433 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6409 (t70) REVERT: B 619 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8225 (mm) REVERT: C 433 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6469 (t70) REVERT: C 619 LEU cc_start: 0.8688 (mm) cc_final: 0.8352 (mm) REVERT: D 433 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6551 (t70) REVERT: D 619 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8255 (mm) outliers start: 85 outliers final: 53 residues processed: 289 average time/residue: 0.3133 time to fit residues: 140.1956 Evaluate side-chains 272 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 212 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 676 LYS Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 464 ASP Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 676 LYS Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20608 Z= 0.148 Angle : 0.529 9.098 27988 Z= 0.261 Chirality : 0.037 0.167 3172 Planarity : 0.003 0.035 3432 Dihedral : 5.064 53.272 2956 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.98 % Favored : 94.86 % Rotamer: Outliers : 2.30 % Allowed : 16.08 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2432 helix: 1.54 (0.14), residues: 1424 sheet: -1.33 (0.48), residues: 76 loop : -2.27 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 328 HIS 0.003 0.001 HIS B 433 PHE 0.007 0.001 PHE B 700 TYR 0.012 0.001 TYR A 466 ARG 0.005 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 2.183 Fit side-chains REVERT: A 428 MET cc_start: 0.5178 (tmm) cc_final: 0.4842 (mtm) REVERT: A 433 HIS cc_start: 0.7377 (OUTLIER) cc_final: 0.6543 (t70) REVERT: A 619 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8132 (mm) REVERT: B 428 MET cc_start: 0.5181 (tmm) cc_final: 0.4800 (mtm) REVERT: B 433 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6464 (t70) REVERT: B 619 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (mm) REVERT: C 433 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.6585 (t70) REVERT: C 619 LEU cc_start: 0.8516 (mm) cc_final: 0.8218 (mm) REVERT: D 428 MET cc_start: 0.5039 (tmm) cc_final: 0.4754 (mtm) REVERT: D 433 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6550 (t70) REVERT: D 619 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8180 (mm) outliers start: 50 outliers final: 26 residues processed: 277 average time/residue: 0.3118 time to fit residues: 133.3719 Evaluate side-chains 245 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 211 optimal weight: 0.2980 chunk 59 optimal weight: 0.0040 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20608 Z= 0.162 Angle : 0.529 12.042 27988 Z= 0.258 Chirality : 0.037 0.150 3172 Planarity : 0.003 0.035 3432 Dihedral : 4.893 52.950 2956 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 2.99 % Allowed : 17.14 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2432 helix: 1.72 (0.14), residues: 1420 sheet: -0.75 (0.48), residues: 76 loop : -2.24 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 328 HIS 0.004 0.001 HIS B 433 PHE 0.008 0.001 PHE B 596 TYR 0.009 0.001 TYR A 466 ARG 0.004 0.000 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 222 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7360 (OUTLIER) cc_final: 0.6561 (t70) REVERT: A 619 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 433 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6513 (t70) REVERT: B 619 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8234 (mm) REVERT: C 428 MET cc_start: 0.5098 (ttt) cc_final: 0.4861 (tmm) REVERT: C 619 LEU cc_start: 0.8547 (mm) cc_final: 0.8230 (mm) REVERT: D 433 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.6517 (t70) REVERT: D 619 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8181 (mm) outliers start: 65 outliers final: 52 residues processed: 275 average time/residue: 0.3206 time to fit residues: 135.1165 Evaluate side-chains 266 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 208 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 0.7980 chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 0.0070 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 40.0000 overall best weight: 3.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20608 Z= 0.325 Angle : 0.617 13.329 27988 Z= 0.303 Chirality : 0.040 0.163 3172 Planarity : 0.004 0.036 3432 Dihedral : 5.226 52.172 2956 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 2.94 % Allowed : 18.06 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2432 helix: 1.55 (0.14), residues: 1416 sheet: -0.59 (0.49), residues: 76 loop : -2.14 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 655 HIS 0.006 0.001 HIS D 433 PHE 0.014 0.001 PHE A 596 TYR 0.011 0.001 TYR C 407 ARG 0.007 0.001 ARG D 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 211 time to evaluate : 2.087 Fit side-chains REVERT: A 433 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6517 (t70) REVERT: A 619 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8225 (mm) REVERT: B 433 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6494 (t70) REVERT: B 619 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 428 MET cc_start: 0.5278 (ttt) cc_final: 0.4994 (tmm) REVERT: C 433 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6519 (t70) REVERT: C 435 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7756 (mp) REVERT: C 619 LEU cc_start: 0.8664 (mm) cc_final: 0.8285 (mm) REVERT: D 433 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6472 (t70) REVERT: D 619 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8239 (mm) outliers start: 64 outliers final: 55 residues processed: 261 average time/residue: 0.3141 time to fit residues: 127.7584 Evaluate side-chains 269 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 206 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 172 optimal weight: 0.0020 chunk 133 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 20608 Z= 0.152 Angle : 0.531 14.234 27988 Z= 0.257 Chirality : 0.037 0.135 3172 Planarity : 0.003 0.037 3432 Dihedral : 4.939 53.144 2956 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.08 % Allowed : 18.34 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2432 helix: 1.79 (0.14), residues: 1416 sheet: -0.35 (0.49), residues: 76 loop : -2.16 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 328 HIS 0.004 0.001 HIS D 433 PHE 0.006 0.001 PHE D 306 TYR 0.009 0.001 TYR B 466 ARG 0.004 0.000 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 229 time to evaluate : 2.247 Fit side-chains REVERT: A 428 MET cc_start: 0.5175 (tmm) cc_final: 0.4807 (mtm) REVERT: A 433 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6598 (t70) REVERT: A 619 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 428 MET cc_start: 0.5144 (tmm) cc_final: 0.4716 (mtm) REVERT: B 433 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.6599 (t70) REVERT: B 619 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8202 (mm) REVERT: C 428 MET cc_start: 0.5247 (ttt) cc_final: 0.4970 (tmm) REVERT: C 433 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6567 (t70) REVERT: C 619 LEU cc_start: 0.8590 (mm) cc_final: 0.8271 (mm) REVERT: D 428 MET cc_start: 0.5106 (tmm) cc_final: 0.4736 (mtm) REVERT: D 433 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6645 (t70) REVERT: D 619 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8169 (mm) outliers start: 67 outliers final: 49 residues processed: 287 average time/residue: 0.3097 time to fit residues: 138.1778 Evaluate side-chains 262 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 160 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20608 Z= 0.237 Angle : 0.585 14.816 27988 Z= 0.279 Chirality : 0.038 0.137 3172 Planarity : 0.004 0.037 3432 Dihedral : 5.048 54.088 2956 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.35 % Allowed : 18.29 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2432 helix: 1.78 (0.14), residues: 1412 sheet: -0.18 (0.50), residues: 76 loop : -2.08 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 173 HIS 0.005 0.001 HIS B 433 PHE 0.010 0.001 PHE B 596 TYR 0.008 0.001 TYR D 407 ARG 0.005 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 212 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6560 (t70) REVERT: A 619 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8234 (mm) REVERT: B 433 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6493 (t70) REVERT: B 619 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8273 (mm) REVERT: C 428 MET cc_start: 0.5293 (ttt) cc_final: 0.4986 (tmm) REVERT: C 433 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.6628 (t70) REVERT: C 619 LEU cc_start: 0.8665 (mm) cc_final: 0.8295 (mm) REVERT: D 433 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6561 (t70) REVERT: D 619 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8273 (mm) outliers start: 73 outliers final: 58 residues processed: 273 average time/residue: 0.3209 time to fit residues: 136.1335 Evaluate side-chains 266 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 201 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 205 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 198 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 218 optimal weight: 0.0980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 20608 Z= 0.148 Angle : 0.552 15.243 27988 Z= 0.264 Chirality : 0.037 0.135 3172 Planarity : 0.003 0.038 3432 Dihedral : 4.944 54.679 2956 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.08 % Allowed : 18.34 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2432 helix: 1.90 (0.14), residues: 1416 sheet: -0.20 (0.49), residues: 76 loop : -2.09 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 173 HIS 0.004 0.001 HIS D 433 PHE 0.009 0.001 PHE C 700 TYR 0.008 0.001 TYR A 466 ARG 0.004 0.000 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 200 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5284 (tmm) cc_final: 0.4853 (mtm) REVERT: A 433 HIS cc_start: 0.7359 (OUTLIER) cc_final: 0.6620 (t70) REVERT: A 619 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8186 (mm) REVERT: B 433 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6610 (t70) REVERT: B 619 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8243 (mm) REVERT: C 428 MET cc_start: 0.5277 (ttt) cc_final: 0.4979 (tmm) REVERT: C 433 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6526 (t70) REVERT: C 619 LEU cc_start: 0.8595 (mm) cc_final: 0.8268 (mm) REVERT: D 433 HIS cc_start: 0.7357 (OUTLIER) cc_final: 0.6602 (t70) REVERT: D 619 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8240 (mm) outliers start: 67 outliers final: 50 residues processed: 264 average time/residue: 0.2810 time to fit residues: 118.9735 Evaluate side-chains 255 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0980 chunk 231 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20608 Z= 0.189 Angle : 0.573 15.706 27988 Z= 0.272 Chirality : 0.037 0.135 3172 Planarity : 0.003 0.038 3432 Dihedral : 4.977 54.859 2956 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.22 % Allowed : 18.34 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2432 helix: 1.92 (0.14), residues: 1412 sheet: 0.01 (0.49), residues: 76 loop : -2.03 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 173 HIS 0.004 0.001 HIS D 433 PHE 0.008 0.001 PHE D 596 TYR 0.007 0.001 TYR A 466 ARG 0.005 0.000 ARG C 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 194 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.5227 (tmm) cc_final: 0.4767 (mtm) REVERT: A 433 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6565 (t70) REVERT: A 619 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8255 (mm) REVERT: B 433 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6518 (t70) REVERT: B 619 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8263 (mm) REVERT: C 428 MET cc_start: 0.5310 (ttt) cc_final: 0.4982 (tmm) REVERT: C 433 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.6533 (t70) REVERT: C 619 LEU cc_start: 0.8616 (mm) cc_final: 0.8254 (mm) REVERT: D 433 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6521 (t70) REVERT: D 619 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8263 (mm) outliers start: 70 outliers final: 60 residues processed: 255 average time/residue: 0.2740 time to fit residues: 112.3701 Evaluate side-chains 261 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 194 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 433 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 433 HIS Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 433 HIS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 517 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.4980 chunk 206 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.193516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131620 restraints weight = 27625.069| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.81 r_work: 0.3345 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20608 Z= 0.173 Angle : 0.561 15.693 27988 Z= 0.266 Chirality : 0.037 0.135 3172 Planarity : 0.003 0.040 3432 Dihedral : 4.969 55.014 2956 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.17 % Allowed : 18.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2432 helix: 1.96 (0.14), residues: 1412 sheet: 0.10 (0.49), residues: 76 loop : -2.01 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 173 HIS 0.004 0.001 HIS D 433 PHE 0.007 0.001 PHE B 596 TYR 0.008 0.001 TYR B 466 ARG 0.004 0.000 ARG C 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4289.00 seconds wall clock time: 78 minutes 36.02 seconds (4716.02 seconds total)