Starting phenix.real_space_refine on Thu Mar 5 08:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.map" model { file = "/net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f5t_31466/03_2026/7f5t_31466.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 112 5.16 5 C 12800 2.51 5 N 3620 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5099 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.20 Number of scatterers: 20436 At special positions: 0 Unit cell: (193.98, 107.06, 94.34, 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 112 16.00 O 3904 8.00 N 3620 7.00 C 12800 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 923.0 milliseconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 20 sheets defined 51.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE A 68 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 95 " --> pdb=" O CYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 163 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 368 through 384 Processing helix chain 'A' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 Processing helix chain 'A' and resid 415 through 433 Processing helix chain 'A' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'A' and resid 527 through 534 Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 614 through 627 Processing helix chain 'A' and resid 633 through 640 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 689 through 700 Processing helix chain 'A' and resid 710 through 714 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 740 through 744 Processing helix chain 'A' and resid 757 through 761 Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.795A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 95 " --> pdb=" O CYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 163 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 180 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 175 through 180' Processing helix chain 'B' and resid 180 through 196 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 349 through 363 Processing helix chain 'B' and resid 368 through 384 Processing helix chain 'B' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 433 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.014A pdb=" N GLN B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 512 Processing helix chain 'B' and resid 527 through 534 Processing helix chain 'B' and resid 546 through 557 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 633 through 640 Processing helix chain 'B' and resid 666 through 678 Processing helix chain 'B' and resid 689 through 700 Processing helix chain 'B' and resid 710 through 714 Processing helix chain 'B' and resid 716 through 720 Processing helix chain 'B' and resid 740 through 744 Processing helix chain 'B' and resid 757 through 761 Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE C 68 " --> pdb=" O GLY C 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 77 through 95 removed outlier: 4.124A pdb=" N LEU C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 95 " --> pdb=" O CYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 115 through 122 removed outlier: 3.691A pdb=" N SER C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 Processing helix chain 'C' and resid 175 through 180 removed outlier: 3.763A pdb=" N TYR C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 180' Processing helix chain 'C' and resid 180 through 196 Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.852A pdb=" N SER C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'C' and resid 321 through 328 Processing helix chain 'C' and resid 349 through 363 Processing helix chain 'C' and resid 368 through 384 Processing helix chain 'C' and resid 384 through 403 removed outlier: 3.777A pdb=" N ILE C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 433 Processing helix chain 'C' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 512 Processing helix chain 'C' and resid 527 through 534 Processing helix chain 'C' and resid 546 through 557 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 609 through 612 Processing helix chain 'C' and resid 614 through 627 Processing helix chain 'C' and resid 633 through 640 Processing helix chain 'C' and resid 666 through 678 Processing helix chain 'C' and resid 689 through 700 Processing helix chain 'C' and resid 710 through 714 Processing helix chain 'C' and resid 716 through 720 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 757 through 761 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.794A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.016A pdb=" N ILE D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 77 through 95 removed outlier: 4.125A pdb=" N LEU D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY D 95 " --> pdb=" O CYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 Processing helix chain 'D' and resid 115 through 122 removed outlier: 3.692A pdb=" N SER D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.762A pdb=" N TYR D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 180 " --> pdb=" O PRO D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 180 through 196 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.851A pdb=" N SER D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 368 through 384 Processing helix chain 'D' and resid 384 through 403 removed outlier: 3.776A pdb=" N ILE D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 Processing helix chain 'D' and resid 415 through 433 Processing helix chain 'D' and resid 471 through 483 removed outlier: 4.015A pdb=" N GLN D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 512 Processing helix chain 'D' and resid 527 through 534 Processing helix chain 'D' and resid 546 through 557 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 614 through 627 Processing helix chain 'D' and resid 633 through 640 Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 689 through 700 Processing helix chain 'D' and resid 710 through 714 Processing helix chain 'D' and resid 716 through 720 Processing helix chain 'D' and resid 740 through 744 Processing helix chain 'D' and resid 757 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG A 58 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE A 250 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL A 60 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 336 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA A 169 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG A 442 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 451 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 751 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL C 705 " --> pdb=" O THR A 746 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP A 748 " --> pdb=" O VAL C 705 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS C 707 " --> pdb=" O TRP A 748 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 750 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASP C 683 " --> pdb=" O PHE C 706 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 572 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS C 607 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE C 574 " --> pdb=" O HIS C 607 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 604 " --> pdb=" O GLU C 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 664 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE C 606 " --> pdb=" O VAL C 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU A 462 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 461 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 542 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 463 " --> pdb=" O ILE A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU A 604 " --> pdb=" O GLU A 662 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 664 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 606 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL A 572 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS A 607 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 574 " --> pdb=" O HIS A 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP A 683 " --> pdb=" O PHE A 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 751 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C 451 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 442 " --> pdb=" O GLN C 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY A 726 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG B 58 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE B 250 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 60 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 336 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 173 removed outlier: 3.932A pdb=" N ALA B 169 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 771 through 772 removed outlier: 3.517A pdb=" N ARG B 442 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 451 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 751 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL D 705 " --> pdb=" O THR B 746 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP B 748 " --> pdb=" O VAL D 705 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS D 707 " --> pdb=" O TRP B 748 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 750 " --> pdb=" O HIS D 707 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP D 683 " --> pdb=" O PHE D 706 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 572 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N HIS D 607 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE D 574 " --> pdb=" O HIS D 607 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU D 604 " --> pdb=" O GLU D 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL D 664 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 606 " --> pdb=" O VAL D 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 487 through 488 removed outlier: 6.645A pdb=" N LEU B 462 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL B 461 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 542 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 463 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 660 through 664 removed outlier: 6.007A pdb=" N LEU B 604 " --> pdb=" O GLU B 662 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 664 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 606 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL B 572 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS B 607 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE B 574 " --> pdb=" O HIS B 607 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASP B 683 " --> pdb=" O PHE B 706 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 751 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 451 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 442 " --> pdb=" O GLN D 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY B 726 " --> pdb=" O VAL B 738 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.840A pdb=" N ARG C 58 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE C 250 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 60 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 336 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA C 169 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU C 462 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 461 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 542 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 463 " --> pdb=" O ILE C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 726 through 728 removed outlier: 3.827A pdb=" N GLY C 726 " --> pdb=" O VAL C 738 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.841A pdb=" N ARG D 58 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D 250 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 60 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 336 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 167 through 173 removed outlier: 3.933A pdb=" N ALA D 169 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 487 through 488 removed outlier: 6.646A pdb=" N LEU D 462 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 461 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 542 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 463 " --> pdb=" O ILE D 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 726 through 728 removed outlier: 3.826A pdb=" N GLY D 726 " --> pdb=" O VAL D 738 " (cutoff:3.500A) 976 hydrogen bonds defined for protein. 2724 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: 3.85 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6350 1.33 - 1.45: 2720 1.45 - 1.57: 11474 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 20728 Sorted by residual: bond pdb=" CA LEU B 53 " pdb=" C LEU B 53 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.56e-02 4.11e+03 1.29e+01 bond pdb=" CA LEU D 53 " pdb=" C LEU D 53 " ideal model delta sigma weight residual 1.523 1.468 0.056 1.56e-02 4.11e+03 1.27e+01 bond pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.25e+01 bond pdb=" CA LEU C 53 " pdb=" C LEU C 53 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" CA VAL D 346 " pdb=" CB VAL D 346 " ideal model delta sigma weight residual 1.540 1.517 0.023 7.70e-03 1.69e+04 8.74e+00 ... (remaining 20723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 25534 1.42 - 2.85: 2071 2.85 - 4.27: 299 4.27 - 5.69: 104 5.69 - 7.12: 28 Bond angle restraints: 28036 Sorted by residual: angle pdb=" C ALA D 345 " pdb=" N VAL D 346 " pdb=" CA VAL D 346 " ideal model delta sigma weight residual 123.33 118.63 4.70 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA C 345 " pdb=" N VAL C 346 " pdb=" CA VAL C 346 " ideal model delta sigma weight residual 123.33 118.64 4.69 8.70e-01 1.32e+00 2.91e+01 angle pdb=" C ALA A 345 " pdb=" N VAL A 346 " pdb=" CA VAL A 346 " ideal model delta sigma weight residual 123.33 118.65 4.68 8.70e-01 1.32e+00 2.90e+01 angle pdb=" C ALA B 345 " pdb=" N VAL B 346 " pdb=" CA VAL B 346 " ideal model delta sigma weight residual 123.33 118.67 4.66 8.70e-01 1.32e+00 2.87e+01 angle pdb=" N ALA A 691 " pdb=" CA ALA A 691 " pdb=" C ALA A 691 " ideal model delta sigma weight residual 111.03 105.16 5.87 1.11e+00 8.12e-01 2.80e+01 ... (remaining 28031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11333 17.73 - 35.45: 1040 35.45 - 53.18: 243 53.18 - 70.90: 36 70.90 - 88.63: 28 Dihedral angle restraints: 12680 sinusoidal: 4932 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ASN B 344 " pdb=" C ASN B 344 " pdb=" N ALA B 345 " pdb=" CA ALA B 345 " ideal model delta harmonic sigma weight residual -180.00 -150.82 -29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ASN A 344 " pdb=" C ASN A 344 " pdb=" N ALA A 345 " pdb=" CA ALA A 345 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ASN C 344 " pdb=" C ASN C 344 " pdb=" N ALA C 345 " pdb=" CA ALA C 345 " ideal model delta harmonic sigma weight residual 180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2196 0.038 - 0.076: 793 0.076 - 0.113: 277 0.113 - 0.151: 34 0.151 - 0.189: 8 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA LEU B 53 " pdb=" N LEU B 53 " pdb=" C LEU B 53 " pdb=" CB LEU B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA LEU D 53 " pdb=" N LEU D 53 " pdb=" C LEU D 53 " pdb=" CB LEU D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA LEU C 53 " pdb=" N LEU C 53 " pdb=" C LEU C 53 " pdb=" CB LEU C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3305 not shown) Planarity restraints: 3632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 597 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ALA B 597 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 597 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS B 598 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 597 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ALA C 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA C 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS C 598 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 597 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ALA A 597 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA A 597 " -0.013 2.00e-02 2.50e+03 pdb=" N CYS A 598 " -0.011 2.00e-02 2.50e+03 ... (remaining 3629 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1288 2.69 - 3.24: 24453 3.24 - 3.80: 34306 3.80 - 4.35: 41978 4.35 - 4.90: 66489 Nonbonded interactions: 168514 Sorted by model distance: nonbonded pdb=" O ASN D 354 " pdb=" OG1 THR D 357 " model vdw 2.141 3.040 nonbonded pdb=" O ASN A 354 " pdb=" OG1 THR A 357 " model vdw 2.141 3.040 nonbonded pdb=" O ASN B 354 " pdb=" OG1 THR B 357 " model vdw 2.142 3.040 nonbonded pdb=" O ASN C 354 " pdb=" OG1 THR C 357 " model vdw 2.142 3.040 nonbonded pdb=" O ALA C 399 " pdb=" OG SER C 402 " model vdw 2.204 3.040 ... (remaining 168509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.110 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.007 0.056 20728 Z= 0.413 Angle : 0.886 7.118 28036 Z= 0.535 Chirality : 0.043 0.189 3308 Planarity : 0.004 0.041 3632 Dihedral : 15.070 88.631 7656 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.25 % Favored : 86.30 % Rotamer: Outliers : 3.48 % Allowed : 7.14 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.13), residues: 2664 helix: -2.50 (0.12), residues: 1136 sheet: -4.18 (0.18), residues: 428 loop : -3.78 (0.16), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 308 TYR 0.017 0.002 TYR B 55 PHE 0.018 0.002 PHE B 642 TRP 0.019 0.003 TRP C 304 HIS 0.008 0.002 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00726 (20728) covalent geometry : angle 0.88552 (28036) hydrogen bonds : bond 0.19093 ( 976) hydrogen bonds : angle 7.78314 ( 2724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 275 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8693 (tp) cc_final: 0.7588 (tt) REVERT: A 154 MET cc_start: 0.7800 (mmm) cc_final: 0.7418 (tpp) REVERT: A 158 ASP cc_start: 0.8232 (m-30) cc_final: 0.7540 (m-30) REVERT: A 178 PHE cc_start: 0.8419 (m-80) cc_final: 0.8186 (m-80) REVERT: B 209 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8706 (p) REVERT: C 153 LEU cc_start: 0.8702 (tp) cc_final: 0.7604 (tt) REVERT: C 154 MET cc_start: 0.7740 (mmm) cc_final: 0.7218 (tpp) REVERT: C 158 ASP cc_start: 0.8235 (m-30) cc_final: 0.7494 (m-30) REVERT: C 178 PHE cc_start: 0.8456 (m-80) cc_final: 0.8171 (m-80) REVERT: C 209 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 240 LEU cc_start: 0.9492 (tt) cc_final: 0.9281 (tp) REVERT: D 178 PHE cc_start: 0.8579 (m-80) cc_final: 0.8289 (m-80) REVERT: D 209 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8625 (p) REVERT: D 240 LEU cc_start: 0.9506 (tt) cc_final: 0.9302 (tp) outliers start: 76 outliers final: 19 residues processed: 329 average time/residue: 0.1522 time to fit residues: 76.1696 Evaluate side-chains 216 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 363 GLN A 369 GLN A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN B 369 GLN B 392 ASN B 607 HIS B 652 HIS C 150 GLN C 363 GLN C 369 GLN C 392 ASN C 607 HIS C 652 HIS ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN D 369 GLN D 392 ASN D 607 HIS D 652 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.034125 restraints weight = 175891.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034768 restraints weight = 131350.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.035163 restraints weight = 105382.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035595 restraints weight = 92808.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035849 restraints weight = 82366.753| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20728 Z= 0.164 Angle : 0.651 7.654 28036 Z= 0.342 Chirality : 0.043 0.233 3308 Planarity : 0.004 0.045 3632 Dihedral : 5.413 28.879 2872 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.39 % Favored : 92.34 % Rotamer: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.15), residues: 2664 helix: -0.81 (0.14), residues: 1180 sheet: -3.10 (0.20), residues: 428 loop : -3.15 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 694 TYR 0.033 0.002 TYR C 157 PHE 0.010 0.002 PHE B 642 TRP 0.013 0.002 TRP A 304 HIS 0.005 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00328 (20728) covalent geometry : angle 0.65077 (28036) hydrogen bonds : bond 0.04354 ( 976) hydrogen bonds : angle 5.71528 ( 2724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 253 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9613 (mtp) cc_final: 0.9277 (mmp) REVERT: A 102 THR cc_start: 0.9022 (p) cc_final: 0.8652 (p) REVERT: A 161 PHE cc_start: 0.9427 (m-80) cc_final: 0.9116 (m-80) REVERT: A 178 PHE cc_start: 0.9079 (m-80) cc_final: 0.8499 (m-80) REVERT: A 503 MET cc_start: 0.9658 (tpt) cc_final: 0.9449 (tpp) REVERT: A 559 HIS cc_start: 0.8741 (t-90) cc_final: 0.8363 (t70) REVERT: A 601 MET cc_start: 0.9091 (ptm) cc_final: 0.8395 (ppp) REVERT: A 677 TYR cc_start: 0.9601 (m-80) cc_final: 0.9288 (m-80) REVERT: B 63 LEU cc_start: 0.9577 (mp) cc_final: 0.9375 (mp) REVERT: B 91 CYS cc_start: 0.9840 (m) cc_final: 0.9537 (p) REVERT: B 161 PHE cc_start: 0.9571 (m-80) cc_final: 0.9047 (m-80) REVERT: B 271 MET cc_start: 0.9561 (ptp) cc_final: 0.9349 (ptp) REVERT: B 538 ILE cc_start: 0.9763 (pt) cc_final: 0.9548 (tp) REVERT: B 559 HIS cc_start: 0.8857 (t-90) cc_final: 0.8514 (t70) REVERT: B 601 MET cc_start: 0.9141 (ptm) cc_final: 0.8414 (ppp) REVERT: B 677 TYR cc_start: 0.9593 (m-80) cc_final: 0.9311 (m-80) REVERT: C 91 CYS cc_start: 0.9864 (m) cc_final: 0.9534 (p) REVERT: C 100 MET cc_start: 0.9587 (mtp) cc_final: 0.9264 (mmp) REVERT: C 102 THR cc_start: 0.9121 (p) cc_final: 0.8733 (p) REVERT: C 161 PHE cc_start: 0.9439 (m-80) cc_final: 0.9103 (m-80) REVERT: C 178 PHE cc_start: 0.9246 (m-80) cc_final: 0.8637 (m-80) REVERT: C 503 MET cc_start: 0.9685 (tpt) cc_final: 0.9459 (tpp) REVERT: C 559 HIS cc_start: 0.8744 (t-90) cc_final: 0.8357 (t70) REVERT: C 601 MET cc_start: 0.8984 (ptm) cc_final: 0.8366 (ppp) REVERT: C 677 TYR cc_start: 0.9612 (m-80) cc_final: 0.9295 (m-80) REVERT: D 63 LEU cc_start: 0.9603 (mp) cc_final: 0.9394 (mp) REVERT: D 153 LEU cc_start: 0.9659 (tt) cc_final: 0.9302 (tt) REVERT: D 154 MET cc_start: 0.9481 (mmt) cc_final: 0.9234 (mmm) REVERT: D 161 PHE cc_start: 0.9553 (m-80) cc_final: 0.9062 (m-80) REVERT: D 178 PHE cc_start: 0.9262 (m-80) cc_final: 0.8634 (m-80) REVERT: D 538 ILE cc_start: 0.9767 (pt) cc_final: 0.9547 (tp) REVERT: D 559 HIS cc_start: 0.8907 (t-90) cc_final: 0.8565 (t70) REVERT: D 601 MET cc_start: 0.9093 (ptm) cc_final: 0.8385 (ppp) REVERT: D 677 TYR cc_start: 0.9584 (m-80) cc_final: 0.9263 (m-80) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.1522 time to fit residues: 59.1614 Evaluate side-chains 184 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 156 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 chunk 59 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 571 HIS ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 707 HIS C 392 ASN C 707 HIS D 150 GLN D 392 ASN D 707 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.033830 restraints weight = 182618.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034393 restraints weight = 136054.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.034991 restraints weight = 111221.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.035340 restraints weight = 95822.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.035694 restraints weight = 83906.829| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20728 Z= 0.161 Angle : 0.616 7.903 28036 Z= 0.323 Chirality : 0.043 0.164 3308 Planarity : 0.004 0.046 3632 Dihedral : 5.151 28.965 2872 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.87 % Favored : 92.98 % Rotamer: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2664 helix: 0.10 (0.15), residues: 1184 sheet: -2.80 (0.20), residues: 472 loop : -2.80 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 50 TYR 0.026 0.002 TYR A 157 PHE 0.011 0.002 PHE D 335 TRP 0.011 0.002 TRP D 304 HIS 0.007 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00328 (20728) covalent geometry : angle 0.61557 (28036) hydrogen bonds : bond 0.03778 ( 976) hydrogen bonds : angle 5.15085 ( 2724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9599 (mtp) cc_final: 0.9113 (mmp) REVERT: A 154 MET cc_start: 0.9234 (mmp) cc_final: 0.8731 (mmm) REVERT: A 157 TYR cc_start: 0.9854 (m-80) cc_final: 0.9163 (m-80) REVERT: A 178 PHE cc_start: 0.9204 (m-80) cc_final: 0.8686 (m-80) REVERT: A 252 MET cc_start: 0.9453 (mmp) cc_final: 0.8678 (mmm) REVERT: A 271 MET cc_start: 0.9613 (ptp) cc_final: 0.9390 (ptp) REVERT: A 503 MET cc_start: 0.9673 (tpt) cc_final: 0.9452 (tpp) REVERT: A 559 HIS cc_start: 0.8735 (t-90) cc_final: 0.8321 (t70) REVERT: A 601 MET cc_start: 0.9149 (ptm) cc_final: 0.8416 (ppp) REVERT: A 677 TYR cc_start: 0.9599 (m-80) cc_final: 0.9245 (m-80) REVERT: B 91 CYS cc_start: 0.9847 (m) cc_final: 0.9551 (p) REVERT: B 154 MET cc_start: 0.9508 (mmm) cc_final: 0.8965 (mmm) REVERT: B 161 PHE cc_start: 0.9616 (m-80) cc_final: 0.9207 (m-80) REVERT: B 252 MET cc_start: 0.9452 (mmp) cc_final: 0.8747 (mmm) REVERT: B 254 ASP cc_start: 0.9686 (p0) cc_final: 0.9278 (m-30) REVERT: B 318 MET cc_start: 0.9420 (mpp) cc_final: 0.9207 (mpp) REVERT: B 538 ILE cc_start: 0.9738 (pt) cc_final: 0.9511 (tp) REVERT: B 559 HIS cc_start: 0.8836 (t-90) cc_final: 0.8461 (t70) REVERT: B 601 MET cc_start: 0.9117 (ptm) cc_final: 0.8198 (ppp) REVERT: B 677 TYR cc_start: 0.9584 (m-80) cc_final: 0.9273 (m-80) REVERT: C 91 CYS cc_start: 0.9792 (m) cc_final: 0.9440 (p) REVERT: C 100 MET cc_start: 0.9603 (mtp) cc_final: 0.9204 (mmp) REVERT: C 153 LEU cc_start: 0.9641 (tp) cc_final: 0.9435 (tp) REVERT: C 154 MET cc_start: 0.9236 (mmp) cc_final: 0.8750 (mmm) REVERT: C 157 TYR cc_start: 0.9834 (m-80) cc_final: 0.9204 (m-80) REVERT: C 161 PHE cc_start: 0.9457 (m-80) cc_final: 0.9203 (m-80) REVERT: C 167 LYS cc_start: 0.9724 (mppt) cc_final: 0.9521 (mmtm) REVERT: C 271 MET cc_start: 0.9599 (ptp) cc_final: 0.9377 (ptp) REVERT: C 503 MET cc_start: 0.9671 (tpt) cc_final: 0.9428 (tpp) REVERT: C 559 HIS cc_start: 0.8722 (t-90) cc_final: 0.8308 (t70) REVERT: C 601 MET cc_start: 0.9140 (ptm) cc_final: 0.8416 (ppp) REVERT: C 677 TYR cc_start: 0.9618 (m-80) cc_final: 0.9275 (m-80) REVERT: D 63 LEU cc_start: 0.9617 (mp) cc_final: 0.9401 (mp) REVERT: D 154 MET cc_start: 0.9565 (mmt) cc_final: 0.9287 (mmm) REVERT: D 161 PHE cc_start: 0.9611 (m-80) cc_final: 0.9111 (m-80) REVERT: D 252 MET cc_start: 0.9394 (mmp) cc_final: 0.8666 (mmm) REVERT: D 254 ASP cc_start: 0.9646 (p0) cc_final: 0.9231 (m-30) REVERT: D 538 ILE cc_start: 0.9731 (pt) cc_final: 0.9503 (tp) REVERT: D 559 HIS cc_start: 0.8861 (t-90) cc_final: 0.8499 (t70) REVERT: D 601 MET cc_start: 0.9147 (ptm) cc_final: 0.8431 (ppp) REVERT: D 677 TYR cc_start: 0.9579 (m-80) cc_final: 0.9251 (m-80) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1407 time to fit residues: 49.6643 Evaluate side-chains 180 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 172 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 259 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 24 optimal weight: 0.0010 chunk 190 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 overall best weight: 3.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN B 392 ASN B 571 HIS C 392 ASN C 571 HIS D 392 ASN D 571 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033997 restraints weight = 184670.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034690 restraints weight = 136675.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.035080 restraints weight = 109556.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.035418 restraints weight = 95779.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035840 restraints weight = 85668.460| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20728 Z= 0.137 Angle : 0.589 7.765 28036 Z= 0.305 Chirality : 0.042 0.160 3308 Planarity : 0.004 0.046 3632 Dihedral : 4.939 29.371 2872 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.98 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2664 helix: 0.66 (0.15), residues: 1196 sheet: -2.23 (0.22), residues: 452 loop : -2.78 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 50 TYR 0.020 0.001 TYR A 157 PHE 0.013 0.001 PHE A 466 TRP 0.010 0.001 TRP D 304 HIS 0.005 0.001 HIS B 272 Details of bonding type rmsd covalent geometry : bond 0.00282 (20728) covalent geometry : angle 0.58931 (28036) hydrogen bonds : bond 0.03383 ( 976) hydrogen bonds : angle 4.87891 ( 2724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9561 (mtp) cc_final: 0.9248 (mmp) REVERT: A 161 PHE cc_start: 0.9494 (m-80) cc_final: 0.9071 (m-80) REVERT: A 254 ASP cc_start: 0.9584 (p0) cc_final: 0.9163 (m-30) REVERT: A 259 TYR cc_start: 0.9502 (m-10) cc_final: 0.9298 (m-80) REVERT: A 271 MET cc_start: 0.9633 (ptp) cc_final: 0.9245 (ppp) REVERT: A 315 CYS cc_start: 0.9621 (p) cc_final: 0.9268 (p) REVERT: A 503 MET cc_start: 0.9660 (tpt) cc_final: 0.9449 (tpp) REVERT: A 559 HIS cc_start: 0.8789 (t-90) cc_final: 0.8368 (t70) REVERT: A 601 MET cc_start: 0.9147 (ptm) cc_final: 0.8328 (ppp) REVERT: A 677 TYR cc_start: 0.9596 (m-80) cc_final: 0.9280 (m-80) REVERT: B 63 LEU cc_start: 0.9728 (mp) cc_final: 0.9368 (mp) REVERT: B 91 CYS cc_start: 0.9834 (m) cc_final: 0.9546 (p) REVERT: B 119 MET cc_start: 0.9265 (mmp) cc_final: 0.9059 (mmm) REVERT: B 154 MET cc_start: 0.9444 (mmm) cc_final: 0.8919 (mmm) REVERT: B 161 PHE cc_start: 0.9662 (m-80) cc_final: 0.9222 (m-80) REVERT: B 167 LYS cc_start: 0.9724 (mppt) cc_final: 0.9477 (mmtm) REVERT: B 254 ASP cc_start: 0.9657 (p0) cc_final: 0.9235 (m-30) REVERT: B 271 MET cc_start: 0.9619 (ptp) cc_final: 0.9253 (ppp) REVERT: B 315 CYS cc_start: 0.9686 (p) cc_final: 0.9294 (p) REVERT: B 318 MET cc_start: 0.9299 (mpp) cc_final: 0.9082 (mpp) REVERT: B 559 HIS cc_start: 0.8843 (t-90) cc_final: 0.8462 (t70) REVERT: B 601 MET cc_start: 0.9148 (ptm) cc_final: 0.8191 (ppp) REVERT: B 677 TYR cc_start: 0.9584 (m-80) cc_final: 0.9282 (m-80) REVERT: C 91 CYS cc_start: 0.9780 (m) cc_final: 0.9444 (p) REVERT: C 100 MET cc_start: 0.9584 (mtp) cc_final: 0.9271 (mmp) REVERT: C 161 PHE cc_start: 0.9474 (m-80) cc_final: 0.9041 (m-80) REVERT: C 167 LYS cc_start: 0.9733 (mppt) cc_final: 0.9493 (mmtm) REVERT: C 254 ASP cc_start: 0.9639 (p0) cc_final: 0.9240 (m-30) REVERT: C 271 MET cc_start: 0.9636 (ptp) cc_final: 0.9264 (ppp) REVERT: C 318 MET cc_start: 0.9338 (mpp) cc_final: 0.9113 (mpp) REVERT: C 503 MET cc_start: 0.9660 (tpt) cc_final: 0.9439 (tpp) REVERT: C 559 HIS cc_start: 0.8783 (t-90) cc_final: 0.8360 (t70) REVERT: C 601 MET cc_start: 0.9151 (ptm) cc_final: 0.8336 (ppp) REVERT: C 677 TYR cc_start: 0.9615 (m-80) cc_final: 0.9301 (m-80) REVERT: D 154 MET cc_start: 0.9592 (mmt) cc_final: 0.9283 (mmm) REVERT: D 161 PHE cc_start: 0.9628 (m-80) cc_final: 0.9117 (m-80) REVERT: D 254 ASP cc_start: 0.9604 (p0) cc_final: 0.9114 (m-30) REVERT: D 271 MET cc_start: 0.9566 (ptp) cc_final: 0.9149 (ppp) REVERT: D 315 CYS cc_start: 0.9634 (p) cc_final: 0.9253 (p) REVERT: D 318 MET cc_start: 0.9436 (mpp) cc_final: 0.9217 (mpp) REVERT: D 559 HIS cc_start: 0.8854 (t-90) cc_final: 0.8463 (t70) REVERT: D 601 MET cc_start: 0.9149 (ptm) cc_final: 0.8336 (ppp) REVERT: D 677 TYR cc_start: 0.9581 (m-80) cc_final: 0.9269 (m-80) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1376 time to fit residues: 47.6478 Evaluate side-chains 195 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 145 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 255 optimal weight: 50.0000 chunk 119 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN C 392 ASN D 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.041823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.033092 restraints weight = 196186.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033709 restraints weight = 146437.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034257 restraints weight = 118441.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034495 restraints weight = 101114.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.034802 restraints weight = 91928.024| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20728 Z= 0.205 Angle : 0.642 6.811 28036 Z= 0.335 Chirality : 0.043 0.233 3308 Planarity : 0.004 0.047 3632 Dihedral : 5.155 34.438 2872 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.37 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.16), residues: 2664 helix: 0.67 (0.15), residues: 1192 sheet: -2.04 (0.22), residues: 448 loop : -2.78 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 50 TYR 0.016 0.002 TYR A 573 PHE 0.013 0.002 PHE A 466 TRP 0.009 0.002 TRP A 304 HIS 0.005 0.001 HIS C 707 Details of bonding type rmsd covalent geometry : bond 0.00402 (20728) covalent geometry : angle 0.64234 (28036) hydrogen bonds : bond 0.03530 ( 976) hydrogen bonds : angle 5.03058 ( 2724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9633 (mtp) cc_final: 0.9321 (mmp) REVERT: A 161 PHE cc_start: 0.9543 (m-80) cc_final: 0.9117 (m-80) REVERT: A 239 MET cc_start: 0.9339 (ppp) cc_final: 0.9129 (ppp) REVERT: A 252 MET cc_start: 0.8517 (tpt) cc_final: 0.8271 (tpp) REVERT: A 254 ASP cc_start: 0.9585 (p0) cc_final: 0.9104 (m-30) REVERT: A 271 MET cc_start: 0.9644 (ptp) cc_final: 0.9310 (ppp) REVERT: A 315 CYS cc_start: 0.9626 (p) cc_final: 0.9413 (p) REVERT: A 503 MET cc_start: 0.9661 (tpt) cc_final: 0.9420 (tpp) REVERT: A 559 HIS cc_start: 0.8778 (t-90) cc_final: 0.8350 (t70) REVERT: A 601 MET cc_start: 0.9185 (ptm) cc_final: 0.8188 (ppp) REVERT: A 677 TYR cc_start: 0.9603 (m-80) cc_final: 0.9248 (m-80) REVERT: B 91 CYS cc_start: 0.9864 (m) cc_final: 0.9599 (p) REVERT: B 154 MET cc_start: 0.9476 (mmm) cc_final: 0.9069 (mmm) REVERT: B 161 PHE cc_start: 0.9651 (m-80) cc_final: 0.9222 (m-80) REVERT: B 167 LYS cc_start: 0.9734 (mppt) cc_final: 0.9486 (mmtm) REVERT: B 559 HIS cc_start: 0.8905 (t-90) cc_final: 0.8514 (t70) REVERT: B 601 MET cc_start: 0.9192 (ptm) cc_final: 0.8273 (ppp) REVERT: B 677 TYR cc_start: 0.9586 (m-80) cc_final: 0.9244 (m-80) REVERT: C 91 CYS cc_start: 0.9810 (m) cc_final: 0.9519 (p) REVERT: C 100 MET cc_start: 0.9650 (mtp) cc_final: 0.9353 (mmp) REVERT: C 161 PHE cc_start: 0.9497 (m-80) cc_final: 0.9090 (m-80) REVERT: C 239 MET cc_start: 0.9393 (ppp) cc_final: 0.9190 (ppp) REVERT: C 254 ASP cc_start: 0.9577 (p0) cc_final: 0.9102 (m-30) REVERT: C 259 TYR cc_start: 0.9526 (m-10) cc_final: 0.9303 (m-80) REVERT: C 271 MET cc_start: 0.9659 (ptp) cc_final: 0.9323 (ppp) REVERT: C 318 MET cc_start: 0.9358 (mpp) cc_final: 0.9103 (mpp) REVERT: C 503 MET cc_start: 0.9669 (tpt) cc_final: 0.9400 (tpp) REVERT: C 559 HIS cc_start: 0.8797 (t-90) cc_final: 0.8364 (t70) REVERT: C 601 MET cc_start: 0.9191 (ptm) cc_final: 0.8199 (ppp) REVERT: C 677 TYR cc_start: 0.9633 (m-80) cc_final: 0.9269 (m-80) REVERT: D 100 MET cc_start: 0.9433 (ttm) cc_final: 0.9161 (ttt) REVERT: D 154 MET cc_start: 0.9590 (mmt) cc_final: 0.9344 (mmm) REVERT: D 161 PHE cc_start: 0.9637 (m-80) cc_final: 0.9140 (m-80) REVERT: D 271 MET cc_start: 0.9607 (ptp) cc_final: 0.9188 (ppp) REVERT: D 315 CYS cc_start: 0.9637 (p) cc_final: 0.9397 (p) REVERT: D 503 MET cc_start: 0.9673 (tpt) cc_final: 0.9455 (tpp) REVERT: D 559 HIS cc_start: 0.8936 (t-90) cc_final: 0.8546 (t-90) REVERT: D 601 MET cc_start: 0.9194 (ptm) cc_final: 0.8218 (ppp) REVERT: D 677 TYR cc_start: 0.9608 (m-80) cc_final: 0.9252 (m-80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1416 time to fit residues: 46.8951 Evaluate side-chains 167 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 225 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN C 392 ASN D 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033148 restraints weight = 192482.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033819 restraints weight = 142447.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034405 restraints weight = 113968.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.034653 restraints weight = 96381.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034966 restraints weight = 87549.620| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20728 Z= 0.142 Angle : 0.588 7.725 28036 Z= 0.303 Chirality : 0.043 0.196 3308 Planarity : 0.004 0.052 3632 Dihedral : 4.953 31.796 2872 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.17 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.16), residues: 2664 helix: 0.96 (0.15), residues: 1188 sheet: -1.77 (0.23), residues: 440 loop : -2.51 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 50 TYR 0.012 0.001 TYR C 157 PHE 0.011 0.001 PHE C 466 TRP 0.010 0.001 TRP D 748 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00292 (20728) covalent geometry : angle 0.58802 (28036) hydrogen bonds : bond 0.03231 ( 976) hydrogen bonds : angle 4.80691 ( 2724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9179 (mp) cc_final: 0.8932 (mt) REVERT: A 161 PHE cc_start: 0.9556 (m-80) cc_final: 0.9129 (m-80) REVERT: A 252 MET cc_start: 0.8689 (tpt) cc_final: 0.8412 (tpp) REVERT: A 271 MET cc_start: 0.9630 (ptp) cc_final: 0.9308 (ppp) REVERT: A 315 CYS cc_start: 0.9735 (p) cc_final: 0.9519 (p) REVERT: A 503 MET cc_start: 0.9648 (tpt) cc_final: 0.9421 (tpp) REVERT: A 559 HIS cc_start: 0.8866 (t-90) cc_final: 0.8492 (t70) REVERT: A 601 MET cc_start: 0.9161 (ptm) cc_final: 0.8290 (ppp) REVERT: A 677 TYR cc_start: 0.9613 (m-80) cc_final: 0.9285 (m-80) REVERT: B 91 CYS cc_start: 0.9852 (m) cc_final: 0.9601 (p) REVERT: B 153 LEU cc_start: 0.9570 (tt) cc_final: 0.9243 (pp) REVERT: B 154 MET cc_start: 0.9466 (mmm) cc_final: 0.9220 (mmm) REVERT: B 161 PHE cc_start: 0.9633 (m-80) cc_final: 0.9193 (m-80) REVERT: B 167 LYS cc_start: 0.9743 (mppt) cc_final: 0.9522 (mmtm) REVERT: B 252 MET cc_start: 0.8317 (tpt) cc_final: 0.8085 (tpp) REVERT: B 271 MET cc_start: 0.9594 (ptp) cc_final: 0.9122 (ppp) REVERT: B 315 CYS cc_start: 0.9764 (p) cc_final: 0.9541 (p) REVERT: B 559 HIS cc_start: 0.8968 (t-90) cc_final: 0.8660 (t-90) REVERT: B 601 MET cc_start: 0.9179 (ptm) cc_final: 0.8238 (ppp) REVERT: B 677 TYR cc_start: 0.9619 (m-80) cc_final: 0.9314 (m-80) REVERT: C 91 CYS cc_start: 0.9807 (m) cc_final: 0.9511 (p) REVERT: C 100 MET cc_start: 0.9662 (mtp) cc_final: 0.9324 (mmp) REVERT: C 161 PHE cc_start: 0.9490 (m-80) cc_final: 0.9112 (m-80) REVERT: C 167 LYS cc_start: 0.9713 (mppt) cc_final: 0.9498 (mmtm) REVERT: C 239 MET cc_start: 0.9362 (ppp) cc_final: 0.9151 (ppp) REVERT: C 254 ASP cc_start: 0.9542 (p0) cc_final: 0.8996 (m-30) REVERT: C 259 TYR cc_start: 0.9534 (m-10) cc_final: 0.9326 (m-80) REVERT: C 271 MET cc_start: 0.9647 (ptp) cc_final: 0.9366 (ppp) REVERT: C 318 MET cc_start: 0.9367 (mpp) cc_final: 0.9098 (mpp) REVERT: C 503 MET cc_start: 0.9646 (tpt) cc_final: 0.9407 (tpp) REVERT: C 559 HIS cc_start: 0.8893 (t-90) cc_final: 0.8497 (t70) REVERT: C 601 MET cc_start: 0.9187 (ptm) cc_final: 0.8189 (ppp) REVERT: C 677 TYR cc_start: 0.9633 (m-80) cc_final: 0.9284 (m-80) REVERT: D 100 MET cc_start: 0.9397 (ttm) cc_final: 0.9127 (ttt) REVERT: D 154 MET cc_start: 0.9572 (mmt) cc_final: 0.9308 (mmm) REVERT: D 161 PHE cc_start: 0.9607 (m-80) cc_final: 0.9085 (m-80) REVERT: D 315 CYS cc_start: 0.9735 (p) cc_final: 0.9510 (p) REVERT: D 503 MET cc_start: 0.9672 (tpt) cc_final: 0.9471 (tpp) REVERT: D 601 MET cc_start: 0.9202 (ptm) cc_final: 0.8254 (ppp) REVERT: D 677 TYR cc_start: 0.9612 (m-80) cc_final: 0.9308 (m-80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1437 time to fit residues: 45.7531 Evaluate side-chains 178 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 171 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 38 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN C 392 ASN D 392 ASN D 559 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.041912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.032352 restraints weight = 189164.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.033065 restraints weight = 140335.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033567 restraints weight = 112868.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.033981 restraints weight = 96803.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034304 restraints weight = 86271.880| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20728 Z= 0.142 Angle : 0.582 6.865 28036 Z= 0.299 Chirality : 0.042 0.170 3308 Planarity : 0.004 0.053 3632 Dihedral : 4.864 32.213 2872 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.70 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.16), residues: 2664 helix: 1.04 (0.15), residues: 1196 sheet: -1.50 (0.24), residues: 432 loop : -2.36 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.013 0.001 TYR A 573 PHE 0.012 0.001 PHE C 466 TRP 0.008 0.001 TRP D 748 HIS 0.006 0.001 HIS D 559 Details of bonding type rmsd covalent geometry : bond 0.00296 (20728) covalent geometry : angle 0.58163 (28036) hydrogen bonds : bond 0.03097 ( 976) hydrogen bonds : angle 4.70582 ( 2724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 PHE cc_start: 0.9564 (m-80) cc_final: 0.9079 (m-80) REVERT: A 239 MET cc_start: 0.9343 (ppp) cc_final: 0.9083 (ppp) REVERT: A 252 MET cc_start: 0.8713 (tpt) cc_final: 0.8418 (tpp) REVERT: A 271 MET cc_start: 0.9622 (ptp) cc_final: 0.9333 (ppp) REVERT: A 503 MET cc_start: 0.9612 (tpt) cc_final: 0.9356 (tpp) REVERT: A 601 MET cc_start: 0.9154 (ptm) cc_final: 0.8192 (ppp) REVERT: A 677 TYR cc_start: 0.9580 (m-80) cc_final: 0.9241 (m-80) REVERT: B 91 CYS cc_start: 0.9851 (m) cc_final: 0.9604 (p) REVERT: B 154 MET cc_start: 0.9476 (mmm) cc_final: 0.9052 (mmm) REVERT: B 161 PHE cc_start: 0.9613 (m-80) cc_final: 0.9093 (m-80) REVERT: B 167 LYS cc_start: 0.9747 (mppt) cc_final: 0.9524 (mmtm) REVERT: B 239 MET cc_start: 0.9437 (ppp) cc_final: 0.9231 (ppp) REVERT: B 252 MET cc_start: 0.8440 (tpt) cc_final: 0.8219 (tpp) REVERT: B 271 MET cc_start: 0.9543 (ptp) cc_final: 0.9055 (ppp) REVERT: B 503 MET cc_start: 0.9629 (tpt) cc_final: 0.9423 (tpp) REVERT: B 559 HIS cc_start: 0.8797 (t-90) cc_final: 0.8498 (t70) REVERT: B 601 MET cc_start: 0.9161 (ptm) cc_final: 0.8228 (ppp) REVERT: B 677 TYR cc_start: 0.9567 (m-80) cc_final: 0.9263 (m-80) REVERT: C 100 MET cc_start: 0.9675 (mtp) cc_final: 0.9375 (mmp) REVERT: C 161 PHE cc_start: 0.9440 (m-80) cc_final: 0.9050 (m-80) REVERT: C 167 LYS cc_start: 0.9710 (mppt) cc_final: 0.9476 (mmtm) REVERT: C 239 MET cc_start: 0.9380 (ppp) cc_final: 0.9165 (ppp) REVERT: C 254 ASP cc_start: 0.9502 (p0) cc_final: 0.8917 (m-30) REVERT: C 271 MET cc_start: 0.9654 (ptp) cc_final: 0.9393 (ppp) REVERT: C 318 MET cc_start: 0.9373 (mpp) cc_final: 0.9082 (mpp) REVERT: C 503 MET cc_start: 0.9604 (tpt) cc_final: 0.9365 (tpp) REVERT: C 559 HIS cc_start: 0.8878 (t-90) cc_final: 0.8534 (t70) REVERT: C 601 MET cc_start: 0.9200 (ptm) cc_final: 0.8200 (ppp) REVERT: C 677 TYR cc_start: 0.9596 (m-80) cc_final: 0.9261 (m-80) REVERT: D 100 MET cc_start: 0.9379 (ttm) cc_final: 0.9102 (ttt) REVERT: D 154 MET cc_start: 0.9577 (mmt) cc_final: 0.9153 (mmm) REVERT: D 161 PHE cc_start: 0.9614 (m-80) cc_final: 0.9071 (m-80) REVERT: D 315 CYS cc_start: 0.9825 (p) cc_final: 0.9625 (p) REVERT: D 503 MET cc_start: 0.9627 (tpt) cc_final: 0.9407 (tpp) REVERT: D 601 MET cc_start: 0.9237 (ptm) cc_final: 0.8271 (ppp) REVERT: D 677 TYR cc_start: 0.9576 (m-80) cc_final: 0.9221 (m-80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1386 time to fit residues: 44.8198 Evaluate side-chains 172 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 174 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 160 optimal weight: 0.6980 chunk 196 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 158 optimal weight: 0.0030 chunk 17 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 overall best weight: 4.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN C 392 ASN D 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.041684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.032117 restraints weight = 190177.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.032844 restraints weight = 139780.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.033357 restraints weight = 112268.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033653 restraints weight = 95630.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.033992 restraints weight = 86194.540| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20728 Z= 0.142 Angle : 0.586 7.383 28036 Z= 0.300 Chirality : 0.042 0.163 3308 Planarity : 0.004 0.055 3632 Dihedral : 4.830 32.353 2872 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.58 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2664 helix: 1.11 (0.15), residues: 1196 sheet: -1.32 (0.23), residues: 432 loop : -2.21 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.012 0.001 TYR C 573 PHE 0.011 0.001 PHE A 466 TRP 0.009 0.001 TRP D 748 HIS 0.010 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00290 (20728) covalent geometry : angle 0.58629 (28036) hydrogen bonds : bond 0.03068 ( 976) hydrogen bonds : angle 4.68168 ( 2724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9870 (tt) cc_final: 0.9602 (mp) REVERT: A 153 LEU cc_start: 0.9661 (tp) cc_final: 0.9446 (tp) REVERT: A 154 MET cc_start: 0.9304 (mmp) cc_final: 0.9027 (mmm) REVERT: A 157 TYR cc_start: 0.9848 (m-80) cc_final: 0.9414 (m-80) REVERT: A 161 PHE cc_start: 0.9578 (m-80) cc_final: 0.9244 (m-80) REVERT: A 239 MET cc_start: 0.9335 (ppp) cc_final: 0.9104 (ppp) REVERT: A 252 MET cc_start: 0.8712 (tpt) cc_final: 0.8402 (tpp) REVERT: A 271 MET cc_start: 0.9620 (ptp) cc_final: 0.9329 (ppp) REVERT: A 503 MET cc_start: 0.9616 (tpt) cc_final: 0.9363 (tpp) REVERT: A 601 MET cc_start: 0.9234 (ptm) cc_final: 0.8250 (ppp) REVERT: A 677 TYR cc_start: 0.9614 (m-80) cc_final: 0.9266 (m-80) REVERT: B 91 CYS cc_start: 0.9876 (m) cc_final: 0.9642 (p) REVERT: B 100 MET cc_start: 0.9452 (tpp) cc_final: 0.9251 (tpp) REVERT: B 161 PHE cc_start: 0.9609 (m-80) cc_final: 0.9106 (m-80) REVERT: B 167 LYS cc_start: 0.9748 (mppt) cc_final: 0.9534 (mmtm) REVERT: B 239 MET cc_start: 0.9409 (ppp) cc_final: 0.9188 (ppp) REVERT: B 252 MET cc_start: 0.8610 (tpt) cc_final: 0.8099 (tpt) REVERT: B 271 MET cc_start: 0.9540 (ptp) cc_final: 0.9056 (ppp) REVERT: B 559 HIS cc_start: 0.8884 (t-90) cc_final: 0.8450 (t70) REVERT: B 601 MET cc_start: 0.9188 (ptm) cc_final: 0.8258 (ppp) REVERT: B 677 TYR cc_start: 0.9602 (m-80) cc_final: 0.9269 (m-80) REVERT: C 91 CYS cc_start: 0.9817 (m) cc_final: 0.9574 (p) REVERT: C 100 MET cc_start: 0.9681 (mtp) cc_final: 0.9369 (mmp) REVERT: C 161 PHE cc_start: 0.9432 (m-80) cc_final: 0.8998 (m-80) REVERT: C 167 LYS cc_start: 0.9719 (mppt) cc_final: 0.9492 (mmtm) REVERT: C 239 MET cc_start: 0.9366 (ppp) cc_final: 0.9160 (ppp) REVERT: C 254 ASP cc_start: 0.9478 (p0) cc_final: 0.8875 (m-30) REVERT: C 271 MET cc_start: 0.9628 (ptp) cc_final: 0.9345 (ppp) REVERT: C 318 MET cc_start: 0.9364 (mpp) cc_final: 0.9095 (mpp) REVERT: C 503 MET cc_start: 0.9606 (tpt) cc_final: 0.9363 (tpp) REVERT: C 601 MET cc_start: 0.9284 (ptm) cc_final: 0.8333 (ppp) REVERT: C 677 TYR cc_start: 0.9627 (m-80) cc_final: 0.9287 (m-80) REVERT: D 78 LEU cc_start: 0.9876 (tt) cc_final: 0.9667 (mp) REVERT: D 100 MET cc_start: 0.9341 (ttm) cc_final: 0.9038 (ttt) REVERT: D 154 MET cc_start: 0.9556 (mmt) cc_final: 0.9227 (mmm) REVERT: D 161 PHE cc_start: 0.9620 (m-80) cc_final: 0.9032 (m-80) REVERT: D 252 MET cc_start: 0.8487 (tpt) cc_final: 0.8251 (tpp) REVERT: D 271 MET cc_start: 0.9240 (pmm) cc_final: 0.8948 (pmm) REVERT: D 503 MET cc_start: 0.9648 (tpt) cc_final: 0.9423 (tpp) REVERT: D 601 MET cc_start: 0.9286 (ptm) cc_final: 0.8394 (ppp) REVERT: D 677 TYR cc_start: 0.9593 (m-80) cc_final: 0.9235 (m-80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1319 time to fit residues: 42.7625 Evaluate side-chains 172 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 226 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 454 GLN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN C 392 ASN D 392 ASN D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.041559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.032161 restraints weight = 190898.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.032894 restraints weight = 139378.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033459 restraints weight = 110635.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.033888 restraints weight = 93315.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034088 restraints weight = 82940.034| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20728 Z= 0.143 Angle : 0.588 7.113 28036 Z= 0.300 Chirality : 0.042 0.158 3308 Planarity : 0.004 0.055 3632 Dihedral : 4.838 32.827 2872 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.66 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2664 helix: 1.10 (0.15), residues: 1200 sheet: -1.19 (0.23), residues: 432 loop : -2.19 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 50 TYR 0.013 0.001 TYR A 573 PHE 0.012 0.002 PHE D 466 TRP 0.009 0.001 TRP D 748 HIS 0.004 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00292 (20728) covalent geometry : angle 0.58801 (28036) hydrogen bonds : bond 0.03050 ( 976) hydrogen bonds : angle 4.68411 ( 2724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9869 (tt) cc_final: 0.9618 (mp) REVERT: A 153 LEU cc_start: 0.9674 (tp) cc_final: 0.9447 (tp) REVERT: A 154 MET cc_start: 0.9270 (mmp) cc_final: 0.8992 (mmm) REVERT: A 157 TYR cc_start: 0.9842 (m-80) cc_final: 0.9406 (m-80) REVERT: A 161 PHE cc_start: 0.9551 (m-80) cc_final: 0.9206 (m-80) REVERT: A 239 MET cc_start: 0.9296 (ppp) cc_final: 0.9059 (ppp) REVERT: A 252 MET cc_start: 0.8796 (tpt) cc_final: 0.8568 (tpp) REVERT: A 271 MET cc_start: 0.9619 (ptp) cc_final: 0.9286 (ppp) REVERT: A 315 CYS cc_start: 0.9872 (p) cc_final: 0.9668 (p) REVERT: A 503 MET cc_start: 0.9602 (tpt) cc_final: 0.9332 (tpp) REVERT: A 601 MET cc_start: 0.9241 (ptm) cc_final: 0.8322 (ppp) REVERT: A 677 TYR cc_start: 0.9591 (m-80) cc_final: 0.9242 (m-80) REVERT: B 78 LEU cc_start: 0.9872 (tt) cc_final: 0.9624 (mp) REVERT: B 91 CYS cc_start: 0.9863 (m) cc_final: 0.9628 (p) REVERT: B 100 MET cc_start: 0.9458 (tpp) cc_final: 0.9241 (tpp) REVERT: B 154 MET cc_start: 0.9258 (mmm) cc_final: 0.8975 (mmm) REVERT: B 161 PHE cc_start: 0.9607 (m-80) cc_final: 0.9071 (m-80) REVERT: B 167 LYS cc_start: 0.9751 (mppt) cc_final: 0.9537 (mmtm) REVERT: B 239 MET cc_start: 0.9399 (ppp) cc_final: 0.9174 (ppp) REVERT: B 252 MET cc_start: 0.8570 (tpt) cc_final: 0.8335 (tpp) REVERT: B 503 MET cc_start: 0.9638 (tpt) cc_final: 0.9378 (tpp) REVERT: B 559 HIS cc_start: 0.8767 (t-90) cc_final: 0.8293 (t70) REVERT: B 601 MET cc_start: 0.9230 (ptm) cc_final: 0.8391 (ppp) REVERT: B 677 TYR cc_start: 0.9575 (m-80) cc_final: 0.9252 (m-80) REVERT: C 100 MET cc_start: 0.9680 (mtp) cc_final: 0.9307 (mmp) REVERT: C 153 LEU cc_start: 0.9663 (tp) cc_final: 0.9446 (tp) REVERT: C 154 MET cc_start: 0.9339 (mmp) cc_final: 0.8997 (mmm) REVERT: C 157 TYR cc_start: 0.9833 (m-80) cc_final: 0.9370 (m-80) REVERT: C 161 PHE cc_start: 0.9421 (m-80) cc_final: 0.9160 (m-80) REVERT: C 167 LYS cc_start: 0.9722 (mppt) cc_final: 0.9489 (mmtm) REVERT: C 239 MET cc_start: 0.9322 (ppp) cc_final: 0.9107 (ppp) REVERT: C 254 ASP cc_start: 0.9466 (p0) cc_final: 0.8843 (m-30) REVERT: C 271 MET cc_start: 0.9631 (ptp) cc_final: 0.9349 (ppp) REVERT: C 318 MET cc_start: 0.9340 (mpp) cc_final: 0.9085 (mpp) REVERT: C 503 MET cc_start: 0.9593 (tpt) cc_final: 0.9324 (tpp) REVERT: C 601 MET cc_start: 0.9279 (ptm) cc_final: 0.8399 (ppp) REVERT: C 677 TYR cc_start: 0.9603 (m-80) cc_final: 0.9257 (m-80) REVERT: D 154 MET cc_start: 0.9539 (mmt) cc_final: 0.9219 (mmm) REVERT: D 161 PHE cc_start: 0.9619 (m-80) cc_final: 0.9074 (m-80) REVERT: D 239 MET cc_start: 0.9410 (ppp) cc_final: 0.9190 (ppp) REVERT: D 252 MET cc_start: 0.8430 (tpt) cc_final: 0.8139 (tpp) REVERT: D 271 MET cc_start: 0.9180 (pmm) cc_final: 0.8930 (pmm) REVERT: D 503 MET cc_start: 0.9632 (tpt) cc_final: 0.9367 (tpp) REVERT: D 601 MET cc_start: 0.9278 (ptm) cc_final: 0.8355 (ppp) REVERT: D 677 TYR cc_start: 0.9552 (m-80) cc_final: 0.9221 (m-80) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1412 time to fit residues: 45.5579 Evaluate side-chains 174 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 219 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 230 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 242 optimal weight: 40.0000 chunk 125 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 392 ASN B 454 GLN ** B 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 454 GLN D 392 ASN ** D 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.028207 restraints weight = 195671.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.028778 restraints weight = 140479.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029286 restraints weight = 112565.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029682 restraints weight = 95432.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.030004 restraints weight = 85373.744| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20728 Z= 0.235 Angle : 0.665 7.288 28036 Z= 0.346 Chirality : 0.043 0.154 3308 Planarity : 0.004 0.054 3632 Dihedral : 5.225 34.755 2872 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2664 helix: 0.88 (0.15), residues: 1192 sheet: -1.32 (0.23), residues: 440 loop : -2.12 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 50 TYR 0.017 0.002 TYR A 573 PHE 0.016 0.002 PHE B 466 TRP 0.008 0.002 TRP B 304 HIS 0.006 0.002 HIS D 652 Details of bonding type rmsd covalent geometry : bond 0.00455 (20728) covalent geometry : angle 0.66500 (28036) hydrogen bonds : bond 0.03514 ( 976) hydrogen bonds : angle 4.97101 ( 2724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.9879 (tt) cc_final: 0.9646 (mp) REVERT: A 154 MET cc_start: 0.9322 (mmp) cc_final: 0.9040 (mmm) REVERT: A 157 TYR cc_start: 0.9804 (m-80) cc_final: 0.9426 (m-80) REVERT: A 161 PHE cc_start: 0.9582 (m-80) cc_final: 0.9259 (m-80) REVERT: A 239 MET cc_start: 0.9321 (ppp) cc_final: 0.9101 (ppp) REVERT: A 252 MET cc_start: 0.8701 (tpt) cc_final: 0.8220 (tpt) REVERT: A 362 MET cc_start: 0.9541 (ppp) cc_final: 0.9277 (ppp) REVERT: A 503 MET cc_start: 0.9654 (tpt) cc_final: 0.9392 (tpp) REVERT: A 601 MET cc_start: 0.9320 (ptm) cc_final: 0.8533 (ppp) REVERT: A 677 TYR cc_start: 0.9613 (m-80) cc_final: 0.9251 (m-80) REVERT: B 78 LEU cc_start: 0.9883 (tt) cc_final: 0.9645 (mp) REVERT: B 91 CYS cc_start: 0.9885 (m) cc_final: 0.9642 (p) REVERT: B 154 MET cc_start: 0.9362 (mmm) cc_final: 0.9071 (mmm) REVERT: B 161 PHE cc_start: 0.9633 (m-80) cc_final: 0.9133 (m-80) REVERT: B 252 MET cc_start: 0.8781 (tpt) cc_final: 0.8121 (tpt) REVERT: B 503 MET cc_start: 0.9671 (tpt) cc_final: 0.9422 (tpp) REVERT: B 525 ARG cc_start: 0.9611 (mmt180) cc_final: 0.8919 (mmp80) REVERT: B 601 MET cc_start: 0.9317 (ptm) cc_final: 0.8538 (ppp) REVERT: B 677 TYR cc_start: 0.9629 (m-80) cc_final: 0.9262 (m-80) REVERT: C 63 LEU cc_start: 0.8911 (mp) cc_final: 0.8655 (mt) REVERT: C 78 LEU cc_start: 0.9880 (tt) cc_final: 0.9626 (mp) REVERT: C 91 CYS cc_start: 0.9796 (m) cc_final: 0.9588 (p) REVERT: C 154 MET cc_start: 0.9374 (mmp) cc_final: 0.9051 (mmm) REVERT: C 157 TYR cc_start: 0.9809 (m-80) cc_final: 0.9411 (m-80) REVERT: C 161 PHE cc_start: 0.9450 (m-80) cc_final: 0.9219 (m-80) REVERT: C 167 LYS cc_start: 0.9736 (mppt) cc_final: 0.9514 (mmtm) REVERT: C 239 MET cc_start: 0.9335 (ppp) cc_final: 0.9124 (ppp) REVERT: C 254 ASP cc_start: 0.9481 (p0) cc_final: 0.8895 (m-30) REVERT: C 318 MET cc_start: 0.9239 (mpp) cc_final: 0.9019 (mpp) REVERT: C 362 MET cc_start: 0.9523 (ppp) cc_final: 0.9296 (ppp) REVERT: C 503 MET cc_start: 0.9641 (tpt) cc_final: 0.9385 (tpp) REVERT: C 601 MET cc_start: 0.9324 (ptm) cc_final: 0.8577 (ppp) REVERT: C 677 TYR cc_start: 0.9629 (m-80) cc_final: 0.9268 (m-80) REVERT: D 154 MET cc_start: 0.9553 (mmt) cc_final: 0.9211 (mmm) REVERT: D 161 PHE cc_start: 0.9647 (m-80) cc_final: 0.9063 (m-80) REVERT: D 239 MET cc_start: 0.9385 (ppp) cc_final: 0.9177 (ppp) REVERT: D 271 MET cc_start: 0.9241 (pmm) cc_final: 0.8982 (pmm) REVERT: D 503 MET cc_start: 0.9665 (tpt) cc_final: 0.9407 (tpp) REVERT: D 601 MET cc_start: 0.9357 (ptm) cc_final: 0.8589 (ppp) REVERT: D 677 TYR cc_start: 0.9612 (m-80) cc_final: 0.9237 (m-80) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1295 time to fit residues: 42.4401 Evaluate side-chains 169 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 204 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN B 392 ASN C 392 ASN ** C 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 ASN D 392 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.028318 restraints weight = 192305.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.028909 restraints weight = 138383.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029427 restraints weight = 110861.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029808 restraints weight = 93940.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.030131 restraints weight = 84118.080| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20728 Z= 0.182 Angle : 0.629 8.981 28036 Z= 0.323 Chirality : 0.043 0.161 3308 Planarity : 0.004 0.054 3632 Dihedral : 5.133 34.470 2872 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.73 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2664 helix: 0.81 (0.15), residues: 1216 sheet: -1.17 (0.23), residues: 440 loop : -2.07 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 50 TYR 0.013 0.002 TYR D 157 PHE 0.013 0.002 PHE D 466 TRP 0.009 0.002 TRP B 304 HIS 0.007 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00365 (20728) covalent geometry : angle 0.62938 (28036) hydrogen bonds : bond 0.03314 ( 976) hydrogen bonds : angle 4.86514 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.08 seconds wall clock time: 49 minutes 7.59 seconds (2947.59 seconds total)