Starting phenix.real_space_refine on Tue Sep 15 02:44:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.cif Found real_map, /net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5zsu_6952/09_2026/5zsu_6952.map" } resolution = 4.25 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= 0.001 sd= 0.008 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 144 5.16 5 C 22779 2.51 5 N 5889 2.21 5 O 6147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.15s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34959 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5843 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 27, 'TRANS': 679} Chain breaks: 2 Chain: "B" Number of atoms: 5810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5810 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 27, 'TRANS': 674} Chain breaks: 2 Restraints were copied for chains: C, E, D, F Time building chain proxies: 12.06, per 1000 atoms: 0.34 Number of scatterers: 34959 At special positions: 0 Unit cell: (150.49, 144.53, 193.7, 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 144 16.00 O 6147 8.00 N 5889 7.00 C 22779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.04 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.04 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8196 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 12 sheets defined 52.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 145 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 234 through 255 removed outlier: 3.627A pdb=" N GLU A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 287 removed outlier: 4.774A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.555A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.510A pdb=" N ALA A 466 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.789A pdb=" N PHE A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.510A pdb=" N LEU A 540 " --> pdb=" O ILE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.508A pdb=" N VAL A 565 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 566 " --> pdb=" O THR A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 566' Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.738A pdb=" N LEU A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE A 610 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 611 " --> pdb=" O HIS A 608 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.509A pdb=" N PHE A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 659 " --> pdb=" O ILE A 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 655 through 659' Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.507A pdb=" N LEU A 681 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 682 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 705 removed outlier: 3.502A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.507A pdb=" N LEU A 727 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 728 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A 730 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL A 750 " --> pdb=" O PRO A 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.503A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 786 removed outlier: 3.511A pdb=" N VAL A 786 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 794 through 806 Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 145 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 233 through 254 removed outlier: 3.685A pdb=" N GLY B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 286 removed outlier: 3.683A pdb=" N TYR B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA B 466 " --> pdb=" O PRO B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 3.677A pdb=" N PHE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU B 540 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP B 564 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 565 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 566 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE B 610 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 611 " --> pdb=" O HIS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.505A pdb=" N PHE B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.504A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU B 681 " --> pdb=" O PRO B 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 682 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 removed outlier: 3.506A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.510A pdb=" N LEU B 727 " --> pdb=" O PRO B 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 728 " --> pdb=" O PRO B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 775 " --> pdb=" O GLU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 786 Processing helix chain 'B' and resid 787 through 793 Processing helix chain 'B' and resid 794 through 806 Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 124 through 145 Processing helix chain 'C' and resid 146 through 166 Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.626A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 287 removed outlier: 4.775A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.556A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 Processing helix chain 'C' and resid 395 through 410 Processing helix chain 'C' and resid 412 through 418 Processing helix chain 'C' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.510A pdb=" N ALA C 466 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 3.788A pdb=" N PHE C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 493 " --> pdb=" O ALA C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 536 " --> pdb=" O ASN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.511A pdb=" N LEU C 540 " --> pdb=" O ILE C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 removed outlier: 3.509A pdb=" N VAL C 565 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 566 " --> pdb=" O THR C 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 566' Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.739A pdb=" N LEU C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET C 590 " --> pdb=" O SER C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 613 removed outlier: 3.504A pdb=" N ILE C 610 " --> pdb=" O PRO C 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 611 " --> pdb=" O HIS C 608 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 612 " --> pdb=" O SER C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.508A pdb=" N PHE C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 638 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE C 658 " --> pdb=" O PRO C 655 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 659 " --> pdb=" O ILE C 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 655 through 659' Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.506A pdb=" N LEU C 681 " --> pdb=" O PRO C 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 682 " --> pdb=" O THR C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.503A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 730 removed outlier: 3.508A pdb=" N LEU C 727 " --> pdb=" O PRO C 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 728 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL C 750 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.502A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 786 removed outlier: 3.511A pdb=" N VAL C 786 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 Processing helix chain 'C' and resid 794 through 806 Processing helix chain 'D' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 145 Proline residue: D 126 - end of helix Processing helix chain 'D' and resid 146 through 166 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 233 through 254 removed outlier: 3.686A pdb=" N GLY D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 286 removed outlier: 3.685A pdb=" N TYR D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 Processing helix chain 'D' and resid 412 through 419 Processing helix chain 'D' and resid 441 through 445 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA D 466 " --> pdb=" O PRO D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.678A pdb=" N PHE D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.501A pdb=" N TYR D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU D 540 " --> pdb=" O ILE D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP D 564 " --> pdb=" O VAL D 561 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 565 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 566 " --> pdb=" O THR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE D 610 " --> pdb=" O PRO D 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 611 " --> pdb=" O HIS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 638 removed outlier: 3.507A pdb=" N PHE D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE D 658 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU D 681 " --> pdb=" O PRO D 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE D 682 " --> pdb=" O THR D 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 683 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 705 removed outlier: 3.504A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 3.510A pdb=" N LEU D 727 " --> pdb=" O PRO D 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 728 " --> pdb=" O PRO D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL D 750 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU D 773 " --> pdb=" O PRO D 770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 775 " --> pdb=" O GLU D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 786 Processing helix chain 'D' and resid 787 through 793 Processing helix chain 'D' and resid 794 through 806 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 124 through 145 Processing helix chain 'E' and resid 146 through 166 Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.627A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 287 removed outlier: 4.774A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 350 through 363 Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.556A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 395 Processing helix chain 'E' and resid 395 through 410 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 441 through 445 removed outlier: 3.506A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.509A pdb=" N ALA E 466 " --> pdb=" O PRO E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 493 removed outlier: 3.788A pdb=" N PHE E 490 " --> pdb=" O PRO E 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 493 " --> pdb=" O ALA E 489 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 536 removed outlier: 3.503A pdb=" N ILE E 535 " --> pdb=" O ASN E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.511A pdb=" N LEU E 540 " --> pdb=" O ILE E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 removed outlier: 3.509A pdb=" N VAL E 565 " --> pdb=" O VAL E 562 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY E 566 " --> pdb=" O THR E 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 562 through 566' Processing helix chain 'E' and resid 583 through 590 removed outlier: 3.739A pdb=" N LEU E 587 " --> pdb=" O VAL E 583 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 613 removed outlier: 3.503A pdb=" N ILE E 610 " --> pdb=" O PRO E 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 611 " --> pdb=" O HIS E 608 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 612 " --> pdb=" O SER E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 removed outlier: 3.508A pdb=" N PHE E 635 " --> pdb=" O GLU E 631 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 637 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 638 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE E 658 " --> pdb=" O PRO E 655 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY E 659 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 655 through 659' Processing helix chain 'E' and resid 678 through 684 removed outlier: 3.506A pdb=" N LEU E 681 " --> pdb=" O PRO E 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 682 " --> pdb=" O THR E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 705 removed outlier: 3.502A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.508A pdb=" N LEU E 727 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE E 728 " --> pdb=" O PRO E 725 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 730 " --> pdb=" O LEU E 727 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 removed outlier: 3.509A pdb=" N VAL E 750 " --> pdb=" O PRO E 747 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 753 " --> pdb=" O VAL E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 775 removed outlier: 3.502A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 782 through 786 removed outlier: 3.512A pdb=" N VAL E 786 " --> pdb=" O GLY E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 Processing helix chain 'E' and resid 794 through 806 Processing helix chain 'F' and resid 22 through 50 removed outlier: 3.681A pdb=" N ASP F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 Processing helix chain 'F' and resid 119 through 145 Proline residue: F 126 - end of helix Processing helix chain 'F' and resid 146 through 166 Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 233 through 254 removed outlier: 3.685A pdb=" N GLY F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 286 removed outlier: 3.685A pdb=" N TYR F 261 " --> pdb=" O GLY F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 395 removed outlier: 3.516A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'F' and resid 441 through 445 Processing helix chain 'F' and resid 462 through 468 removed outlier: 3.504A pdb=" N ALA F 466 " --> pdb=" O PRO F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.677A pdb=" N PHE F 490 " --> pdb=" O PRO F 486 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 493 " --> pdb=" O ALA F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.501A pdb=" N TYR F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.505A pdb=" N LEU F 540 " --> pdb=" O ILE F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 566 removed outlier: 3.507A pdb=" N ASP F 564 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 565 " --> pdb=" O VAL F 562 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 566 " --> pdb=" O THR F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 588 Processing helix chain 'F' and resid 607 through 613 removed outlier: 3.502A pdb=" N ILE F 610 " --> pdb=" O PRO F 607 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 611 " --> pdb=" O HIS F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 638 removed outlier: 3.506A pdb=" N PHE F 635 " --> pdb=" O GLU F 631 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 638 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 659 removed outlier: 3.505A pdb=" N ILE F 658 " --> pdb=" O PRO F 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 684 removed outlier: 3.503A pdb=" N LEU F 681 " --> pdb=" O PRO F 678 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE F 682 " --> pdb=" O THR F 679 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR F 683 " --> pdb=" O GLN F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 705 removed outlier: 3.505A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 730 removed outlier: 3.509A pdb=" N LEU F 727 " --> pdb=" O PRO F 724 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 728 " --> pdb=" O PRO F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.506A pdb=" N VAL F 750 " --> pdb=" O PRO F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 775 removed outlier: 3.508A pdb=" N LEU F 773 " --> pdb=" O PRO F 770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 775 " --> pdb=" O GLU F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 782 through 786 Processing helix chain 'F' and resid 787 through 793 Processing helix chain 'F' and resid 794 through 806 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.644A pdb=" N THR A 307 " --> pdb=" O CYS A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.412A pdb=" N LEU A 451 " --> pdb=" O TRP A 475 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 596 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 690 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.536A pdb=" N LEU B 428 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 596 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 690 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 57 removed outlier: 4.643A pdb=" N THR C 307 " --> pdb=" O CYS C 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 427 through 429 removed outlier: 6.412A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 596 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 690 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 57 removed outlier: 4.820A pdb=" N THR D 307 " --> pdb=" O CYS D 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 427 through 429 removed outlier: 6.537A pdb=" N LEU D 428 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU D 451 " --> pdb=" O TRP D 475 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 596 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 690 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 4.643A pdb=" N THR E 307 " --> pdb=" O CYS E 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 427 through 429 removed outlier: 6.413A pdb=" N LEU E 451 " --> pdb=" O TRP E 475 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 596 " --> pdb=" O ASP E 620 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 removed outlier: 4.820A pdb=" N THR F 307 " --> pdb=" O CYS F 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 427 through 429 removed outlier: 6.537A pdb=" N LEU F 428 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU F 451 " --> pdb=" O TRP F 475 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU F 596 " --> pdb=" O ASP F 620 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU F 690 " --> pdb=" O ALA F 714 " (cutoff:3.500A) 1550 hydrogen bonds defined for protein. 4308 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: 6.93 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10810 1.34 - 1.46: 7908 1.46 - 1.58: 16829 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 35745 Sorted by residual: bond pdb=" C HIS D 312 " pdb=" N PRO D 313 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.79e+00 bond pdb=" C HIS C 312 " pdb=" N PRO C 313 " ideal model delta sigma weight residual 1.334 1.310 0.023 8.40e-03 1.42e+04 7.59e+00 bond pdb=" C HIS F 312 " pdb=" N PRO F 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.37e+00 bond pdb=" C HIS A 312 " pdb=" N PRO A 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.26e+00 bond pdb=" C HIS B 312 " pdb=" N PRO B 313 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.22e+00 ... (remaining 35740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 47125 2.95 - 5.89: 1115 5.89 - 8.84: 173 8.84 - 11.78: 28 11.78 - 14.73: 12 Bond angle restraints: 48453 Sorted by residual: angle pdb=" CA TYR E 477 " pdb=" CB TYR E 477 " pdb=" CG TYR E 477 " ideal model delta sigma weight residual 113.90 122.54 -8.64 1.80e+00 3.09e-01 2.31e+01 angle pdb=" CA TYR A 477 " pdb=" CB TYR A 477 " pdb=" CG TYR A 477 " ideal model delta sigma weight residual 113.90 122.53 -8.63 1.80e+00 3.09e-01 2.30e+01 angle pdb=" CA TYR C 477 " pdb=" CB TYR C 477 " pdb=" CG TYR C 477 " ideal model delta sigma weight residual 113.90 122.51 -8.61 1.80e+00 3.09e-01 2.29e+01 angle pdb=" C LEU D 430 " pdb=" N HIS D 431 " pdb=" CA HIS D 431 " ideal model delta sigma weight residual 121.97 129.44 -7.47 1.73e+00 3.34e-01 1.87e+01 angle pdb=" C LEU B 430 " pdb=" N HIS B 431 " pdb=" CA HIS B 431 " ideal model delta sigma weight residual 121.97 129.40 -7.43 1.73e+00 3.34e-01 1.85e+01 ... (remaining 48448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 19952 14.85 - 29.71: 1303 29.71 - 44.56: 336 44.56 - 59.41: 27 59.41 - 74.27: 9 Dihedral angle restraints: 21627 sinusoidal: 9048 harmonic: 12579 Sorted by residual: dihedral pdb=" CA ASP C 371 " pdb=" C ASP C 371 " pdb=" N PHE C 372 " pdb=" CA PHE C 372 " ideal model delta harmonic sigma weight residual -180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ASP A 371 " pdb=" C ASP A 371 " pdb=" N PHE A 372 " pdb=" CA PHE A 372 " ideal model delta harmonic sigma weight residual 180.00 -136.44 -43.56 0 5.00e+00 4.00e-02 7.59e+01 dihedral pdb=" CA ASP E 371 " pdb=" C ASP E 371 " pdb=" N PHE E 372 " pdb=" CA PHE E 372 " ideal model delta harmonic sigma weight residual -180.00 -136.47 -43.53 0 5.00e+00 4.00e-02 7.58e+01 ... (remaining 21624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4072 0.059 - 0.119: 1199 0.119 - 0.178: 258 0.178 - 0.238: 54 0.238 - 0.297: 15 Chirality restraints: 5598 Sorted by residual: chirality pdb=" CB ILE D 715 " pdb=" CA ILE D 715 " pdb=" CG1 ILE D 715 " pdb=" CG2 ILE D 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE B 715 " pdb=" CA ILE B 715 " pdb=" CG1 ILE B 715 " pdb=" CG2 ILE B 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE F 715 " pdb=" CA ILE F 715 " pdb=" CG1 ILE F 715 " pdb=" CG2 ILE F 715 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 5595 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 456 " -0.054 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO E 457 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 457 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 457 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 456 " 0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO A 457 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 456 " 0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 457 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 457 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 457 " 0.045 5.00e-02 4.00e+02 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9287 2.81 - 3.33: 33307 3.33 - 3.85: 59074 3.85 - 4.38: 67959 4.38 - 4.90: 109594 Nonbonded interactions: 279221 Sorted by model distance: nonbonded pdb=" O LYS D 249 " pdb=" OG1 THR D 252 " model vdw 2.286 3.040 nonbonded pdb=" O LYS B 249 " pdb=" OG1 THR B 252 " model vdw 2.286 3.040 nonbonded pdb=" O LYS F 249 " pdb=" OG1 THR F 252 " model vdw 2.287 3.040 nonbonded pdb=" O PRO B 147 " pdb=" OG SER B 150 " model vdw 2.309 3.040 nonbonded pdb=" O PRO F 147 " pdb=" OG SER F 150 " model vdw 2.309 3.040 ... (remaining 279216 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 34.790 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.006 0.076 35757 Z= 0.292 Angle : 1.137 14.728 48477 Z= 0.591 Chirality : 0.060 0.297 5598 Planarity : 0.007 0.083 5994 Dihedral : 10.785 74.266 13395 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 0.76 % Allowed : 5.42 % Favored : 93.82 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.45 (0.10), residues: 4191 helix: -2.93 (0.08), residues: 1992 sheet: -2.48 (0.21), residues: 465 loop : -2.95 (0.13), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 688 TYR 0.045 0.003 TYR C 477 PHE 0.025 0.003 PHE F 353 TRP 0.044 0.004 TRP E 647 HIS 0.030 0.004 HIS F 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (35745) covalent geometry : angle 1.13659 / 0.59 (48453) SS BOND : bond 0.00418 / 0.25 ( 12) SS BOND : angle 1.37661 / 1.09 ( 24) hydrogen bonds : bond 0.20807 / 13.35 ( 1550) hydrogen bonds : angle 10.84327 / 7.52 ( 4308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 919 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8607 (mt) cc_final: 0.8352 (mm) REVERT: A 233 ASP cc_start: 0.8479 (m-30) cc_final: 0.7950 (t0) REVERT: A 402 LEU cc_start: 0.8619 (tm) cc_final: 0.8159 (tp) REVERT: A 473 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7636 (tt0) REVERT: A 476 LEU cc_start: 0.8988 (mt) cc_final: 0.8419 (pp) REVERT: A 518 LEU cc_start: 0.8942 (tp) cc_final: 0.8537 (tp) REVERT: A 592 ASN cc_start: 0.7953 (m-40) cc_final: 0.7680 (t0) REVERT: A 593 LEU cc_start: 0.8813 (tp) cc_final: 0.8530 (tp) REVERT: A 595 GLU cc_start: 0.8502 (tt0) cc_final: 0.7168 (tm-30) REVERT: A 654 ILE cc_start: 0.7705 (mt) cc_final: 0.7452 (mm) REVERT: A 707 LEU cc_start: 0.8852 (mt) cc_final: 0.8387 (tp) REVERT: A 758 GLN cc_start: 0.8719 (mt0) cc_final: 0.8503 (pp30) REVERT: B 35 MET cc_start: 0.8004 (ttm) cc_final: 0.7681 (ttm) REVERT: B 115 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8155 (tm-30) REVERT: B 255 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7753 (mp0) REVERT: B 280 CYS cc_start: 0.8698 (m) cc_final: 0.8195 (t) REVERT: B 321 LEU cc_start: 0.8911 (pp) cc_final: 0.8316 (mp) REVERT: B 367 ASP cc_start: 0.7169 (m-30) cc_final: 0.6338 (t0) REVERT: B 473 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7103 (mp0) REVERT: B 482 LYS cc_start: 0.8188 (mttt) cc_final: 0.7711 (tppt) REVERT: B 492 ARG cc_start: 0.8821 (mtt180) cc_final: 0.8536 (mtm110) REVERT: B 622 LYS cc_start: 0.8181 (mttt) cc_final: 0.7894 (mttp) REVERT: B 623 ASP cc_start: 0.8361 (m-30) cc_final: 0.8090 (t0) REVERT: B 629 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5506 (mt) REVERT: B 689 TYR cc_start: 0.6608 (t80) cc_final: 0.6223 (t80) REVERT: B 694 HIS cc_start: 0.7858 (t-90) cc_final: 0.7469 (t-90) REVERT: B 707 LEU cc_start: 0.8384 (mt) cc_final: 0.7956 (tp) REVERT: B 716 THR cc_start: 0.7590 (t) cc_final: 0.5898 (m) REVERT: C 101 LEU cc_start: 0.8728 (mt) cc_final: 0.8416 (mm) REVERT: C 128 LEU cc_start: 0.9304 (mt) cc_final: 0.8991 (tt) REVERT: C 394 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7054 (tt) REVERT: C 402 LEU cc_start: 0.8413 (tm) cc_final: 0.8015 (tp) REVERT: C 414 ASP cc_start: 0.8388 (m-30) cc_final: 0.7945 (p0) REVERT: C 476 LEU cc_start: 0.9001 (mt) cc_final: 0.8614 (pp) REVERT: C 495 LEU cc_start: 0.9135 (pp) cc_final: 0.8796 (mp) REVERT: C 498 LEU cc_start: 0.9127 (tp) cc_final: 0.8560 (tp) REVERT: C 515 LEU cc_start: 0.8989 (pt) cc_final: 0.8693 (pp) REVERT: C 518 LEU cc_start: 0.8674 (tp) cc_final: 0.8353 (tp) REVERT: C 543 LEU cc_start: 0.7940 (mp) cc_final: 0.7530 (mp) REVERT: C 658 ILE cc_start: 0.8864 (tt) cc_final: 0.8656 (pt) REVERT: C 799 LYS cc_start: 0.8939 (mttt) cc_final: 0.8713 (mmmt) REVERT: D 52 MET cc_start: 0.7804 (ttm) cc_final: 0.7281 (ttp) REVERT: D 102 ASP cc_start: 0.8210 (t0) cc_final: 0.7962 (t0) REVERT: D 115 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8236 (tm-30) REVERT: D 124 TYR cc_start: 0.8744 (m-80) cc_final: 0.8002 (m-80) REVERT: D 367 ASP cc_start: 0.7110 (m-30) cc_final: 0.6682 (t70) REVERT: D 455 LEU cc_start: 0.8421 (mt) cc_final: 0.8018 (mt) REVERT: D 473 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7120 (mp0) REVERT: D 474 LEU cc_start: 0.8898 (tp) cc_final: 0.8645 (tp) REVERT: D 482 LYS cc_start: 0.7915 (mttt) cc_final: 0.7379 (tppt) REVERT: D 500 ILE cc_start: 0.8944 (mp) cc_final: 0.8727 (mm) REVERT: D 571 LYS cc_start: 0.8473 (mttt) cc_final: 0.7797 (mtmm) REVERT: D 623 ASP cc_start: 0.8165 (m-30) cc_final: 0.7724 (t0) REVERT: D 629 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5723 (mt) REVERT: D 635 PHE cc_start: 0.7992 (m-80) cc_final: 0.7686 (m-80) REVERT: D 668 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7654 (m-10) REVERT: D 689 TYR cc_start: 0.6538 (t80) cc_final: 0.6236 (t80) REVERT: D 707 LEU cc_start: 0.8603 (mt) cc_final: 0.8164 (tp) REVERT: D 788 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7965 (tp30) REVERT: E 337 MET cc_start: 0.8453 (tmm) cc_final: 0.8169 (tmm) REVERT: E 402 LEU cc_start: 0.8286 (tm) cc_final: 0.7777 (tp) REVERT: E 448 LEU cc_start: 0.9087 (tp) cc_final: 0.8882 (tp) REVERT: E 473 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7580 (mp0) REVERT: E 476 LEU cc_start: 0.8995 (mt) cc_final: 0.8543 (pp) REVERT: E 482 LYS cc_start: 0.8715 (mttt) cc_final: 0.8418 (tptp) REVERT: E 498 LEU cc_start: 0.9109 (tp) cc_final: 0.8736 (tp) REVERT: E 518 LEU cc_start: 0.8888 (tp) cc_final: 0.8201 (tp) REVERT: E 543 LEU cc_start: 0.8164 (mp) cc_final: 0.7948 (mp) REVERT: F 35 MET cc_start: 0.8296 (ttm) cc_final: 0.7956 (ttp) REVERT: F 115 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 336 CYS cc_start: 0.8139 (m) cc_final: 0.7747 (m) REVERT: F 343 MET cc_start: 0.8001 (mmp) cc_final: 0.7639 (tpp) REVERT: F 473 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7226 (mp0) REVERT: F 476 LEU cc_start: 0.9060 (mt) cc_final: 0.8781 (pp) REVERT: F 482 LYS cc_start: 0.7608 (mttt) cc_final: 0.7006 (tppt) REVERT: F 492 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8366 (ttp-110) REVERT: F 623 ASP cc_start: 0.8571 (m-30) cc_final: 0.8213 (t0) REVERT: F 629 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.6095 (mt) REVERT: F 689 TYR cc_start: 0.6926 (t80) cc_final: 0.6601 (t80) REVERT: F 707 LEU cc_start: 0.8498 (mt) cc_final: 0.8051 (tp) REVERT: F 788 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8082 (tp30) outliers start: 30 outliers final: 1 residues processed: 940 average time/residue: 0.2367 time to fit residues: 351.9244 Evaluate side-chains 527 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 521 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 615 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 ASN A 744 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 HIS B 709 ASN B 718 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN C 615 ASN C 695 ASN C 709 ASN C 718 ASN C 744 GLN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 614 HIS D 650 HIS D 709 ASN D 718 ASN ** D 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN E 408 ASN E 592 ASN E 615 ASN ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN E 718 ASN E 744 GLN ** F 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 HIS ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN F 526 ASN F 614 HIS F 708 GLN F 709 ASN F 718 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.111285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086531 restraints weight = 101598.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088332 restraints weight = 58715.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088056 restraints weight = 35270.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088262 restraints weight = 35817.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.088441 restraints weight = 32076.297| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35757 Z= 0.198 Angle : 0.818 11.390 48477 Z= 0.427 Chirality : 0.047 0.242 5598 Planarity : 0.006 0.068 5994 Dihedral : 6.634 40.017 4617 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.10 (0.12), residues: 4191 helix: -1.69 (0.10), residues: 2103 sheet: -1.65 (0.22), residues: 468 loop : -2.52 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 804 TYR 0.032 0.002 TYR C 281 PHE 0.038 0.002 PHE E 164 TRP 0.040 0.002 TRP A 168 HIS 0.029 0.002 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (35745) covalent geometry : angle 0.81791 / 0.43 (48453) SS BOND : bond 0.00254 / 0.17 ( 12) SS BOND : angle 1.16294 / 0.79 ( 24) hydrogen bonds : bond 0.06953 / 4.52 ( 1550) hydrogen bonds : angle 6.55048 / 4.53 ( 4308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 640 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 157 VAL cc_start: 0.8562 (m) cc_final: 0.8349 (p) REVERT: A 170 THR cc_start: 0.8570 (m) cc_final: 0.8284 (m) REVERT: A 332 TYR cc_start: 0.8985 (t80) cc_final: 0.8544 (t80) REVERT: A 402 LEU cc_start: 0.8635 (tt) cc_final: 0.8017 (tp) REVERT: A 498 LEU cc_start: 0.9149 (tp) cc_final: 0.8764 (tp) REVERT: A 518 LEU cc_start: 0.8856 (tp) cc_final: 0.8539 (tp) REVERT: A 520 GLU cc_start: 0.8216 (pt0) cc_final: 0.7908 (pt0) REVERT: A 593 LEU cc_start: 0.9139 (tp) cc_final: 0.8893 (tt) REVERT: A 654 ILE cc_start: 0.7767 (mt) cc_final: 0.7426 (mm) REVERT: A 707 LEU cc_start: 0.8725 (mt) cc_final: 0.8254 (tp) REVERT: B 35 MET cc_start: 0.8030 (ttm) cc_final: 0.7683 (ttm) REVERT: B 367 ASP cc_start: 0.6882 (m-30) cc_final: 0.6539 (t0) REVERT: B 374 PHE cc_start: 0.6454 (t80) cc_final: 0.6019 (t80) REVERT: B 448 LEU cc_start: 0.8317 (tp) cc_final: 0.8103 (tp) REVERT: B 473 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7043 (mp0) REVERT: B 482 LYS cc_start: 0.8220 (mttt) cc_final: 0.7538 (tppt) REVERT: B 501 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7646 (mtmt) REVERT: B 694 HIS cc_start: 0.7383 (t-90) cc_final: 0.7150 (t-90) REVERT: B 707 LEU cc_start: 0.8473 (mt) cc_final: 0.7788 (tp) REVERT: C 128 LEU cc_start: 0.9373 (mt) cc_final: 0.9152 (tt) REVERT: C 332 TYR cc_start: 0.8911 (t80) cc_final: 0.8471 (t80) REVERT: C 402 LEU cc_start: 0.8451 (tt) cc_final: 0.7747 (tt) REVERT: C 414 ASP cc_start: 0.8325 (m-30) cc_final: 0.7829 (p0) REVERT: C 498 LEU cc_start: 0.9194 (tp) cc_final: 0.8789 (tp) REVERT: C 518 LEU cc_start: 0.8614 (tp) cc_final: 0.8182 (tp) REVERT: C 543 LEU cc_start: 0.8053 (mp) cc_final: 0.7769 (mp) REVERT: C 546 LEU cc_start: 0.8299 (mm) cc_final: 0.7762 (mm) REVERT: C 574 ILE cc_start: 0.8368 (mp) cc_final: 0.8136 (mp) REVERT: C 799 LYS cc_start: 0.9150 (mttt) cc_final: 0.8949 (mmmt) REVERT: D 292 ASP cc_start: 0.7939 (p0) cc_final: 0.7730 (p0) REVERT: D 374 PHE cc_start: 0.6609 (t80) cc_final: 0.6148 (t80) REVERT: D 428 LEU cc_start: 0.7694 (mm) cc_final: 0.7310 (mm) REVERT: D 473 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6796 (mp0) REVERT: D 482 LYS cc_start: 0.7768 (mttt) cc_final: 0.7312 (tppt) REVERT: D 576 ASN cc_start: 0.8011 (m-40) cc_final: 0.7607 (t0) REVERT: D 623 ASP cc_start: 0.7626 (m-30) cc_final: 0.7161 (t0) REVERT: D 635 PHE cc_start: 0.7795 (m-80) cc_final: 0.7406 (m-80) REVERT: D 788 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7919 (tp30) REVERT: E 52 MET cc_start: 0.8413 (ttp) cc_final: 0.7010 (ttm) REVERT: E 337 MET cc_start: 0.7991 (tmm) cc_final: 0.7682 (tmm) REVERT: E 402 LEU cc_start: 0.8472 (tt) cc_final: 0.8065 (tt) REVERT: E 434 MET cc_start: 0.7916 (tpp) cc_final: 0.7707 (tpp) REVERT: E 476 LEU cc_start: 0.8802 (mt) cc_final: 0.8514 (tt) REVERT: E 498 LEU cc_start: 0.9245 (tp) cc_final: 0.8923 (tp) REVERT: E 518 LEU cc_start: 0.8794 (tp) cc_final: 0.8293 (tp) REVERT: E 574 ILE cc_start: 0.8359 (mp) cc_final: 0.8147 (mp) REVERT: F 161 LEU cc_start: 0.8460 (tp) cc_final: 0.8093 (pp) REVERT: F 332 TYR cc_start: 0.8809 (t80) cc_final: 0.8098 (t80) REVERT: F 336 CYS cc_start: 0.8250 (m) cc_final: 0.7602 (m) REVERT: F 374 PHE cc_start: 0.7456 (t80) cc_final: 0.7114 (t80) REVERT: F 428 LEU cc_start: 0.8047 (mm) cc_final: 0.7608 (mm) REVERT: F 455 LEU cc_start: 0.8592 (mt) cc_final: 0.8375 (mt) REVERT: F 473 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6859 (mp0) REVERT: F 482 LYS cc_start: 0.7589 (mttt) cc_final: 0.6960 (tppt) REVERT: F 500 ILE cc_start: 0.9138 (mt) cc_final: 0.8895 (mm) REVERT: F 501 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8544 (mtpp) REVERT: F 534 TYR cc_start: 0.7891 (m-10) cc_final: 0.6644 (m-10) REVERT: F 635 PHE cc_start: 0.7730 (m-80) cc_final: 0.7510 (m-80) REVERT: F 762 ARG cc_start: 0.8892 (tpt170) cc_final: 0.8125 (tpm170) REVERT: F 788 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8107 (tp30) outliers start: 3 outliers final: 0 residues processed: 643 average time/residue: 0.2265 time to fit residues: 237.2566 Evaluate side-chains 436 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 389 optimal weight: 10.0000 chunk 402 optimal weight: 0.0370 chunk 235 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 378 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 overall best weight: 4.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 695 ASN A 709 ASN B 132 HIS B 253 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 HIS ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN C 624 ASN C 744 GLN ** C 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 155 HIS ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS E 624 ASN E 695 ASN F 132 HIS F 253 HIS F 288 ASN F 312 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 608 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080486 restraints weight = 103199.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.082781 restraints weight = 56131.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083406 restraints weight = 32588.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083788 restraints weight = 28568.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083915 restraints weight = 23728.533| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35757 Z= 0.263 Angle : 0.869 13.838 48477 Z= 0.449 Chirality : 0.050 0.300 5598 Planarity : 0.005 0.061 5994 Dihedral : 6.460 41.505 4617 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.18 % Allowed : 6.26 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.73 (0.12), residues: 4191 helix: -1.34 (0.10), residues: 2091 sheet: -1.29 (0.23), residues: 468 loop : -2.47 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 765 TYR 0.033 0.003 TYR D 477 PHE 0.034 0.003 PHE E 164 TRP 0.032 0.003 TRP E 647 HIS 0.018 0.002 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.26 (35745) covalent geometry : angle 0.86794 / 0.45 (48453) SS BOND : bond 0.00435 / 0.26 ( 12) SS BOND : angle 2.19884 / 1.37 ( 24) hydrogen bonds : bond 0.06904 / 4.49 ( 1550) hydrogen bonds : angle 6.04466 / 4.19 ( 4308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 507 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 55 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 265 MET cc_start: 0.7512 (mmp) cc_final: 0.6938 (tpp) REVERT: A 402 LEU cc_start: 0.8887 (tt) cc_final: 0.7644 (tt) REVERT: A 498 LEU cc_start: 0.9211 (tp) cc_final: 0.9001 (tp) REVERT: A 520 GLU cc_start: 0.8213 (pt0) cc_final: 0.7870 (pt0) REVERT: A 654 ILE cc_start: 0.7854 (mt) cc_final: 0.7242 (mm) REVERT: A 689 TYR cc_start: 0.7639 (t80) cc_final: 0.7337 (t80) REVERT: A 707 LEU cc_start: 0.8884 (mt) cc_final: 0.8392 (tp) REVERT: B 25 ASP cc_start: 0.8731 (m-30) cc_final: 0.8187 (t70) REVERT: B 37 MET cc_start: 0.7889 (tmm) cc_final: 0.7528 (tmm) REVERT: B 367 ASP cc_start: 0.6840 (m-30) cc_final: 0.6318 (t0) REVERT: B 448 LEU cc_start: 0.8404 (tp) cc_final: 0.8200 (mm) REVERT: B 482 LYS cc_start: 0.8441 (mttt) cc_final: 0.7840 (tppt) REVERT: B 576 ASN cc_start: 0.7452 (m-40) cc_final: 0.7224 (m110) REVERT: B 590 MET cc_start: 0.5047 (mmp) cc_final: 0.4147 (tpp) REVERT: B 623 ASP cc_start: 0.7627 (t0) cc_final: 0.7270 (t0) REVERT: B 635 PHE cc_start: 0.7596 (m-80) cc_final: 0.7126 (m-80) REVERT: B 694 HIS cc_start: 0.7232 (t-90) cc_final: 0.6912 (t-90) REVERT: B 707 LEU cc_start: 0.8578 (mt) cc_final: 0.7744 (tp) REVERT: B 762 ARG cc_start: 0.8401 (tpm170) cc_final: 0.8068 (tpm170) REVERT: C 52 MET cc_start: 0.7657 (ttp) cc_final: 0.6826 (ttm) REVERT: C 128 LEU cc_start: 0.9502 (mt) cc_final: 0.9296 (tp) REVERT: C 169 THR cc_start: 0.8412 (p) cc_final: 0.8030 (p) REVERT: C 265 MET cc_start: 0.8459 (mmm) cc_final: 0.7927 (tpp) REVERT: C 402 LEU cc_start: 0.8851 (tt) cc_final: 0.8438 (tp) REVERT: C 498 LEU cc_start: 0.9232 (tp) cc_final: 0.8823 (tp) REVERT: C 518 LEU cc_start: 0.8630 (tp) cc_final: 0.8382 (tp) REVERT: C 653 TYR cc_start: 0.6826 (t80) cc_final: 0.6282 (t80) REVERT: C 654 ILE cc_start: 0.7781 (mm) cc_final: 0.7568 (mm) REVERT: C 799 LYS cc_start: 0.9169 (mttt) cc_final: 0.8941 (mmmt) REVERT: D 25 ASP cc_start: 0.8732 (m-30) cc_final: 0.8272 (t70) REVERT: D 375 MET cc_start: 0.8274 (ptp) cc_final: 0.7962 (ptt) REVERT: D 433 PHE cc_start: 0.7273 (m-10) cc_final: 0.6756 (m-10) REVERT: D 455 LEU cc_start: 0.8116 (mt) cc_final: 0.7897 (mt) REVERT: D 473 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6977 (mp0) REVERT: D 482 LYS cc_start: 0.7630 (mttt) cc_final: 0.7375 (tppt) REVERT: D 635 PHE cc_start: 0.7753 (m-80) cc_final: 0.7436 (m-80) REVERT: D 707 LEU cc_start: 0.8726 (mt) cc_final: 0.8103 (tp) REVERT: D 762 ARG cc_start: 0.8937 (tpm170) cc_final: 0.8514 (tpm170) REVERT: D 788 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8031 (tp30) REVERT: E 337 MET cc_start: 0.8131 (tmm) cc_final: 0.7901 (tmm) REVERT: E 402 LEU cc_start: 0.8903 (tt) cc_final: 0.8518 (tt) REVERT: E 476 LEU cc_start: 0.8916 (mt) cc_final: 0.8570 (tt) REVERT: E 574 ILE cc_start: 0.8524 (mp) cc_final: 0.8209 (mp) REVERT: E 654 ILE cc_start: 0.7767 (mm) cc_final: 0.7194 (mm) REVERT: E 689 TYR cc_start: 0.7927 (t80) cc_final: 0.7589 (t80) REVERT: F 25 ASP cc_start: 0.8720 (m-30) cc_final: 0.8508 (t70) REVERT: F 161 LEU cc_start: 0.8574 (tp) cc_final: 0.8224 (pp) REVERT: F 332 TYR cc_start: 0.8950 (t80) cc_final: 0.8742 (t80) REVERT: F 336 CYS cc_start: 0.8395 (m) cc_final: 0.8015 (m) REVERT: F 374 PHE cc_start: 0.7941 (t80) cc_final: 0.7223 (t80) REVERT: F 473 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6691 (mp0) REVERT: F 482 LYS cc_start: 0.7693 (mttt) cc_final: 0.7102 (tppt) REVERT: F 501 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8519 (mtpp) REVERT: F 683 TYR cc_start: 0.7451 (t80) cc_final: 0.7223 (t80) REVERT: F 707 LEU cc_start: 0.8718 (mp) cc_final: 0.7985 (tp) REVERT: F 762 ARG cc_start: 0.9178 (tpt170) cc_final: 0.8320 (tpm170) outliers start: 7 outliers final: 5 residues processed: 512 average time/residue: 0.2118 time to fit residues: 182.3767 Evaluate side-chains 390 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 384 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 358 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 385 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 300 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 387 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 184 optimal weight: 0.0470 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS A 312 HIS ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 370 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 132 HIS D 155 HIS D 288 ASN D 370 ASN D 708 GLN E 116 ASN E 312 HIS ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084022 restraints weight = 100908.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086410 restraints weight = 55577.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.086913 restraints weight = 36819.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.087642 restraints weight = 27074.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087765 restraints weight = 22617.054| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35757 Z= 0.144 Angle : 0.743 10.618 48477 Z= 0.380 Chirality : 0.046 0.255 5598 Planarity : 0.004 0.056 5994 Dihedral : 6.036 35.906 4617 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.35 (0.12), residues: 4191 helix: -1.00 (0.11), residues: 2097 sheet: -1.15 (0.24), residues: 468 loop : -2.31 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 749 TYR 0.032 0.002 TYR E 477 PHE 0.059 0.002 PHE D 250 TRP 0.030 0.002 TRP C 168 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (35745) covalent geometry : angle 0.74115 / 0.38 (48453) SS BOND : bond 0.00233 / 0.15 ( 12) SS BOND : angle 2.30265 / 1.38 ( 24) hydrogen bonds : bond 0.05911 / 3.84 ( 1550) hydrogen bonds : angle 5.50350 / 3.81 ( 4308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 544 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.8502 (m) cc_final: 0.8287 (p) REVERT: A 265 MET cc_start: 0.7279 (mmp) cc_final: 0.6719 (tpp) REVERT: A 402 LEU cc_start: 0.8783 (tt) cc_final: 0.7630 (tt) REVERT: A 414 ASP cc_start: 0.8433 (m-30) cc_final: 0.8181 (m-30) REVERT: A 498 LEU cc_start: 0.9222 (tp) cc_final: 0.8926 (tp) REVERT: A 520 GLU cc_start: 0.8103 (pt0) cc_final: 0.7787 (pt0) REVERT: A 654 ILE cc_start: 0.7824 (mt) cc_final: 0.7223 (mm) REVERT: A 707 LEU cc_start: 0.8732 (mt) cc_final: 0.8385 (tp) REVERT: B 25 ASP cc_start: 0.8362 (m-30) cc_final: 0.8016 (t70) REVERT: B 35 MET cc_start: 0.7794 (ttm) cc_final: 0.7380 (ttp) REVERT: B 420 LEU cc_start: 0.7459 (mt) cc_final: 0.7252 (pt) REVERT: B 482 LYS cc_start: 0.8258 (mttt) cc_final: 0.7676 (tppt) REVERT: B 576 ASN cc_start: 0.7847 (m-40) cc_final: 0.7624 (m110) REVERT: B 590 MET cc_start: 0.5144 (mmp) cc_final: 0.4560 (tpt) REVERT: B 623 ASP cc_start: 0.7176 (t0) cc_final: 0.6870 (t0) REVERT: B 635 PHE cc_start: 0.7932 (m-80) cc_final: 0.7574 (m-80) REVERT: B 694 HIS cc_start: 0.7328 (t-90) cc_final: 0.7038 (t-90) REVERT: B 704 ILE cc_start: 0.7560 (pt) cc_final: 0.7355 (pt) REVERT: B 707 LEU cc_start: 0.8541 (mt) cc_final: 0.7726 (tp) REVERT: B 762 ARG cc_start: 0.8386 (tpm170) cc_final: 0.8029 (tpm170) REVERT: C 128 LEU cc_start: 0.9238 (mt) cc_final: 0.8981 (tt) REVERT: C 402 LEU cc_start: 0.8609 (tt) cc_final: 0.7391 (tt) REVERT: C 414 ASP cc_start: 0.8517 (m-30) cc_final: 0.8103 (p0) REVERT: C 498 LEU cc_start: 0.9187 (tp) cc_final: 0.8940 (tp) REVERT: C 518 LEU cc_start: 0.8598 (tp) cc_final: 0.8390 (tp) REVERT: C 571 LYS cc_start: 0.8466 (mttt) cc_final: 0.8190 (mppt) REVERT: D 25 ASP cc_start: 0.8359 (m-30) cc_final: 0.8072 (t70) REVERT: D 115 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8281 (tm-30) REVERT: D 428 LEU cc_start: 0.7690 (mm) cc_final: 0.7240 (mm) REVERT: D 482 LYS cc_start: 0.7563 (mttt) cc_final: 0.7252 (tppt) REVERT: D 590 MET cc_start: 0.6634 (tpt) cc_final: 0.5866 (tpp) REVERT: D 623 ASP cc_start: 0.7051 (t0) cc_final: 0.6581 (t0) REVERT: D 635 PHE cc_start: 0.7834 (m-80) cc_final: 0.7587 (m-80) REVERT: D 762 ARG cc_start: 0.8853 (tpm170) cc_final: 0.8502 (tpm170) REVERT: D 788 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7843 (tp30) REVERT: E 128 LEU cc_start: 0.9313 (tt) cc_final: 0.8996 (tt) REVERT: E 160 LEU cc_start: 0.7523 (tp) cc_final: 0.7309 (tp) REVERT: E 265 MET cc_start: 0.7288 (mmp) cc_final: 0.6849 (tpp) REVERT: E 337 MET cc_start: 0.8126 (tmm) cc_final: 0.7925 (tmm) REVERT: E 574 ILE cc_start: 0.8303 (mp) cc_final: 0.7978 (mp) REVERT: E 654 ILE cc_start: 0.7950 (mm) cc_final: 0.7460 (mm) REVERT: F 161 LEU cc_start: 0.8549 (tp) cc_final: 0.8192 (pp) REVERT: F 374 PHE cc_start: 0.7543 (t80) cc_final: 0.7032 (t80) REVERT: F 428 LEU cc_start: 0.7730 (mm) cc_final: 0.7369 (mm) REVERT: F 473 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6627 (mp0) REVERT: F 482 LYS cc_start: 0.7673 (mttt) cc_final: 0.7085 (tppt) REVERT: F 501 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8424 (mtpp) REVERT: F 552 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7655 (tmtt) REVERT: F 576 ASN cc_start: 0.7710 (m-40) cc_final: 0.7213 (m110) REVERT: F 590 MET cc_start: 0.6736 (tpt) cc_final: 0.6171 (tpp) REVERT: F 623 ASP cc_start: 0.7556 (t0) cc_final: 0.7094 (t0) REVERT: F 635 PHE cc_start: 0.7581 (m-80) cc_final: 0.7374 (m-80) REVERT: F 707 LEU cc_start: 0.8575 (mp) cc_final: 0.7806 (tp) REVERT: F 762 ARG cc_start: 0.9221 (tpt170) cc_final: 0.8267 (tpm170) outliers start: 4 outliers final: 0 residues processed: 547 average time/residue: 0.1972 time to fit residues: 182.9778 Evaluate side-chains 395 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 184 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 335 optimal weight: 10.0000 chunk 408 optimal weight: 10.0000 chunk 387 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 695 ASN C 312 HIS D 132 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.110528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084869 restraints weight = 102199.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086683 restraints weight = 58348.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.087141 restraints weight = 34408.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087455 restraints weight = 29502.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087530 restraints weight = 28178.955| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 35757 Z= 0.147 Angle : 0.728 10.561 48477 Z= 0.369 Chirality : 0.045 0.202 5598 Planarity : 0.004 0.053 5994 Dihedral : 5.809 34.713 4617 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.05 % Allowed : 3.26 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.11 (0.13), residues: 4191 helix: -0.83 (0.11), residues: 2094 sheet: -0.97 (0.24), residues: 483 loop : -2.20 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 671 TYR 0.033 0.002 TYR B 477 PHE 0.031 0.002 PHE E 164 TRP 0.022 0.001 TRP E 647 HIS 0.009 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (35745) covalent geometry : angle 0.72719 / 0.37 (48453) SS BOND : bond 0.00362 / 0.15 ( 12) SS BOND : angle 1.68579 / 1.04 ( 24) hydrogen bonds : bond 0.05605 / 3.62 ( 1550) hydrogen bonds : angle 5.29553 / 3.66 ( 4308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 531 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 265 MET cc_start: 0.7384 (mmp) cc_final: 0.6846 (tpp) REVERT: A 414 ASP cc_start: 0.8593 (m-30) cc_final: 0.8351 (m-30) REVERT: A 448 LEU cc_start: 0.8964 (mp) cc_final: 0.8730 (mp) REVERT: A 468 LEU cc_start: 0.8123 (mp) cc_final: 0.7773 (mt) REVERT: A 498 LEU cc_start: 0.9234 (tp) cc_final: 0.8949 (tp) REVERT: A 520 GLU cc_start: 0.8079 (pt0) cc_final: 0.7771 (pt0) REVERT: A 654 ILE cc_start: 0.7894 (mt) cc_final: 0.7258 (mm) REVERT: A 707 LEU cc_start: 0.8813 (mt) cc_final: 0.8340 (tp) REVERT: B 25 ASP cc_start: 0.8377 (m-30) cc_final: 0.8046 (t70) REVERT: B 35 MET cc_start: 0.8234 (ttm) cc_final: 0.7757 (ttp) REVERT: B 337 MET cc_start: 0.7657 (ttt) cc_final: 0.7405 (tmm) REVERT: B 427 LYS cc_start: 0.6937 (mttm) cc_final: 0.6502 (mttp) REVERT: B 482 LYS cc_start: 0.8327 (mttt) cc_final: 0.7764 (tppt) REVERT: B 501 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8205 (mtpt) REVERT: B 576 ASN cc_start: 0.7955 (m-40) cc_final: 0.7720 (m110) REVERT: B 590 MET cc_start: 0.5027 (mmp) cc_final: 0.4592 (tpp) REVERT: B 623 ASP cc_start: 0.7200 (t0) cc_final: 0.6901 (t0) REVERT: B 635 PHE cc_start: 0.7958 (m-80) cc_final: 0.7619 (m-80) REVERT: B 694 HIS cc_start: 0.7735 (t-90) cc_final: 0.7368 (t70) REVERT: B 707 LEU cc_start: 0.8553 (mt) cc_final: 0.7742 (tp) REVERT: B 762 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7988 (tpm170) REVERT: C 128 LEU cc_start: 0.9302 (mt) cc_final: 0.9081 (tt) REVERT: C 265 MET cc_start: 0.8256 (mmm) cc_final: 0.7884 (tpp) REVERT: C 321 LEU cc_start: 0.8870 (pp) cc_final: 0.8301 (mt) REVERT: C 402 LEU cc_start: 0.8682 (tt) cc_final: 0.7498 (tt) REVERT: C 498 LEU cc_start: 0.9169 (tp) cc_final: 0.8857 (tp) REVERT: C 518 LEU cc_start: 0.8664 (tp) cc_final: 0.8436 (tp) REVERT: C 654 ILE cc_start: 0.7814 (mm) cc_final: 0.7463 (mm) REVERT: D 25 ASP cc_start: 0.8428 (m-30) cc_final: 0.8143 (t70) REVERT: D 428 LEU cc_start: 0.7780 (mm) cc_final: 0.7385 (mm) REVERT: D 433 PHE cc_start: 0.7128 (m-10) cc_final: 0.6505 (m-10) REVERT: D 482 LYS cc_start: 0.7536 (mttt) cc_final: 0.7202 (tppt) REVERT: D 501 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7762 (mtmt) REVERT: D 576 ASN cc_start: 0.7836 (m-40) cc_final: 0.7301 (t0) REVERT: D 590 MET cc_start: 0.6571 (tpt) cc_final: 0.5846 (tpp) REVERT: D 623 ASP cc_start: 0.7246 (t0) cc_final: 0.6732 (t0) REVERT: D 635 PHE cc_start: 0.7843 (m-80) cc_final: 0.7636 (m-80) REVERT: D 707 LEU cc_start: 0.8638 (mt) cc_final: 0.8220 (tp) REVERT: D 762 ARG cc_start: 0.8698 (tpm170) cc_final: 0.8246 (tpm170) REVERT: D 788 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7867 (tp30) REVERT: E 128 LEU cc_start: 0.9234 (tt) cc_final: 0.8848 (tt) REVERT: E 161 LEU cc_start: 0.7858 (mm) cc_final: 0.7577 (pp) REVERT: E 283 VAL cc_start: 0.9262 (t) cc_final: 0.9043 (p) REVERT: E 337 MET cc_start: 0.8072 (tmm) cc_final: 0.7824 (tmm) REVERT: E 402 LEU cc_start: 0.8601 (tt) cc_final: 0.8329 (tp) REVERT: E 574 ILE cc_start: 0.8357 (mp) cc_final: 0.8157 (mp) REVERT: E 654 ILE cc_start: 0.7979 (mm) cc_final: 0.7469 (mm) REVERT: F 35 MET cc_start: 0.8075 (ttm) cc_final: 0.7708 (ttp) REVERT: F 332 TYR cc_start: 0.8749 (t80) cc_final: 0.8281 (t80) REVERT: F 337 MET cc_start: 0.7707 (tmm) cc_final: 0.7361 (tmm) REVERT: F 374 PHE cc_start: 0.7143 (t80) cc_final: 0.6823 (t80) REVERT: F 428 LEU cc_start: 0.7814 (mm) cc_final: 0.7375 (mm) REVERT: F 433 PHE cc_start: 0.7381 (m-10) cc_final: 0.7019 (m-10) REVERT: F 474 LEU cc_start: 0.9068 (tp) cc_final: 0.8539 (tp) REVERT: F 482 LYS cc_start: 0.7639 (mttt) cc_final: 0.7090 (tppt) REVERT: F 501 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8369 (mtpp) REVERT: F 576 ASN cc_start: 0.7690 (m-40) cc_final: 0.7249 (m110) REVERT: F 590 MET cc_start: 0.6483 (tpt) cc_final: 0.6177 (tpp) REVERT: F 623 ASP cc_start: 0.7917 (t0) cc_final: 0.7580 (t0) REVERT: F 707 LEU cc_start: 0.8431 (mp) cc_final: 0.7679 (tp) REVERT: F 762 ARG cc_start: 0.9181 (tpt170) cc_final: 0.8239 (tpm170) outliers start: 2 outliers final: 0 residues processed: 533 average time/residue: 0.2069 time to fit residues: 186.2174 Evaluate side-chains 389 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 339 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 376 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 ASN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 712 ASN ** F 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 526 ASN F 532 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.108686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082070 restraints weight = 102149.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.084071 restraints weight = 58136.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.084591 restraints weight = 33944.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084852 restraints weight = 28578.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085089 restraints weight = 27447.599| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35757 Z= 0.191 Angle : 0.770 11.531 48477 Z= 0.394 Chirality : 0.047 0.197 5598 Planarity : 0.004 0.054 5994 Dihedral : 5.797 35.247 4617 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % 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: -2.10 (0.13), residues: 4191 helix: -0.81 (0.11), residues: 2091 sheet: -1.13 (0.24), residues: 498 loop : -2.15 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 671 TYR 0.034 0.002 TYR A 325 PHE 0.028 0.002 PHE E 164 TRP 0.024 0.002 TRP E 647 HIS 0.013 0.002 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (35745) covalent geometry : angle 0.76839 / 0.39 (48453) SS BOND : bond 0.00396 / 0.21 ( 12) SS BOND : angle 2.02986 / 1.31 ( 24) hydrogen bonds : bond 0.05869 / 3.80 ( 1550) hydrogen bonds : angle 5.30353 / 3.67 ( 4308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 1.317 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: A 128 LEU cc_start: 0.9450 (tp) cc_final: 0.9072 (tp) REVERT: A 265 MET cc_start: 0.7628 (mmp) cc_final: 0.7061 (tpp) REVERT: A 283 VAL cc_start: 0.9281 (t) cc_final: 0.9042 (p) REVERT: A 414 ASP cc_start: 0.8639 (m-30) cc_final: 0.8399 (m-30) REVERT: A 498 LEU cc_start: 0.9199 (tp) cc_final: 0.8922 (tp) REVERT: A 520 GLU cc_start: 0.8242 (pt0) cc_final: 0.7973 (pt0) REVERT: A 571 LYS cc_start: 0.8502 (mttt) cc_final: 0.8256 (mtpt) REVERT: A 654 ILE cc_start: 0.7979 (mt) cc_final: 0.7316 (mm) REVERT: A 707 LEU cc_start: 0.8897 (mt) cc_final: 0.8483 (tp) REVERT: A 758 GLN cc_start: 0.7674 (pp30) cc_final: 0.7327 (pp30) REVERT: B 35 MET cc_start: 0.8281 (ttm) cc_final: 0.7990 (ttp) REVERT: B 128 LEU cc_start: 0.9356 (tt) cc_final: 0.8871 (tt) REVERT: B 374 PHE cc_start: 0.8114 (t80) cc_final: 0.7909 (t80) REVERT: B 474 LEU cc_start: 0.8796 (tp) cc_final: 0.8525 (tp) REVERT: B 482 LYS cc_start: 0.8407 (mttt) cc_final: 0.7820 (mmmt) REVERT: B 501 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8219 (mtpt) REVERT: B 590 MET cc_start: 0.5094 (mmp) cc_final: 0.4681 (tpp) REVERT: B 623 ASP cc_start: 0.7168 (t0) cc_final: 0.6963 (t0) REVERT: B 635 PHE cc_start: 0.8072 (m-80) cc_final: 0.7786 (m-80) REVERT: B 694 HIS cc_start: 0.7434 (t-90) cc_final: 0.7139 (t-90) REVERT: B 707 LEU cc_start: 0.8561 (mt) cc_final: 0.7680 (tp) REVERT: B 762 ARG cc_start: 0.8434 (tpm170) cc_final: 0.8011 (tpm170) REVERT: C 128 LEU cc_start: 0.9399 (mt) cc_final: 0.9034 (tt) REVERT: C 265 MET cc_start: 0.8256 (mmm) cc_final: 0.7696 (tpp) REVERT: C 402 LEU cc_start: 0.8709 (tt) cc_final: 0.7531 (tt) REVERT: C 498 LEU cc_start: 0.9167 (tp) cc_final: 0.8844 (tp) REVERT: C 654 ILE cc_start: 0.7868 (mm) cc_final: 0.7520 (mm) REVERT: D 25 ASP cc_start: 0.8647 (m-30) cc_final: 0.8332 (t70) REVERT: D 37 MET cc_start: 0.8113 (ttp) cc_final: 0.7736 (tmm) REVERT: D 427 LYS cc_start: 0.7263 (mppt) cc_final: 0.7006 (mppt) REVERT: D 482 LYS cc_start: 0.7587 (mttt) cc_final: 0.7293 (tppt) REVERT: D 501 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7792 (mtmt) REVERT: D 590 MET cc_start: 0.6206 (tpt) cc_final: 0.5337 (tpp) REVERT: D 623 ASP cc_start: 0.7359 (t0) cc_final: 0.6766 (t0) REVERT: D 635 PHE cc_start: 0.8070 (m-80) cc_final: 0.7852 (m-80) REVERT: D 704 ILE cc_start: 0.7658 (pt) cc_final: 0.7437 (pt) REVERT: D 707 LEU cc_start: 0.8697 (mt) cc_final: 0.8292 (tp) REVERT: D 762 ARG cc_start: 0.8393 (tpm170) cc_final: 0.8186 (tpm170) REVERT: D 788 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7942 (tp30) REVERT: E 161 LEU cc_start: 0.8006 (mm) cc_final: 0.7631 (pp) REVERT: E 265 MET cc_start: 0.6992 (mmp) cc_final: 0.6748 (tpp) REVERT: E 337 MET cc_start: 0.8023 (tmm) cc_final: 0.7804 (tmm) REVERT: E 402 LEU cc_start: 0.8673 (tt) cc_final: 0.8272 (tp) REVERT: E 414 ASP cc_start: 0.8372 (m-30) cc_final: 0.8110 (m-30) REVERT: E 571 LYS cc_start: 0.8519 (mttt) cc_final: 0.8285 (mttm) REVERT: E 574 ILE cc_start: 0.8416 (mp) cc_final: 0.8115 (mp) REVERT: E 654 ILE cc_start: 0.7981 (mm) cc_final: 0.7435 (mm) REVERT: F 35 MET cc_start: 0.8162 (ttm) cc_final: 0.7828 (ttp) REVERT: F 337 MET cc_start: 0.7513 (tmm) cc_final: 0.7189 (tmm) REVERT: F 374 PHE cc_start: 0.7485 (t80) cc_final: 0.7088 (t80) REVERT: F 428 LEU cc_start: 0.7892 (mm) cc_final: 0.7572 (mm) REVERT: F 482 LYS cc_start: 0.7610 (mttt) cc_final: 0.7134 (tppt) REVERT: F 501 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8300 (mtpp) REVERT: F 576 ASN cc_start: 0.8084 (m-40) cc_final: 0.7870 (m110) REVERT: F 623 ASP cc_start: 0.7895 (t0) cc_final: 0.7678 (t0) REVERT: F 645 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7885 (mmmm) REVERT: F 707 LEU cc_start: 0.8536 (mp) cc_final: 0.7780 (tp) REVERT: F 762 ARG cc_start: 0.9094 (tpt170) cc_final: 0.8248 (tpm170) outliers start: 1 outliers final: 1 residues processed: 493 average time/residue: 0.2002 time to fit residues: 167.8354 Evaluate side-chains 379 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 262 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 96 optimal weight: 0.0670 chunk 236 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 239 GLN B 288 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.110056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.083826 restraints weight = 102040.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085558 restraints weight = 57623.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086202 restraints weight = 32229.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.086458 restraints weight = 28439.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086635 restraints weight = 26152.497| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35757 Z= 0.149 Angle : 0.732 10.805 48477 Z= 0.370 Chirality : 0.046 0.209 5598 Planarity : 0.004 0.056 5994 Dihedral : 5.657 33.630 4617 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.03 % Allowed : 1.93 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.99 (0.13), residues: 4191 helix: -0.69 (0.11), residues: 2085 sheet: -1.10 (0.25), residues: 477 loop : -2.11 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 671 TYR 0.036 0.002 TYR D 477 PHE 0.029 0.002 PHE D 250 TRP 0.025 0.002 TRP E 647 HIS 0.013 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (35745) covalent geometry : angle 0.73146 / 0.37 (48453) SS BOND : bond 0.00309 / 0.17 ( 12) SS BOND : angle 1.68566 / 1.05 ( 24) hydrogen bonds : bond 0.05555 / 3.60 ( 1550) hydrogen bonds : angle 5.14067 / 3.56 ( 4308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 1.413 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: A 265 MET cc_start: 0.7528 (mmp) cc_final: 0.6972 (tpp) REVERT: A 283 VAL cc_start: 0.9240 (t) cc_final: 0.8981 (p) REVERT: A 332 TYR cc_start: 0.8941 (t80) cc_final: 0.8027 (t80) REVERT: A 414 ASP cc_start: 0.8644 (m-30) cc_final: 0.8402 (m-30) REVERT: A 498 LEU cc_start: 0.9202 (tp) cc_final: 0.8895 (tp) REVERT: A 520 GLU cc_start: 0.8080 (pt0) cc_final: 0.7773 (pt0) REVERT: A 654 ILE cc_start: 0.7956 (mt) cc_final: 0.7291 (mm) REVERT: A 707 LEU cc_start: 0.8791 (mt) cc_final: 0.8381 (tp) REVERT: A 758 GLN cc_start: 0.7667 (pp30) cc_final: 0.7404 (pp30) REVERT: B 128 LEU cc_start: 0.9241 (tt) cc_final: 0.8707 (tt) REVERT: B 337 MET cc_start: 0.7473 (tmm) cc_final: 0.7208 (tmm) REVERT: B 343 MET cc_start: 0.7830 (mmp) cc_final: 0.7592 (mmm) REVERT: B 374 PHE cc_start: 0.8085 (t80) cc_final: 0.7835 (t80) REVERT: B 427 LYS cc_start: 0.6526 (mppt) cc_final: 0.6282 (mppt) REVERT: B 482 LYS cc_start: 0.8398 (mttt) cc_final: 0.7791 (mmmt) REVERT: B 501 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8287 (mtpt) REVERT: B 590 MET cc_start: 0.4883 (mmp) cc_final: 0.4592 (tpp) REVERT: B 623 ASP cc_start: 0.7354 (t0) cc_final: 0.6909 (t0) REVERT: B 635 PHE cc_start: 0.8085 (m-80) cc_final: 0.7840 (m-80) REVERT: B 704 ILE cc_start: 0.7666 (pt) cc_final: 0.7360 (pt) REVERT: B 707 LEU cc_start: 0.8623 (mt) cc_final: 0.7639 (tp) REVERT: B 762 ARG cc_start: 0.8399 (tpm170) cc_final: 0.7975 (tpm170) REVERT: B 788 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7423 (tp30) REVERT: C 35 MET cc_start: 0.8407 (ttm) cc_final: 0.7734 (ttt) REVERT: C 128 LEU cc_start: 0.9378 (mt) cc_final: 0.9090 (tt) REVERT: C 265 MET cc_start: 0.8153 (mmm) cc_final: 0.7594 (tpp) REVERT: C 321 LEU cc_start: 0.8999 (pp) cc_final: 0.8479 (mp) REVERT: C 402 LEU cc_start: 0.8721 (tt) cc_final: 0.7621 (tt) REVERT: C 498 LEU cc_start: 0.9225 (tp) cc_final: 0.8949 (tp) REVERT: C 519 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 654 ILE cc_start: 0.7876 (mm) cc_final: 0.7508 (mm) REVERT: C 689 TYR cc_start: 0.7991 (t80) cc_final: 0.7664 (t80) REVERT: D 25 ASP cc_start: 0.8599 (m-30) cc_final: 0.8340 (t70) REVERT: D 37 MET cc_start: 0.8095 (ttp) cc_final: 0.7681 (tmm) REVERT: D 427 LYS cc_start: 0.7278 (mppt) cc_final: 0.7057 (mppt) REVERT: D 428 LEU cc_start: 0.7504 (mm) cc_final: 0.7259 (mm) REVERT: D 448 LEU cc_start: 0.7939 (tt) cc_final: 0.7720 (tt) REVERT: D 474 LEU cc_start: 0.9046 (tp) cc_final: 0.8190 (tp) REVERT: D 482 LYS cc_start: 0.7558 (mttt) cc_final: 0.7266 (tppt) REVERT: D 501 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7866 (mtmt) REVERT: D 590 MET cc_start: 0.5538 (tpt) cc_final: 0.5002 (tpp) REVERT: D 623 ASP cc_start: 0.7291 (t0) cc_final: 0.6861 (t0) REVERT: D 635 PHE cc_start: 0.8066 (m-80) cc_final: 0.7860 (m-80) REVERT: D 707 LEU cc_start: 0.8718 (mt) cc_final: 0.8266 (tp) REVERT: D 762 ARG cc_start: 0.8354 (tpm170) cc_final: 0.8121 (tpm170) REVERT: D 788 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7894 (tp30) REVERT: E 161 LEU cc_start: 0.8073 (mm) cc_final: 0.7515 (pp) REVERT: E 265 MET cc_start: 0.7194 (mmp) cc_final: 0.6828 (tpp) REVERT: E 337 MET cc_start: 0.7972 (tmm) cc_final: 0.7772 (tmm) REVERT: E 402 LEU cc_start: 0.8628 (tt) cc_final: 0.8298 (tp) REVERT: E 414 ASP cc_start: 0.8348 (m-30) cc_final: 0.8099 (m-30) REVERT: E 654 ILE cc_start: 0.8019 (mm) cc_final: 0.7471 (mm) REVERT: F 35 MET cc_start: 0.7958 (ttm) cc_final: 0.7713 (ttp) REVERT: F 276 ILE cc_start: 0.8852 (mm) cc_final: 0.8619 (tp) REVERT: F 337 MET cc_start: 0.7440 (tmm) cc_final: 0.7133 (tmm) REVERT: F 374 PHE cc_start: 0.7243 (t80) cc_final: 0.6981 (t80) REVERT: F 482 LYS cc_start: 0.7556 (mttt) cc_final: 0.7034 (mmmt) REVERT: F 501 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8332 (mtpp) REVERT: F 576 ASN cc_start: 0.8052 (m-40) cc_final: 0.7833 (m110) REVERT: F 623 ASP cc_start: 0.7830 (t0) cc_final: 0.7618 (t0) REVERT: F 645 LYS cc_start: 0.8226 (mmtm) cc_final: 0.8002 (mmmm) REVERT: F 707 LEU cc_start: 0.8477 (mp) cc_final: 0.7730 (tp) REVERT: F 762 ARG cc_start: 0.9087 (tpt170) cc_final: 0.8218 (tpm170) outliers start: 1 outliers final: 1 residues processed: 496 average time/residue: 0.2054 time to fit residues: 172.6767 Evaluate side-chains 368 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 186 optimal weight: 20.0000 chunk 245 optimal weight: 0.0270 chunk 55 optimal weight: 9.9990 chunk 292 optimal weight: 0.8980 chunk 407 optimal weight: 0.3980 chunk 319 optimal weight: 10.0000 chunk 354 optimal weight: 9.9990 chunk 328 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 289 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 overall best weight: 2.4640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 ASN C 267 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.108955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.081650 restraints weight = 102127.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.084220 restraints weight = 54682.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085287 restraints weight = 30020.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085465 restraints weight = 25560.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085609 restraints weight = 21810.025| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35757 Z= 0.177 Angle : 0.762 11.100 48477 Z= 0.389 Chirality : 0.047 0.199 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.661 34.439 4617 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.03 % Allowed : 1.81 % Favored : 98.17 % 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: -2.02 (0.13), residues: 4191 helix: -0.72 (0.11), residues: 2097 sheet: -1.12 (0.25), residues: 477 loop : -2.13 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 671 TYR 0.039 0.002 TYR D 477 PHE 0.037 0.002 PHE D 250 TRP 0.057 0.002 TRP E 168 HIS 0.019 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (35745) covalent geometry : angle 0.76128 / 0.39 (48453) SS BOND : bond 0.00293 / 0.18 ( 12) SS BOND : angle 1.75361 / 1.09 ( 24) hydrogen bonds : bond 0.05737 / 3.70 ( 1550) hydrogen bonds : angle 5.19164 / 3.60 ( 4308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 1.406 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: A 128 LEU cc_start: 0.9260 (tp) cc_final: 0.8987 (tt) REVERT: A 265 MET cc_start: 0.7583 (mmp) cc_final: 0.6955 (tpp) REVERT: A 283 VAL cc_start: 0.9278 (t) cc_final: 0.9005 (p) REVERT: A 498 LEU cc_start: 0.9348 (tp) cc_final: 0.9026 (tp) REVERT: A 520 GLU cc_start: 0.8257 (pt0) cc_final: 0.7837 (pt0) REVERT: A 707 LEU cc_start: 0.8835 (mt) cc_final: 0.8491 (tp) REVERT: B 35 MET cc_start: 0.8105 (ttm) cc_final: 0.7750 (ttt) REVERT: B 128 LEU cc_start: 0.9262 (tt) cc_final: 0.8737 (tt) REVERT: B 337 MET cc_start: 0.7367 (tmm) cc_final: 0.7088 (tmm) REVERT: B 482 LYS cc_start: 0.8412 (mttt) cc_final: 0.7823 (mmmt) REVERT: B 501 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8278 (mtpt) REVERT: B 590 MET cc_start: 0.5038 (mmp) cc_final: 0.4772 (tpp) REVERT: B 623 ASP cc_start: 0.7477 (t0) cc_final: 0.7038 (t0) REVERT: B 635 PHE cc_start: 0.8051 (m-80) cc_final: 0.7801 (m-80) REVERT: B 704 ILE cc_start: 0.7700 (pt) cc_final: 0.7394 (pt) REVERT: B 707 LEU cc_start: 0.8609 (mt) cc_final: 0.7573 (tp) REVERT: B 762 ARG cc_start: 0.8354 (tpm170) cc_final: 0.7767 (tpm170) REVERT: B 788 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7498 (tp30) REVERT: C 35 MET cc_start: 0.8236 (ttm) cc_final: 0.7471 (ttt) REVERT: C 265 MET cc_start: 0.8213 (mmm) cc_final: 0.7703 (tpp) REVERT: C 402 LEU cc_start: 0.8784 (tt) cc_final: 0.8254 (tp) REVERT: C 498 LEU cc_start: 0.9228 (tp) cc_final: 0.8947 (tp) REVERT: C 519 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7877 (mt-10) REVERT: C 571 LYS cc_start: 0.8546 (mppt) cc_final: 0.8312 (mmtm) REVERT: C 654 ILE cc_start: 0.7914 (mm) cc_final: 0.7674 (mm) REVERT: C 689 TYR cc_start: 0.8077 (t80) cc_final: 0.7735 (t80) REVERT: D 25 ASP cc_start: 0.8663 (m-30) cc_final: 0.8400 (t70) REVERT: D 37 MET cc_start: 0.8254 (ttp) cc_final: 0.7830 (tmm) REVERT: D 238 GLU cc_start: 0.8594 (pm20) cc_final: 0.8393 (pm20) REVERT: D 427 LYS cc_start: 0.7082 (mppt) cc_final: 0.6784 (mppt) REVERT: D 451 LEU cc_start: 0.8602 (tp) cc_final: 0.8395 (tp) REVERT: D 482 LYS cc_start: 0.7498 (mttt) cc_final: 0.7238 (tppt) REVERT: D 590 MET cc_start: 0.4800 (tpt) cc_final: 0.4520 (tpp) REVERT: D 623 ASP cc_start: 0.7502 (t0) cc_final: 0.6997 (t0) REVERT: D 707 LEU cc_start: 0.8736 (mt) cc_final: 0.8280 (tp) REVERT: D 788 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7738 (tp30) REVERT: E 161 LEU cc_start: 0.8198 (mm) cc_final: 0.7550 (pp) REVERT: E 337 MET cc_start: 0.8127 (tmm) cc_final: 0.7850 (tmm) REVERT: E 402 LEU cc_start: 0.8705 (tt) cc_final: 0.8216 (tp) REVERT: E 414 ASP cc_start: 0.8121 (m-30) cc_final: 0.7807 (m-30) REVERT: E 571 LYS cc_start: 0.8528 (mttt) cc_final: 0.8294 (mttm) REVERT: E 599 ILE cc_start: 0.8838 (mm) cc_final: 0.8627 (mt) REVERT: E 654 ILE cc_start: 0.8139 (mm) cc_final: 0.7566 (mm) REVERT: F 35 MET cc_start: 0.8096 (ttm) cc_final: 0.7819 (ttp) REVERT: F 128 LEU cc_start: 0.9168 (tt) cc_final: 0.8817 (tt) REVERT: F 276 ILE cc_start: 0.8951 (mm) cc_final: 0.8739 (tp) REVERT: F 337 MET cc_start: 0.7524 (tmm) cc_final: 0.7214 (tmm) REVERT: F 374 PHE cc_start: 0.7244 (t80) cc_final: 0.7011 (t80) REVERT: F 482 LYS cc_start: 0.7525 (mttt) cc_final: 0.7099 (tppt) REVERT: F 501 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8250 (mtpp) REVERT: F 576 ASN cc_start: 0.8016 (m-40) cc_final: 0.7809 (m110) REVERT: F 590 MET cc_start: 0.6517 (tpp) cc_final: 0.6155 (tpp) REVERT: F 645 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7960 (mmmm) REVERT: F 707 LEU cc_start: 0.8406 (mp) cc_final: 0.7607 (tp) REVERT: F 762 ARG cc_start: 0.9086 (tpt170) cc_final: 0.8246 (tpm170) outliers start: 1 outliers final: 0 residues processed: 463 average time/residue: 0.2029 time to fit residues: 159.3974 Evaluate side-chains 367 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 216 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 347 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 263 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS C 132 HIS C 712 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 HIS ** F 575 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 = 0.3908 r_free = 0.3908 target = 0.111394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084168 restraints weight = 101283.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086472 restraints weight = 51720.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087915 restraints weight = 31376.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088793 restraints weight = 22020.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089329 restraints weight = 17552.834| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35757 Z= 0.134 Angle : 0.737 12.944 48477 Z= 0.369 Chirality : 0.046 0.212 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.511 34.269 4617 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.08 % Allowed : 1.09 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.85 (0.13), residues: 4191 helix: -0.57 (0.11), residues: 2061 sheet: -1.20 (0.24), residues: 510 loop : -1.98 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 671 TYR 0.037 0.002 TYR D 477 PHE 0.035 0.002 PHE F 250 TRP 0.025 0.002 TRP F 342 HIS 0.035 0.001 HIS F 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (35745) covalent geometry : angle 0.73658 / 0.37 (48453) SS BOND : bond 0.00198 / 0.12 ( 12) SS BOND : angle 1.35554 / 0.83 ( 24) hydrogen bonds : bond 0.05422 / 3.52 ( 1550) hydrogen bonds : angle 5.03238 / 3.50 ( 4308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 498 time to evaluate : 1.446 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: A 134 LEU cc_start: 0.8849 (tp) cc_final: 0.8598 (tt) REVERT: A 169 THR cc_start: 0.8739 (t) cc_final: 0.8418 (p) REVERT: A 265 MET cc_start: 0.7412 (mmp) cc_final: 0.6806 (tpp) REVERT: A 283 VAL cc_start: 0.9228 (t) cc_final: 0.8909 (p) REVERT: A 402 LEU cc_start: 0.8801 (tt) cc_final: 0.7451 (tt) REVERT: A 414 ASP cc_start: 0.8187 (m-30) cc_final: 0.7961 (m-30) REVERT: A 498 LEU cc_start: 0.9279 (tp) cc_final: 0.9029 (tp) REVERT: A 520 GLU cc_start: 0.8273 (pt0) cc_final: 0.7823 (pt0) REVERT: A 654 ILE cc_start: 0.8307 (mm) cc_final: 0.8046 (mm) REVERT: A 707 LEU cc_start: 0.8825 (mt) cc_final: 0.8370 (tp) REVERT: B 35 MET cc_start: 0.8097 (ttm) cc_final: 0.7746 (ttt) REVERT: B 128 LEU cc_start: 0.9250 (tt) cc_final: 0.8740 (tt) REVERT: B 337 MET cc_start: 0.7631 (tmm) cc_final: 0.7306 (tmm) REVERT: B 427 LYS cc_start: 0.6420 (mttt) cc_final: 0.5824 (mttp) REVERT: B 482 LYS cc_start: 0.8336 (mttt) cc_final: 0.7780 (mmmt) REVERT: B 501 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8232 (mtpt) REVERT: B 623 ASP cc_start: 0.7421 (t0) cc_final: 0.6957 (t0) REVERT: B 635 PHE cc_start: 0.8052 (m-80) cc_final: 0.7822 (m-80) REVERT: B 704 ILE cc_start: 0.7659 (pt) cc_final: 0.7341 (pt) REVERT: B 707 LEU cc_start: 0.8519 (mt) cc_final: 0.7456 (tp) REVERT: B 762 ARG cc_start: 0.8359 (tpm170) cc_final: 0.7761 (tpm170) REVERT: B 788 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7501 (tp30) REVERT: C 35 MET cc_start: 0.8210 (ttm) cc_final: 0.7509 (ttt) REVERT: C 134 LEU cc_start: 0.9035 (tp) cc_final: 0.8784 (tt) REVERT: C 265 MET cc_start: 0.8104 (mmm) cc_final: 0.7608 (tpp) REVERT: C 321 LEU cc_start: 0.9214 (pp) cc_final: 0.8438 (mp) REVERT: C 402 LEU cc_start: 0.8416 (tt) cc_final: 0.7461 (tt) REVERT: C 498 LEU cc_start: 0.9265 (tp) cc_final: 0.9008 (tp) REVERT: C 654 ILE cc_start: 0.7878 (mm) cc_final: 0.7629 (mm) REVERT: C 689 TYR cc_start: 0.8026 (t80) cc_final: 0.7699 (t80) REVERT: D 25 ASP cc_start: 0.8560 (m-30) cc_final: 0.8317 (t70) REVERT: D 37 MET cc_start: 0.8121 (ttp) cc_final: 0.7768 (tmm) REVERT: D 337 MET cc_start: 0.8094 (ttp) cc_final: 0.7859 (tmm) REVERT: D 474 LEU cc_start: 0.9164 (tp) cc_final: 0.8355 (tp) REVERT: D 623 ASP cc_start: 0.7362 (t0) cc_final: 0.6881 (t0) REVERT: D 704 ILE cc_start: 0.7727 (pt) cc_final: 0.7475 (pt) REVERT: D 707 LEU cc_start: 0.8665 (mt) cc_final: 0.8205 (tp) REVERT: D 762 ARG cc_start: 0.8274 (tpm170) cc_final: 0.7836 (tpm170) REVERT: D 788 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7726 (tp30) REVERT: E 265 MET cc_start: 0.6946 (mmp) cc_final: 0.6483 (ttt) REVERT: E 337 MET cc_start: 0.8004 (tmm) cc_final: 0.7776 (tmm) REVERT: E 402 LEU cc_start: 0.8915 (tt) cc_final: 0.8415 (tp) REVERT: E 414 ASP cc_start: 0.8198 (m-30) cc_final: 0.7987 (m-30) REVERT: E 519 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8144 (mt-10) REVERT: E 571 LYS cc_start: 0.8507 (mttt) cc_final: 0.8065 (mtpt) REVERT: E 654 ILE cc_start: 0.8125 (mm) cc_final: 0.7561 (mm) REVERT: F 35 MET cc_start: 0.8091 (ttm) cc_final: 0.7786 (ttp) REVERT: F 128 LEU cc_start: 0.9135 (tt) cc_final: 0.8585 (tt) REVERT: F 337 MET cc_start: 0.7465 (tmm) cc_final: 0.7045 (tmm) REVERT: F 374 PHE cc_start: 0.6740 (t80) cc_final: 0.6473 (t80) REVERT: F 482 LYS cc_start: 0.7371 (mttt) cc_final: 0.7032 (tppt) REVERT: F 501 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8296 (mtpp) REVERT: F 590 MET cc_start: 0.6383 (tpp) cc_final: 0.6012 (tpp) REVERT: F 623 ASP cc_start: 0.7880 (t0) cc_final: 0.7429 (t0) REVERT: F 645 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7837 (mmtm) REVERT: F 707 LEU cc_start: 0.8330 (mp) cc_final: 0.7612 (tp) REVERT: F 762 ARG cc_start: 0.9009 (tpt170) cc_final: 0.8254 (tpm170) outliers start: 3 outliers final: 1 residues processed: 501 average time/residue: 0.2033 time to fit residues: 172.6597 Evaluate side-chains 382 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 251 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 315 optimal weight: 2.9990 chunk 409 optimal weight: 20.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 712 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.109970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.083377 restraints weight = 102853.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085552 restraints weight = 57648.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087056 restraints weight = 32364.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087217 restraints weight = 24746.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087339 restraints weight = 21467.318| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35757 Z= 0.155 Angle : 0.758 11.245 48477 Z= 0.381 Chirality : 0.046 0.180 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.511 34.146 4617 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -1.87 (0.13), residues: 4191 helix: -0.61 (0.11), residues: 2070 sheet: -1.20 (0.24), residues: 510 loop : -1.97 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.035 0.002 TYR B 689 PHE 0.042 0.002 PHE D 250 TRP 0.024 0.002 TRP B 511 HIS 0.026 0.001 HIS F 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (35745) covalent geometry : angle 0.75725 / 0.38 (48453) SS BOND : bond 0.00282 / 0.18 ( 12) SS BOND : angle 1.67077 / 1.05 ( 24) hydrogen bonds : bond 0.05500 / 3.56 ( 1550) hydrogen bonds : angle 5.07255 / 3.52 ( 4308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8382 Ramachandran restraints generated. 4191 Oldfield, 0 Emsley, 4191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.629 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: A 169 THR cc_start: 0.8905 (t) cc_final: 0.8589 (p) REVERT: A 265 MET cc_start: 0.7543 (mmp) cc_final: 0.6965 (tpp) REVERT: A 283 VAL cc_start: 0.9187 (t) cc_final: 0.8966 (p) REVERT: A 402 LEU cc_start: 0.8781 (tt) cc_final: 0.7426 (tt) REVERT: A 414 ASP cc_start: 0.8329 (m-30) cc_final: 0.8066 (m-30) REVERT: A 498 LEU cc_start: 0.9330 (tp) cc_final: 0.8993 (tp) REVERT: A 520 GLU cc_start: 0.8088 (pt0) cc_final: 0.7812 (pt0) REVERT: A 654 ILE cc_start: 0.8348 (mm) cc_final: 0.8104 (mm) REVERT: A 707 LEU cc_start: 0.8853 (mt) cc_final: 0.8497 (tp) REVERT: B 35 MET cc_start: 0.8090 (ttm) cc_final: 0.7715 (ttp) REVERT: B 128 LEU cc_start: 0.9249 (tt) cc_final: 0.8663 (tt) REVERT: B 337 MET cc_start: 0.7461 (tmm) cc_final: 0.7199 (tmm) REVERT: B 427 LYS cc_start: 0.6446 (mttt) cc_final: 0.5835 (mttp) REVERT: B 482 LYS cc_start: 0.8264 (mttt) cc_final: 0.7796 (tppt) REVERT: B 590 MET cc_start: 0.5163 (tpt) cc_final: 0.4795 (tpp) REVERT: B 623 ASP cc_start: 0.7463 (t0) cc_final: 0.7009 (t0) REVERT: B 635 PHE cc_start: 0.8079 (m-80) cc_final: 0.7833 (m-80) REVERT: B 704 ILE cc_start: 0.7704 (pt) cc_final: 0.7380 (pt) REVERT: B 707 LEU cc_start: 0.8599 (mt) cc_final: 0.7566 (tp) REVERT: B 762 ARG cc_start: 0.8435 (tpm170) cc_final: 0.7880 (tpm170) REVERT: B 788 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7420 (tp30) REVERT: C 35 MET cc_start: 0.8277 (ttm) cc_final: 0.8011 (ttt) REVERT: C 134 LEU cc_start: 0.9057 (tp) cc_final: 0.8828 (tt) REVERT: C 265 MET cc_start: 0.8198 (mmm) cc_final: 0.7807 (tpp) REVERT: C 321 LEU cc_start: 0.9218 (pp) cc_final: 0.8457 (mp) REVERT: C 498 LEU cc_start: 0.9282 (tp) cc_final: 0.9015 (tp) REVERT: C 654 ILE cc_start: 0.7896 (mm) cc_final: 0.7652 (mm) REVERT: C 689 TYR cc_start: 0.8023 (t80) cc_final: 0.7663 (t80) REVERT: D 25 ASP cc_start: 0.8649 (m-30) cc_final: 0.8387 (t70) REVERT: D 37 MET cc_start: 0.8182 (ttp) cc_final: 0.7809 (tmm) REVERT: D 115 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 128 LEU cc_start: 0.9170 (tt) cc_final: 0.8676 (tt) REVERT: D 474 LEU cc_start: 0.8989 (tp) cc_final: 0.8215 (tp) REVERT: D 476 LEU cc_start: 0.8108 (mt) cc_final: 0.7908 (mt) REVERT: D 590 MET cc_start: 0.5754 (tpt) cc_final: 0.5550 (tpp) REVERT: D 623 ASP cc_start: 0.7437 (t0) cc_final: 0.6955 (t0) REVERT: D 704 ILE cc_start: 0.7666 (pt) cc_final: 0.7409 (pt) REVERT: D 707 LEU cc_start: 0.8721 (mt) cc_final: 0.8131 (tp) REVERT: D 762 ARG cc_start: 0.8366 (tpm170) cc_final: 0.7923 (tpm170) REVERT: D 788 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7707 (tp30) REVERT: E 265 MET cc_start: 0.6965 (mmp) cc_final: 0.6692 (ttt) REVERT: E 337 MET cc_start: 0.8132 (tmm) cc_final: 0.7854 (tmm) REVERT: E 402 LEU cc_start: 0.8880 (tt) cc_final: 0.7979 (tt) REVERT: E 414 ASP cc_start: 0.8199 (m-30) cc_final: 0.7924 (m-30) REVERT: E 519 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8148 (mt-10) REVERT: E 571 LYS cc_start: 0.8496 (mttt) cc_final: 0.8047 (mtpp) REVERT: E 654 ILE cc_start: 0.8163 (mm) cc_final: 0.7604 (mm) REVERT: F 35 MET cc_start: 0.8161 (ttm) cc_final: 0.7686 (ttp) REVERT: F 128 LEU cc_start: 0.9204 (tt) cc_final: 0.8742 (tt) REVERT: F 250 PHE cc_start: 0.8041 (m-80) cc_final: 0.7671 (m-80) REVERT: F 337 MET cc_start: 0.7452 (tmm) cc_final: 0.7052 (tmm) REVERT: F 428 LEU cc_start: 0.7320 (mm) cc_final: 0.7090 (mm) REVERT: F 448 LEU cc_start: 0.7915 (tt) cc_final: 0.7655 (tt) REVERT: F 453 LEU cc_start: 0.7818 (mt) cc_final: 0.7431 (mt) REVERT: F 482 LYS cc_start: 0.7275 (mttt) cc_final: 0.7040 (tppt) REVERT: F 501 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8347 (mtpp) REVERT: F 590 MET cc_start: 0.6422 (tpp) cc_final: 0.6055 (tpp) REVERT: F 623 ASP cc_start: 0.7609 (t0) cc_final: 0.7252 (t0) REVERT: F 645 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7829 (mmtm) REVERT: F 707 LEU cc_start: 0.8479 (mp) cc_final: 0.7743 (tp) REVERT: F 762 ARG cc_start: 0.9031 (tpt170) cc_final: 0.8321 (tpm170) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.2064 time to fit residues: 164.4668 Evaluate side-chains 373 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 0.0870 chunk 125 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 132 optimal weight: 0.0470 chunk 232 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 354 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN ** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.112161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085118 restraints weight = 101565.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088002 restraints weight = 52593.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088567 restraints weight = 30715.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089128 restraints weight = 24457.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089350 restraints weight = 21272.394| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35757 Z= 0.130 Angle : 0.741 10.982 48477 Z= 0.368 Chirality : 0.045 0.207 5598 Planarity : 0.004 0.057 5994 Dihedral : 5.358 33.559 4617 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.81 (0.13), residues: 4191 helix: -0.55 (0.11), residues: 2052 sheet: -1.19 (0.24), residues: 510 loop : -1.93 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 403 TYR 0.034 0.002 TYR D 477 PHE 0.034 0.002 PHE D 250 TRP 0.049 0.002 TRP A 168 HIS 0.023 0.001 HIS F 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (35745) covalent geometry : angle 0.74075 / 0.37 (48453) SS BOND : bond 0.00231 / 0.17 ( 12) SS BOND : angle 1.31842 / 0.82 ( 24) hydrogen bonds : bond 0.05165 / 3.37 ( 1550) hydrogen bonds : angle 4.96027 / 3.44 ( 4308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6012.85 seconds wall clock time: 105 minutes 8.36 seconds (6308.36 seconds total)