Starting phenix.real_space_refine on Wed Mar 4 07:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.map" model { file = "/net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a46_11629/03_2026/7a46_11629.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.094 sd= 2.381 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 28 5.16 5 C 7343 2.51 5 N 1967 2.21 5 O 2163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11501 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1643 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.56, per 1000 atoms: 0.14 Number of scatterers: 11501 At special positions: 0 Unit cell: (104.223, 102.096, 125.493, 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 28 16.00 O 2163 8.00 N 1967 7.00 C 7343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 572.4 milliseconds 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 54.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid -15 through 0 Processing helix chain 'A' and resid 518 through 533 Processing helix chain 'A' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 638 through 656 Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 711 Processing helix chain 'B' and resid -14 through 0 Processing helix chain 'B' and resid 518 through 533 Processing helix chain 'B' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 558 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 711 Processing helix chain 'C' and resid -14 through 0 Processing helix chain 'C' and resid 518 through 533 Processing helix chain 'C' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU C 558 " --> pdb=" O GLY C 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 638 through 656 Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 711 Processing helix chain 'D' and resid -14 through 0 Processing helix chain 'D' and resid 518 through 533 Processing helix chain 'D' and resid 538 through 571 removed outlier: 5.640A pdb=" N THR D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU D 558 " --> pdb=" O GLY D 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 614 No H-bonds generated for 'chain 'D' and resid 612 through 614' Processing helix chain 'D' and resid 638 through 656 Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 Processing helix chain 'E' and resid -14 through 0 Processing helix chain 'E' and resid 518 through 533 Processing helix chain 'E' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR E 557 " --> pdb=" O PHE E 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU E 558 " --> pdb=" O GLY E 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 638 through 656 Processing helix chain 'E' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 711 Processing helix chain 'F' and resid -14 through 0 Processing helix chain 'F' and resid 518 through 533 Processing helix chain 'F' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR F 557 " --> pdb=" O PHE F 553 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU F 558 " --> pdb=" O GLY F 554 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 638 through 656 Processing helix chain 'F' and resid 656 through 661 removed outlier: 3.678A pdb=" N GLY F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 711 Processing helix chain 'G' and resid -14 through 0 Processing helix chain 'G' and resid 518 through 533 Processing helix chain 'G' and resid 538 through 571 removed outlier: 5.641A pdb=" N THR G 557 " --> pdb=" O PHE G 553 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU G 558 " --> pdb=" O GLY G 554 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL G 559 " --> pdb=" O SER G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 614 No H-bonds generated for 'chain 'G' and resid 612 through 614' Processing helix chain 'G' and resid 638 through 656 Processing helix chain 'G' and resid 656 through 661 removed outlier: 3.679A pdb=" N GLY G 661 " --> pdb=" O GLU G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 692 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 579 through 582 removed outlier: 6.746A pdb=" N GLY A 598 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET A 592 " --> pdb=" O SER A 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER A 596 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY G 598 " --> pdb=" O GLU G 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET G 592 " --> pdb=" O SER G 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER G 596 " --> pdb=" O MET G 592 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE F 617 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY F 598 " --> pdb=" O GLU F 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET F 592 " --> pdb=" O SER F 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER F 596 " --> pdb=" O MET F 592 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY E 598 " --> pdb=" O GLU E 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET E 592 " --> pdb=" O SER E 596 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER E 596 " --> pdb=" O MET E 592 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 617 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY D 598 " --> pdb=" O GLU D 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET D 592 " --> pdb=" O SER D 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER D 596 " --> pdb=" O MET D 592 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 617 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 598 " --> pdb=" O GLU C 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET C 592 " --> pdb=" O SER C 596 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER C 596 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 617 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 598 " --> pdb=" O GLU B 590 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET B 592 " --> pdb=" O SER B 596 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER B 596 " --> pdb=" O MET B 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL A 627 " --> pdb=" O PHE A 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 675 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 681 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 683 " --> pdb=" O GLY A 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 671 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER A 685 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 669 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL B 627 " --> pdb=" O PHE B 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU B 675 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 681 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 683 " --> pdb=" O GLY B 671 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY B 671 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B 685 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 669 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL C 627 " --> pdb=" O PHE C 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU C 675 " --> pdb=" O ALA C 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 681 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 683 " --> pdb=" O GLY C 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 671 " --> pdb=" O ARG C 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER C 685 " --> pdb=" O PHE C 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 669 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL D 627 " --> pdb=" O PHE D 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU D 675 " --> pdb=" O ALA D 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR D 681 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 683 " --> pdb=" O GLY D 671 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY D 671 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER D 685 " --> pdb=" O PHE D 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE D 669 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL E 627 " --> pdb=" O PHE E 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU E 675 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR E 681 " --> pdb=" O VAL E 673 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 683 " --> pdb=" O GLY E 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY E 671 " --> pdb=" O ARG E 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER E 685 " --> pdb=" O PHE E 669 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE E 669 " --> pdb=" O SER E 685 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 625 through 634 removed outlier: 3.914A pdb=" N VAL F 627 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU F 675 " --> pdb=" O ALA F 679 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR F 681 " --> pdb=" O VAL F 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG F 683 " --> pdb=" O GLY F 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY F 671 " --> pdb=" O ARG F 683 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER F 685 " --> pdb=" O PHE F 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE F 669 " --> pdb=" O SER F 685 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 625 through 634 removed outlier: 3.915A pdb=" N VAL G 627 " --> pdb=" O PHE G 686 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 679 " --> pdb=" O LEU G 675 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU G 675 " --> pdb=" O ALA G 679 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR G 681 " --> pdb=" O VAL G 673 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG G 683 " --> pdb=" O GLY G 671 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY G 671 " --> pdb=" O ARG G 683 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER G 685 " --> pdb=" O PHE G 669 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE G 669 " --> pdb=" O SER G 685 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2208 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: 1.92 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3838 1.34 - 1.45: 1524 1.45 - 1.57: 6251 1.57 - 1.68: 0 1.68 - 1.80: 56 Bond restraints: 11669 Sorted by residual: bond pdb=" N GLY E 625 " pdb=" CA GLY E 625 " ideal model delta sigma weight residual 1.454 1.442 0.013 9.90e-03 1.02e+04 1.60e+00 bond pdb=" N GLY D 625 " pdb=" CA GLY D 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.47e+00 bond pdb=" N GLY B 625 " pdb=" CA GLY B 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.44e+00 bond pdb=" N GLY C 625 " pdb=" CA GLY C 625 " ideal model delta sigma weight residual 1.454 1.442 0.012 9.90e-03 1.02e+04 1.43e+00 bond pdb=" N GLY G 625 " pdb=" CA GLY G 625 " ideal model delta sigma weight residual 1.454 1.443 0.012 9.90e-03 1.02e+04 1.42e+00 ... (remaining 11664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 14922 1.12 - 2.24: 793 2.24 - 3.36: 126 3.36 - 4.48: 21 4.48 - 5.61: 21 Bond angle restraints: 15883 Sorted by residual: angle pdb=" N GLY C 534 " pdb=" CA GLY C 534 " pdb=" C GLY C 534 " ideal model delta sigma weight residual 113.18 118.79 -5.61 2.37e+00 1.78e-01 5.60e+00 angle pdb=" N GLY D 534 " pdb=" CA GLY D 534 " pdb=" C GLY D 534 " ideal model delta sigma weight residual 113.18 118.78 -5.60 2.37e+00 1.78e-01 5.58e+00 angle pdb=" N GLY G 534 " pdb=" CA GLY G 534 " pdb=" C GLY G 534 " ideal model delta sigma weight residual 113.18 118.78 -5.60 2.37e+00 1.78e-01 5.57e+00 angle pdb=" N GLY B 534 " pdb=" CA GLY B 534 " pdb=" C GLY B 534 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.57e+00 angle pdb=" N GLY F 534 " pdb=" CA GLY F 534 " pdb=" C GLY F 534 " ideal model delta sigma weight residual 113.18 118.77 -5.59 2.37e+00 1.78e-01 5.57e+00 ... (remaining 15878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 6167 11.70 - 23.39: 477 23.39 - 35.09: 125 35.09 - 46.78: 91 46.78 - 58.48: 35 Dihedral angle restraints: 6895 sinusoidal: 2471 harmonic: 4424 Sorted by residual: dihedral pdb=" CA ASP B 634 " pdb=" CB ASP B 634 " pdb=" CG ASP B 634 " pdb=" OD1 ASP B 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 634 " pdb=" CB ASP A 634 " pdb=" CG ASP A 634 " pdb=" OD1 ASP A 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP G 634 " pdb=" CB ASP G 634 " pdb=" CG ASP G 634 " pdb=" OD1 ASP G 634 " ideal model delta sinusoidal sigma weight residual -30.00 -88.44 58.44 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1079 0.026 - 0.052: 538 0.052 - 0.077: 180 0.077 - 0.103: 114 0.103 - 0.129: 56 Chirality restraints: 1967 Sorted by residual: chirality pdb=" CA VAL B 633 " pdb=" N VAL B 633 " pdb=" C VAL B 633 " pdb=" CB VAL B 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL G 633 " pdb=" N VAL G 633 " pdb=" C VAL G 633 " pdb=" CB VAL G 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL E 633 " pdb=" N VAL E 633 " pdb=" C VAL E 633 " pdb=" CB VAL E 633 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1964 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 560 " -0.004 2.00e-02 2.50e+03 7.09e-03 5.03e-01 pdb=" C LYS D 560 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS D 560 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP D 561 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 560 " 0.004 2.00e-02 2.50e+03 7.07e-03 5.00e-01 pdb=" C LYS C 560 " -0.012 2.00e-02 2.50e+03 pdb=" O LYS C 560 " 0.005 2.00e-02 2.50e+03 pdb=" N ASP C 561 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 560 " 0.003 2.00e-02 2.50e+03 6.98e-03 4.88e-01 pdb=" C LYS B 560 " -0.012 2.00e-02 2.50e+03 pdb=" O LYS B 560 " 0.005 2.00e-02 2.50e+03 pdb=" N ASP B 561 " 0.004 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2121 2.76 - 3.30: 11725 3.30 - 3.83: 18486 3.83 - 4.37: 20340 4.37 - 4.90: 37249 Nonbonded interactions: 89921 Sorted by model distance: nonbonded pdb=" OD1 ASP C 561 " pdb=" N SER C 612 " model vdw 2.225 3.120 nonbonded pdb=" OD1 ASP B 561 " pdb=" N SER B 612 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP E 561 " pdb=" N SER E 612 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP D 561 " pdb=" N SER D 612 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP A 561 " pdb=" N SER A 612 " model vdw 2.227 3.120 ... (remaining 89916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 11669 Z= 0.301 Angle : 0.610 5.606 15883 Z= 0.350 Chirality : 0.041 0.129 1967 Planarity : 0.002 0.017 2030 Dihedral : 12.011 58.478 4039 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.95 % Allowed : 5.36 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1435 helix: -0.51 (0.19), residues: 616 sheet: -1.31 (0.31), residues: 273 loop : -1.30 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 714 TYR 0.009 0.001 TYR B 606 PHE 0.008 0.001 PHE G 680 TRP 0.009 0.001 TRP C 694 HIS 0.004 0.001 HIS A 707 Details of bonding type rmsd covalent geometry : bond 0.00657 (11669) covalent geometry : angle 0.60979 (15883) hydrogen bonds : bond 0.15464 ( 760) hydrogen bonds : angle 5.81730 ( 2208) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 496 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 572 ASN cc_start: 0.8870 (t0) cc_final: 0.8661 (t0) REVERT: A 612 SER cc_start: 0.9502 (p) cc_final: 0.9234 (m) REVERT: A 638 ASP cc_start: 0.8392 (t0) cc_final: 0.7982 (t0) REVERT: A 644 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7632 (tp40) REVERT: A 652 GLU cc_start: 0.8865 (tt0) cc_final: 0.8556 (tt0) REVERT: A 656 ASN cc_start: 0.8701 (t0) cc_final: 0.8073 (t0) REVERT: A 659 ILE cc_start: 0.8992 (mm) cc_final: 0.8740 (mp) REVERT: A 660 ARG cc_start: 0.8871 (tpt90) cc_final: 0.8527 (tpt170) REVERT: A 676 SER cc_start: 0.8478 (m) cc_final: 0.8008 (p) REVERT: A 681 THR cc_start: 0.8567 (m) cc_final: 0.8281 (p) REVERT: A 685 SER cc_start: 0.8892 (m) cc_final: 0.8349 (p) REVERT: B 527 MET cc_start: 0.9311 (mtt) cc_final: 0.9107 (mtt) REVERT: B 572 ASN cc_start: 0.8939 (t0) cc_final: 0.8721 (t0) REVERT: B 590 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 602 ASP cc_start: 0.8913 (p0) cc_final: 0.8658 (p0) REVERT: B 612 SER cc_start: 0.9526 (p) cc_final: 0.9316 (m) REVERT: B 637 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 638 ASP cc_start: 0.8460 (t0) cc_final: 0.8078 (t0) REVERT: B 641 LYS cc_start: 0.8781 (tttt) cc_final: 0.8559 (tttm) REVERT: B 652 GLU cc_start: 0.8712 (tt0) cc_final: 0.8411 (tt0) REVERT: B 656 ASN cc_start: 0.8247 (t0) cc_final: 0.7922 (t0) REVERT: B 659 ILE cc_start: 0.8880 (mm) cc_final: 0.8551 (mp) REVERT: B 666 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8921 (mm-30) REVERT: B 668 ASN cc_start: 0.8528 (t0) cc_final: 0.8105 (t0) REVERT: B 676 SER cc_start: 0.8969 (m) cc_final: 0.8475 (p) REVERT: B 685 SER cc_start: 0.8780 (m) cc_final: 0.8358 (p) REVERT: C 638 ASP cc_start: 0.8413 (t0) cc_final: 0.7970 (t0) REVERT: C 668 ASN cc_start: 0.8471 (t0) cc_final: 0.8267 (t0) REVERT: C 676 SER cc_start: 0.9077 (m) cc_final: 0.8596 (p) REVERT: C 681 THR cc_start: 0.8801 (m) cc_final: 0.8584 (p) REVERT: C 685 SER cc_start: 0.9051 (m) cc_final: 0.8642 (p) REVERT: D 612 SER cc_start: 0.9499 (p) cc_final: 0.9145 (m) REVERT: D 637 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 638 ASP cc_start: 0.8398 (t0) cc_final: 0.8059 (t0) REVERT: D 641 LYS cc_start: 0.8904 (tttt) cc_final: 0.8660 (ttpp) REVERT: D 648 ASP cc_start: 0.8831 (m-30) cc_final: 0.8583 (m-30) REVERT: D 668 ASN cc_start: 0.8763 (t0) cc_final: 0.8375 (t0) REVERT: D 676 SER cc_start: 0.9151 (m) cc_final: 0.8800 (p) REVERT: D 693 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: D 703 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8391 (mm110) REVERT: E 612 SER cc_start: 0.9594 (p) cc_final: 0.9229 (m) REVERT: E 613 SER cc_start: 0.9545 (m) cc_final: 0.9181 (p) REVERT: E 626 SER cc_start: 0.9289 (m) cc_final: 0.8967 (p) REVERT: E 638 ASP cc_start: 0.8456 (t0) cc_final: 0.7908 (t0) REVERT: E 648 ASP cc_start: 0.8834 (m-30) cc_final: 0.8505 (m-30) REVERT: E 660 ARG cc_start: 0.8838 (tpt90) cc_final: 0.8548 (tpt170) REVERT: E 664 ILE cc_start: 0.9546 (mm) cc_final: 0.9346 (OUTLIER) REVERT: E 666 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8889 (tp30) REVERT: E 668 ASN cc_start: 0.8689 (t0) cc_final: 0.8011 (t0) REVERT: E 676 SER cc_start: 0.8834 (m) cc_final: 0.8380 (p) REVERT: E 681 THR cc_start: 0.8621 (m) cc_final: 0.8385 (p) REVERT: E 685 SER cc_start: 0.9108 (m) cc_final: 0.8693 (p) REVERT: E 720 TYR cc_start: 0.7415 (m-10) cc_final: 0.7135 (m-10) REVERT: F 572 ASN cc_start: 0.9065 (t0) cc_final: 0.8855 (t0) REVERT: F 612 SER cc_start: 0.9550 (p) cc_final: 0.9286 (m) REVERT: F 638 ASP cc_start: 0.8478 (t0) cc_final: 0.8026 (t0) REVERT: F 656 ASN cc_start: 0.8112 (t0) cc_final: 0.7836 (t0) REVERT: F 659 ILE cc_start: 0.9010 (mm) cc_final: 0.8808 (mp) REVERT: F 668 ASN cc_start: 0.8595 (t0) cc_final: 0.8253 (t0) REVERT: F 676 SER cc_start: 0.8949 (m) cc_final: 0.8431 (p) REVERT: G 567 PHE cc_start: 0.9102 (m-10) cc_final: 0.8881 (m-10) REVERT: G 571 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8262 (mt-10) REVERT: G 572 ASN cc_start: 0.9086 (t0) cc_final: 0.8822 (t0) REVERT: G 660 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8537 (tpt170) REVERT: G 668 ASN cc_start: 0.8855 (t0) cc_final: 0.8218 (t0) REVERT: G 676 SER cc_start: 0.8929 (m) cc_final: 0.8499 (p) REVERT: G 685 SER cc_start: 0.9093 (m) cc_final: 0.8632 (p) REVERT: G 693 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8604 (mp10) outliers start: 70 outliers final: 35 residues processed: 544 average time/residue: 0.5041 time to fit residues: 298.6644 Evaluate side-chains 434 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 398 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 PHE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 526 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 568 ILE Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 526 ILE Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.0010 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 GLN C 569 GLN D 569 GLN E 569 GLN ** E 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 ASN F 569 GLN F 643 ASN F 644 GLN G 601 GLN G 630 ASN G 703 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086264 restraints weight = 17592.941| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.69 r_work: 0.2773 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11669 Z= 0.125 Angle : 0.589 8.680 15883 Z= 0.298 Chirality : 0.042 0.187 1967 Planarity : 0.003 0.029 2030 Dihedral : 6.012 41.850 1686 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.59 % Allowed : 20.75 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1435 helix: 1.52 (0.18), residues: 644 sheet: -0.59 (0.31), residues: 273 loop : -0.24 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 622 TYR 0.010 0.001 TYR E 606 PHE 0.008 0.001 PHE E 680 TRP 0.009 0.001 TRP B 694 HIS 0.002 0.001 HIS G 607 Details of bonding type rmsd covalent geometry : bond 0.00266 (11669) covalent geometry : angle 0.58877 (15883) hydrogen bonds : bond 0.04348 ( 760) hydrogen bonds : angle 3.99788 ( 2208) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 463 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9002 (t0) cc_final: 0.8727 (t0) REVERT: A 575 ASN cc_start: 0.8559 (m-40) cc_final: 0.8127 (m-40) REVERT: A 578 ASP cc_start: 0.8699 (m-30) cc_final: 0.8372 (m-30) REVERT: A 613 SER cc_start: 0.9507 (t) cc_final: 0.9051 (p) REVERT: A 647 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: A 654 MET cc_start: 0.9130 (mmm) cc_final: 0.8919 (mmm) REVERT: A 656 ASN cc_start: 0.7935 (t0) cc_final: 0.7710 (t0) REVERT: A 659 ILE cc_start: 0.9008 (mm) cc_final: 0.8771 (mp) REVERT: A 660 ARG cc_start: 0.8659 (tpt90) cc_final: 0.8421 (tpp-160) REVERT: A 668 ASN cc_start: 0.8877 (t0) cc_final: 0.8289 (t0) REVERT: A 676 SER cc_start: 0.8683 (m) cc_final: 0.8222 (p) REVERT: A 681 THR cc_start: 0.8442 (m) cc_final: 0.8109 (p) REVERT: A 685 SER cc_start: 0.8900 (m) cc_final: 0.8403 (p) REVERT: A 703 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8480 (tp40) REVERT: B 572 ASN cc_start: 0.9172 (t0) cc_final: 0.8859 (t0) REVERT: B 578 ASP cc_start: 0.8581 (m-30) cc_final: 0.8056 (m-30) REVERT: B 613 SER cc_start: 0.9502 (m) cc_final: 0.9186 (p) REVERT: B 626 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8816 (p) REVERT: B 634 ASP cc_start: 0.8834 (t0) cc_final: 0.8629 (t0) REVERT: B 660 ARG cc_start: 0.8790 (tpp-160) cc_final: 0.8412 (tpm170) REVERT: B 668 ASN cc_start: 0.8527 (t0) cc_final: 0.8080 (t0) REVERT: B 676 SER cc_start: 0.9109 (m) cc_final: 0.8602 (p) REVERT: B 685 SER cc_start: 0.8805 (m) cc_final: 0.8468 (p) REVERT: C 572 ASN cc_start: 0.9084 (t0) cc_final: 0.8614 (t0) REVERT: C 596 SER cc_start: 0.9500 (p) cc_final: 0.8826 (p) REVERT: C 626 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8517 (p) REVERT: C 655 GLU cc_start: 0.9108 (tp30) cc_final: 0.8858 (tp30) REVERT: C 658 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8963 (mp0) REVERT: C 660 ARG cc_start: 0.8446 (tpt90) cc_final: 0.8158 (tpp-160) REVERT: C 676 SER cc_start: 0.9118 (m) cc_final: 0.8655 (p) REVERT: C 685 SER cc_start: 0.8903 (m) cc_final: 0.8538 (p) REVERT: D 613 SER cc_start: 0.9453 (t) cc_final: 0.9204 (p) REVERT: D 624 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8572 (pp) REVERT: D 626 SER cc_start: 0.9096 (OUTLIER) cc_final: 0.8677 (p) REVERT: D 652 GLU cc_start: 0.9127 (tt0) cc_final: 0.8598 (tt0) REVERT: D 655 GLU cc_start: 0.9204 (tp30) cc_final: 0.8873 (tp30) REVERT: D 660 ARG cc_start: 0.8987 (tpp-160) cc_final: 0.8777 (tpm170) REVERT: D 666 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9090 (mm-30) REVERT: D 668 ASN cc_start: 0.8713 (t0) cc_final: 0.8314 (t0) REVERT: D 676 SER cc_start: 0.9242 (m) cc_final: 0.8868 (p) REVERT: E 560 LYS cc_start: 0.8419 (tttt) cc_final: 0.8139 (ptpt) REVERT: E 575 ASN cc_start: 0.8489 (m-40) cc_final: 0.8183 (m110) REVERT: E 578 ASP cc_start: 0.8677 (m-30) cc_final: 0.8251 (m-30) REVERT: E 612 SER cc_start: 0.9566 (p) cc_final: 0.9358 (m) REVERT: E 613 SER cc_start: 0.9448 (m) cc_final: 0.9112 (p) REVERT: E 626 SER cc_start: 0.9140 (m) cc_final: 0.8550 (p) REVERT: E 648 ASP cc_start: 0.8900 (m-30) cc_final: 0.8611 (m-30) REVERT: E 652 GLU cc_start: 0.8993 (tt0) cc_final: 0.8630 (tt0) REVERT: E 655 GLU cc_start: 0.9190 (tp30) cc_final: 0.8891 (tp30) REVERT: E 660 ARG cc_start: 0.8816 (tpt90) cc_final: 0.8499 (tpt170) REVERT: E 666 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9053 (tp30) REVERT: E 668 ASN cc_start: 0.8634 (t0) cc_final: 0.7931 (t0) REVERT: E 676 SER cc_start: 0.8941 (m) cc_final: 0.8484 (p) REVERT: E 681 THR cc_start: 0.8455 (m) cc_final: 0.8216 (p) REVERT: E 685 SER cc_start: 0.8984 (m) cc_final: 0.8653 (p) REVERT: E 720 TYR cc_start: 0.8036 (m-10) cc_final: 0.7701 (m-10) REVERT: F 572 ASN cc_start: 0.9270 (t0) cc_final: 0.8926 (t0) REVERT: F 575 ASN cc_start: 0.8149 (m-40) cc_final: 0.7669 (m-40) REVERT: F 578 ASP cc_start: 0.8532 (m-30) cc_final: 0.7927 (m-30) REVERT: F 590 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8843 (mt-10) REVERT: F 626 SER cc_start: 0.9070 (m) cc_final: 0.8550 (p) REVERT: F 634 ASP cc_start: 0.8954 (t0) cc_final: 0.8738 (t0) REVERT: F 652 GLU cc_start: 0.8995 (tt0) cc_final: 0.8553 (tt0) REVERT: F 655 GLU cc_start: 0.9078 (tp30) cc_final: 0.8796 (tp30) REVERT: F 658 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8970 (mp0) REVERT: F 659 ILE cc_start: 0.8864 (mm) cc_final: 0.8569 (mp) REVERT: F 660 ARG cc_start: 0.9012 (tpp-160) cc_final: 0.8781 (tpm170) REVERT: F 668 ASN cc_start: 0.8512 (t0) cc_final: 0.7991 (t0) REVERT: F 676 SER cc_start: 0.9015 (m) cc_final: 0.8488 (p) REVERT: F 685 SER cc_start: 0.8927 (m) cc_final: 0.8646 (p) REVERT: F 723 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7934 (tt) REVERT: G 574 MET cc_start: 0.9147 (ttm) cc_final: 0.8923 (mtm) REVERT: G 578 ASP cc_start: 0.8705 (m-30) cc_final: 0.8476 (m-30) REVERT: G 590 GLU cc_start: 0.9045 (tt0) cc_final: 0.8805 (mt-10) REVERT: G 612 SER cc_start: 0.9524 (p) cc_final: 0.9238 (m) REVERT: G 626 SER cc_start: 0.9141 (m) cc_final: 0.8560 (p) REVERT: G 634 ASP cc_start: 0.8725 (t0) cc_final: 0.8485 (t0) REVERT: G 652 GLU cc_start: 0.9030 (tt0) cc_final: 0.8622 (tt0) REVERT: G 655 GLU cc_start: 0.9205 (tp30) cc_final: 0.8939 (tp30) REVERT: G 660 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8342 (tpt170) REVERT: G 668 ASN cc_start: 0.8779 (t0) cc_final: 0.8175 (t0) REVERT: G 676 SER cc_start: 0.8998 (m) cc_final: 0.8580 (p) REVERT: G 685 SER cc_start: 0.8984 (m) cc_final: 0.8599 (p) REVERT: G 713 VAL cc_start: 0.9537 (t) cc_final: 0.9211 (p) outliers start: 54 outliers final: 25 residues processed: 486 average time/residue: 0.5019 time to fit residues: 265.5191 Evaluate side-chains 443 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 411 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 703 GLN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 570 PHE Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 702 SER Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 624 ILE Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 723 LEU Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 61 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN A 630 ASN A 644 GLN A 693 GLN C 668 ASN D 575 ASN D 630 ASN D 644 GLN E 630 ASN G 575 ASN G 630 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.082939 restraints weight = 17908.049| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.73 r_work: 0.2725 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11669 Z= 0.265 Angle : 0.633 8.473 15883 Z= 0.325 Chirality : 0.043 0.195 1967 Planarity : 0.003 0.042 2030 Dihedral : 4.858 39.562 1645 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.10 % Allowed : 22.87 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1435 helix: 2.02 (0.18), residues: 644 sheet: -0.19 (0.31), residues: 273 loop : -0.06 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 591 TYR 0.015 0.001 TYR E 606 PHE 0.010 0.001 PHE E 680 TRP 0.011 0.002 TRP E 694 HIS 0.004 0.001 HIS B 707 Details of bonding type rmsd covalent geometry : bond 0.00604 (11669) covalent geometry : angle 0.63347 (15883) hydrogen bonds : bond 0.04544 ( 760) hydrogen bonds : angle 4.00044 ( 2208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 424 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9119 (t0) cc_final: 0.8882 (t0) REVERT: A 575 ASN cc_start: 0.8301 (m-40) cc_final: 0.7837 (m-40) REVERT: A 578 ASP cc_start: 0.8707 (m-30) cc_final: 0.8291 (m-30) REVERT: A 638 ASP cc_start: 0.8171 (t0) cc_final: 0.7705 (t0) REVERT: A 668 ASN cc_start: 0.8783 (t0) cc_final: 0.8154 (t0) REVERT: A 676 SER cc_start: 0.8655 (m) cc_final: 0.8207 (p) REVERT: A 681 THR cc_start: 0.8446 (m) cc_final: 0.8144 (p) REVERT: A 685 SER cc_start: 0.8901 (m) cc_final: 0.8419 (p) REVERT: B 572 ASN cc_start: 0.9182 (t0) cc_final: 0.8932 (t0) REVERT: B 613 SER cc_start: 0.9565 (m) cc_final: 0.9297 (p) REVERT: B 626 SER cc_start: 0.9278 (m) cc_final: 0.8768 (p) REVERT: B 638 ASP cc_start: 0.8144 (t0) cc_final: 0.7540 (t0) REVERT: B 641 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8585 (ttpt) REVERT: B 660 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8498 (tpm170) REVERT: B 668 ASN cc_start: 0.8603 (t0) cc_final: 0.8160 (t0) REVERT: B 676 SER cc_start: 0.8913 (m) cc_final: 0.8415 (p) REVERT: B 685 SER cc_start: 0.8791 (m) cc_final: 0.8425 (p) REVERT: C 560 LYS cc_start: 0.8723 (tttt) cc_final: 0.8516 (tppp) REVERT: C 572 ASN cc_start: 0.9010 (t0) cc_final: 0.8643 (t0) REVERT: C 626 SER cc_start: 0.9232 (m) cc_final: 0.8705 (p) REVERT: C 655 GLU cc_start: 0.9116 (tp30) cc_final: 0.8869 (tp30) REVERT: C 676 SER cc_start: 0.8852 (m) cc_final: 0.8393 (p) REVERT: C 685 SER cc_start: 0.9003 (m) cc_final: 0.8505 (p) REVERT: D 590 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8907 (mt-10) REVERT: D 613 SER cc_start: 0.9439 (t) cc_final: 0.9163 (p) REVERT: D 626 SER cc_start: 0.9162 (m) cc_final: 0.8856 (p) REVERT: D 638 ASP cc_start: 0.8111 (t0) cc_final: 0.7642 (t0) REVERT: D 652 GLU cc_start: 0.8971 (tt0) cc_final: 0.8319 (tt0) REVERT: D 655 GLU cc_start: 0.9236 (tp30) cc_final: 0.8886 (tp30) REVERT: D 660 ARG cc_start: 0.8897 (tpp-160) cc_final: 0.8623 (tpm170) REVERT: D 666 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9072 (mm-30) REVERT: D 668 ASN cc_start: 0.8662 (t0) cc_final: 0.8297 (t0) REVERT: D 676 SER cc_start: 0.9034 (m) cc_final: 0.8648 (p) REVERT: D 693 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8339 (pm20) REVERT: E 560 LYS cc_start: 0.8534 (tttt) cc_final: 0.8176 (ptpt) REVERT: E 574 MET cc_start: 0.9427 (mtt) cc_final: 0.9220 (mtt) REVERT: E 575 ASN cc_start: 0.8437 (m-40) cc_final: 0.7942 (m-40) REVERT: E 578 ASP cc_start: 0.8590 (m-30) cc_final: 0.8111 (m-30) REVERT: E 590 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8790 (mt-10) REVERT: E 602 ASP cc_start: 0.9081 (p0) cc_final: 0.8844 (p0) REVERT: E 612 SER cc_start: 0.9597 (p) cc_final: 0.9359 (m) REVERT: E 613 SER cc_start: 0.9530 (m) cc_final: 0.9234 (p) REVERT: E 622 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.7874 (mmt-90) REVERT: E 626 SER cc_start: 0.9164 (m) cc_final: 0.8467 (p) REVERT: E 648 ASP cc_start: 0.8996 (m-30) cc_final: 0.8766 (m-30) REVERT: E 652 GLU cc_start: 0.8904 (tt0) cc_final: 0.8586 (tt0) REVERT: E 655 GLU cc_start: 0.9177 (tp30) cc_final: 0.8733 (tp30) REVERT: E 660 ARG cc_start: 0.8859 (tpt90) cc_final: 0.8431 (tpt170) REVERT: E 666 GLU cc_start: 0.9299 (mm-30) cc_final: 0.9090 (tp30) REVERT: E 668 ASN cc_start: 0.8620 (t0) cc_final: 0.8129 (t0) REVERT: E 676 SER cc_start: 0.8818 (m) cc_final: 0.8384 (p) REVERT: E 681 THR cc_start: 0.8517 (m) cc_final: 0.8247 (p) REVERT: E 685 SER cc_start: 0.8959 (m) cc_final: 0.8618 (p) REVERT: E 720 TYR cc_start: 0.7981 (m-10) cc_final: 0.7614 (m-10) REVERT: F 572 ASN cc_start: 0.9287 (t0) cc_final: 0.8887 (t0) REVERT: F 575 ASN cc_start: 0.8126 (m-40) cc_final: 0.7616 (m-40) REVERT: F 578 ASP cc_start: 0.8512 (m-30) cc_final: 0.7928 (m-30) REVERT: F 626 SER cc_start: 0.9098 (m) cc_final: 0.8653 (p) REVERT: F 634 ASP cc_start: 0.9051 (t0) cc_final: 0.8791 (t0) REVERT: F 638 ASP cc_start: 0.8221 (t0) cc_final: 0.7730 (t0) REVERT: F 652 GLU cc_start: 0.8978 (tt0) cc_final: 0.8559 (tt0) REVERT: F 655 GLU cc_start: 0.9085 (tp30) cc_final: 0.8840 (tp30) REVERT: F 660 ARG cc_start: 0.8802 (tpp-160) cc_final: 0.8561 (tpt170) REVERT: F 668 ASN cc_start: 0.8608 (t0) cc_final: 0.8280 (t0) REVERT: F 676 SER cc_start: 0.8832 (m) cc_final: 0.8344 (p) REVERT: F 703 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8488 (mm-40) REVERT: G 572 ASN cc_start: 0.9058 (t0) cc_final: 0.8752 (t0) REVERT: G 575 ASN cc_start: 0.8357 (m-40) cc_final: 0.7994 (m-40) REVERT: G 578 ASP cc_start: 0.8558 (m-30) cc_final: 0.8254 (m-30) REVERT: G 612 SER cc_start: 0.9602 (p) cc_final: 0.9343 (m) REVERT: G 626 SER cc_start: 0.9304 (m) cc_final: 0.8813 (p) REVERT: G 652 GLU cc_start: 0.8919 (tt0) cc_final: 0.8650 (tt0) REVERT: G 655 GLU cc_start: 0.9181 (tp30) cc_final: 0.8952 (tp30) REVERT: G 660 ARG cc_start: 0.8613 (tpt90) cc_final: 0.8307 (tpt170) REVERT: G 668 ASN cc_start: 0.8770 (t0) cc_final: 0.8206 (t0) REVERT: G 676 SER cc_start: 0.8903 (m) cc_final: 0.8483 (p) REVERT: G 685 SER cc_start: 0.8929 (m) cc_final: 0.8540 (p) REVERT: G 693 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8511 (pm20) outliers start: 60 outliers final: 41 residues processed: 459 average time/residue: 0.5267 time to fit residues: 262.3052 Evaluate side-chains 454 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 409 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 616 THR Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain E residue 702 SER Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 616 THR Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN D 575 ASN E 703 GLN F 643 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.084616 restraints weight = 17687.127| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.78 r_work: 0.2763 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11669 Z= 0.160 Angle : 0.597 9.049 15883 Z= 0.300 Chirality : 0.042 0.176 1967 Planarity : 0.003 0.034 2030 Dihedral : 4.350 35.886 1641 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.25 % Allowed : 25.77 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.22), residues: 1435 helix: 2.41 (0.19), residues: 644 sheet: -0.00 (0.31), residues: 273 loop : 0.17 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 591 TYR 0.012 0.001 TYR F 720 PHE 0.012 0.001 PHE A 567 TRP 0.010 0.001 TRP B 694 HIS 0.003 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00362 (11669) covalent geometry : angle 0.59672 (15883) hydrogen bonds : bond 0.04088 ( 760) hydrogen bonds : angle 3.76154 ( 2208) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 429 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9171 (t0) cc_final: 0.8903 (t0) REVERT: A 575 ASN cc_start: 0.8292 (m-40) cc_final: 0.7863 (m-40) REVERT: A 578 ASP cc_start: 0.8685 (m-30) cc_final: 0.8326 (m-30) REVERT: A 596 SER cc_start: 0.9578 (p) cc_final: 0.9371 (m) REVERT: A 652 GLU cc_start: 0.9043 (tt0) cc_final: 0.8793 (tt0) REVERT: A 668 ASN cc_start: 0.8749 (t0) cc_final: 0.8072 (t0) REVERT: A 676 SER cc_start: 0.8743 (m) cc_final: 0.8287 (p) REVERT: A 681 THR cc_start: 0.8516 (m) cc_final: 0.8198 (p) REVERT: A 685 SER cc_start: 0.8900 (m) cc_final: 0.8414 (p) REVERT: B 572 ASN cc_start: 0.9125 (t0) cc_final: 0.8915 (t0) REVERT: B 613 SER cc_start: 0.9503 (m) cc_final: 0.9174 (p) REVERT: B 626 SER cc_start: 0.9207 (m) cc_final: 0.8690 (p) REVERT: B 652 GLU cc_start: 0.9114 (tt0) cc_final: 0.8740 (tt0) REVERT: B 660 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8523 (tpt170) REVERT: B 668 ASN cc_start: 0.8663 (t0) cc_final: 0.8227 (t0) REVERT: B 676 SER cc_start: 0.8958 (m) cc_final: 0.8448 (p) REVERT: B 681 THR cc_start: 0.8480 (m) cc_final: 0.8242 (p) REVERT: B 685 SER cc_start: 0.8836 (m) cc_final: 0.8461 (p) REVERT: C 560 LYS cc_start: 0.8626 (tttt) cc_final: 0.8258 (pttt) REVERT: C 572 ASN cc_start: 0.9028 (t0) cc_final: 0.8579 (t0) REVERT: C 626 SER cc_start: 0.9148 (m) cc_final: 0.8527 (p) REVERT: C 655 GLU cc_start: 0.9102 (tp30) cc_final: 0.8876 (tp30) REVERT: C 676 SER cc_start: 0.8909 (m) cc_final: 0.8450 (p) REVERT: C 685 SER cc_start: 0.9044 (m) cc_final: 0.8559 (p) REVERT: D 560 LYS cc_start: 0.8476 (tttt) cc_final: 0.8124 (pttt) REVERT: D 570 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: D 613 SER cc_start: 0.9435 (t) cc_final: 0.9077 (p) REVERT: D 626 SER cc_start: 0.9105 (m) cc_final: 0.8788 (p) REVERT: D 655 GLU cc_start: 0.9225 (tp30) cc_final: 0.8919 (tp30) REVERT: D 660 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8615 (tpm170) REVERT: D 666 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9103 (mm-30) REVERT: D 668 ASN cc_start: 0.8734 (t0) cc_final: 0.8382 (t0) REVERT: D 676 SER cc_start: 0.9091 (m) cc_final: 0.8654 (p) REVERT: D 693 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: E 560 LYS cc_start: 0.8442 (tttt) cc_final: 0.8087 (pttt) REVERT: E 575 ASN cc_start: 0.8342 (m-40) cc_final: 0.7552 (m-40) REVERT: E 578 ASP cc_start: 0.8474 (m-30) cc_final: 0.7948 (m-30) REVERT: E 590 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8786 (mt-10) REVERT: E 602 ASP cc_start: 0.9062 (p0) cc_final: 0.8830 (p0) REVERT: E 612 SER cc_start: 0.9634 (p) cc_final: 0.9416 (m) REVERT: E 613 SER cc_start: 0.9508 (m) cc_final: 0.9225 (p) REVERT: E 626 SER cc_start: 0.9106 (m) cc_final: 0.8353 (p) REVERT: E 648 ASP cc_start: 0.9009 (m-30) cc_final: 0.8784 (m-30) REVERT: E 652 GLU cc_start: 0.8844 (tt0) cc_final: 0.8485 (tt0) REVERT: E 655 GLU cc_start: 0.9162 (tp30) cc_final: 0.8768 (tp30) REVERT: E 660 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8470 (tpt170) REVERT: E 666 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9065 (tp30) REVERT: E 668 ASN cc_start: 0.8664 (t0) cc_final: 0.8153 (t0) REVERT: E 676 SER cc_start: 0.8866 (m) cc_final: 0.8425 (p) REVERT: E 681 THR cc_start: 0.8572 (m) cc_final: 0.8296 (p) REVERT: E 685 SER cc_start: 0.8990 (m) cc_final: 0.8668 (p) REVERT: E 720 TYR cc_start: 0.8004 (m-10) cc_final: 0.7631 (m-10) REVERT: F 572 ASN cc_start: 0.9286 (t0) cc_final: 0.8896 (t0) REVERT: F 575 ASN cc_start: 0.8240 (m-40) cc_final: 0.7821 (m-40) REVERT: F 578 ASP cc_start: 0.8418 (m-30) cc_final: 0.8005 (m-30) REVERT: F 626 SER cc_start: 0.9091 (m) cc_final: 0.8592 (p) REVERT: F 634 ASP cc_start: 0.8985 (t0) cc_final: 0.8751 (t0) REVERT: F 652 GLU cc_start: 0.8981 (tt0) cc_final: 0.8525 (tt0) REVERT: F 660 ARG cc_start: 0.8767 (tpp-160) cc_final: 0.8525 (tpt170) REVERT: F 668 ASN cc_start: 0.8668 (t0) cc_final: 0.8349 (t0) REVERT: F 676 SER cc_start: 0.8904 (m) cc_final: 0.8429 (p) REVERT: F 703 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8478 (mm-40) REVERT: G 572 ASN cc_start: 0.9012 (t0) cc_final: 0.8773 (t0) REVERT: G 575 ASN cc_start: 0.8449 (m-40) cc_final: 0.8163 (m110) REVERT: G 578 ASP cc_start: 0.8596 (m-30) cc_final: 0.8301 (m-30) REVERT: G 590 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8787 (mt-10) REVERT: G 612 SER cc_start: 0.9610 (p) cc_final: 0.9313 (m) REVERT: G 626 SER cc_start: 0.9268 (m) cc_final: 0.8722 (p) REVERT: G 634 ASP cc_start: 0.8878 (t0) cc_final: 0.8675 (t0) REVERT: G 652 GLU cc_start: 0.8931 (tt0) cc_final: 0.8683 (tt0) REVERT: G 655 GLU cc_start: 0.9162 (tp30) cc_final: 0.8839 (tp30) REVERT: G 660 ARG cc_start: 0.8585 (tpt90) cc_final: 0.8265 (tpt170) REVERT: G 668 ASN cc_start: 0.8765 (t0) cc_final: 0.8214 (t0) REVERT: G 676 SER cc_start: 0.8963 (m) cc_final: 0.8529 (p) REVERT: G 685 SER cc_start: 0.8977 (m) cc_final: 0.8566 (p) REVERT: G 693 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: G 713 VAL cc_start: 0.9632 (t) cc_final: 0.9301 (p) outliers start: 50 outliers final: 35 residues processed: 455 average time/residue: 0.5608 time to fit residues: 275.7194 Evaluate side-chains 453 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN C 668 ASN C 693 GLN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.085439 restraints weight = 17680.511| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.80 r_work: 0.2790 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11669 Z= 0.151 Angle : 0.592 9.204 15883 Z= 0.298 Chirality : 0.042 0.179 1967 Planarity : 0.003 0.034 2030 Dihedral : 4.116 34.820 1638 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.25 % Allowed : 26.96 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.23), residues: 1435 helix: 2.58 (0.19), residues: 644 sheet: 0.13 (0.31), residues: 273 loop : 0.32 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 697 TYR 0.014 0.001 TYR F 720 PHE 0.015 0.001 PHE A 567 TRP 0.009 0.001 TRP E 694 HIS 0.003 0.001 HIS B 707 Details of bonding type rmsd covalent geometry : bond 0.00340 (11669) covalent geometry : angle 0.59200 (15883) hydrogen bonds : bond 0.03911 ( 760) hydrogen bonds : angle 3.66918 ( 2208) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 425 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9122 (t0) cc_final: 0.8810 (t0) REVERT: A 575 ASN cc_start: 0.8274 (m-40) cc_final: 0.7785 (m-40) REVERT: A 578 ASP cc_start: 0.8766 (m-30) cc_final: 0.8360 (m-30) REVERT: A 622 ARG cc_start: 0.8816 (mmp80) cc_final: 0.8418 (mmp80) REVERT: A 655 GLU cc_start: 0.9183 (tp30) cc_final: 0.8914 (tp30) REVERT: A 660 ARG cc_start: 0.8753 (tpt90) cc_final: 0.8377 (tpt170) REVERT: A 664 ILE cc_start: 0.9271 (tp) cc_final: 0.8987 (pp) REVERT: A 668 ASN cc_start: 0.8754 (t0) cc_final: 0.8077 (t0) REVERT: A 676 SER cc_start: 0.8734 (m) cc_final: 0.8272 (p) REVERT: A 685 SER cc_start: 0.8903 (m) cc_final: 0.8425 (p) REVERT: B 560 LYS cc_start: 0.8428 (tttt) cc_final: 0.8014 (pttt) REVERT: B 613 SER cc_start: 0.9489 (m) cc_final: 0.9147 (p) REVERT: B 626 SER cc_start: 0.9182 (m) cc_final: 0.8693 (p) REVERT: B 652 GLU cc_start: 0.9074 (tt0) cc_final: 0.8696 (tt0) REVERT: B 658 GLU cc_start: 0.9259 (tp30) cc_final: 0.8939 (mp0) REVERT: B 660 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8463 (tpm170) REVERT: B 668 ASN cc_start: 0.8682 (t0) cc_final: 0.8234 (t0) REVERT: B 676 SER cc_start: 0.8945 (m) cc_final: 0.8434 (p) REVERT: B 685 SER cc_start: 0.8846 (m) cc_final: 0.8468 (p) REVERT: C 560 LYS cc_start: 0.8556 (tttt) cc_final: 0.8215 (pttt) REVERT: C 572 ASN cc_start: 0.9033 (t0) cc_final: 0.8691 (t0) REVERT: C 575 ASN cc_start: 0.8292 (m-40) cc_final: 0.8019 (m110) REVERT: C 578 ASP cc_start: 0.8634 (m-30) cc_final: 0.8396 (m-30) REVERT: C 626 SER cc_start: 0.9064 (m) cc_final: 0.8658 (p) REVERT: C 676 SER cc_start: 0.8897 (m) cc_final: 0.8452 (p) REVERT: C 685 SER cc_start: 0.9057 (m) cc_final: 0.8561 (p) REVERT: C 693 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8580 (pm20) REVERT: D 560 LYS cc_start: 0.8458 (tttt) cc_final: 0.8092 (pttt) REVERT: D 626 SER cc_start: 0.9112 (m) cc_final: 0.8806 (p) REVERT: D 655 GLU cc_start: 0.9208 (tp30) cc_final: 0.8923 (tp30) REVERT: D 660 ARG cc_start: 0.8885 (tpp-160) cc_final: 0.8592 (tpp-160) REVERT: D 666 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9143 (mm-30) REVERT: D 668 ASN cc_start: 0.8749 (t0) cc_final: 0.8400 (t0) REVERT: D 676 SER cc_start: 0.9083 (m) cc_final: 0.8650 (p) REVERT: D 693 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: D 723 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7677 (tt) REVERT: E 560 LYS cc_start: 0.8489 (tttt) cc_final: 0.8161 (pttt) REVERT: E 575 ASN cc_start: 0.8303 (m-40) cc_final: 0.7546 (m-40) REVERT: E 578 ASP cc_start: 0.8492 (m-30) cc_final: 0.7993 (m-30) REVERT: E 590 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8750 (mt-10) REVERT: E 602 ASP cc_start: 0.9005 (p0) cc_final: 0.8778 (p0) REVERT: E 612 SER cc_start: 0.9591 (p) cc_final: 0.9346 (m) REVERT: E 626 SER cc_start: 0.9084 (m) cc_final: 0.8345 (p) REVERT: E 652 GLU cc_start: 0.8745 (tt0) cc_final: 0.8426 (tt0) REVERT: E 655 GLU cc_start: 0.9163 (tp30) cc_final: 0.8802 (tp30) REVERT: E 660 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8436 (tpt170) REVERT: E 666 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9063 (tp30) REVERT: E 668 ASN cc_start: 0.8680 (t0) cc_final: 0.8169 (t0) REVERT: E 676 SER cc_start: 0.8848 (m) cc_final: 0.8406 (p) REVERT: E 685 SER cc_start: 0.9012 (m) cc_final: 0.8676 (p) REVERT: E 720 TYR cc_start: 0.7997 (m-10) cc_final: 0.7687 (m-10) REVERT: F 572 ASN cc_start: 0.9253 (t0) cc_final: 0.8936 (t0) REVERT: F 578 ASP cc_start: 0.8495 (m-30) cc_final: 0.8084 (m-30) REVERT: F 626 SER cc_start: 0.9100 (m) cc_final: 0.8658 (p) REVERT: F 634 ASP cc_start: 0.8947 (t0) cc_final: 0.8714 (t0) REVERT: F 652 GLU cc_start: 0.8967 (tt0) cc_final: 0.8555 (tt0) REVERT: F 660 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8700 (tpp-160) REVERT: F 668 ASN cc_start: 0.8686 (t0) cc_final: 0.8447 (t0) REVERT: F 676 SER cc_start: 0.8927 (m) cc_final: 0.8435 (p) REVERT: F 693 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: F 703 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8485 (mm-40) REVERT: G 572 ASN cc_start: 0.8929 (t0) cc_final: 0.8501 (t0) REVERT: G 575 ASN cc_start: 0.8362 (m-40) cc_final: 0.8023 (m110) REVERT: G 578 ASP cc_start: 0.8565 (m-30) cc_final: 0.8251 (m-30) REVERT: G 590 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8771 (mt-10) REVERT: G 612 SER cc_start: 0.9608 (p) cc_final: 0.9307 (m) REVERT: G 622 ARG cc_start: 0.8685 (mmp80) cc_final: 0.8213 (mmp80) REVERT: G 626 SER cc_start: 0.9252 (m) cc_final: 0.8653 (p) REVERT: G 634 ASP cc_start: 0.8872 (t0) cc_final: 0.8654 (t0) REVERT: G 652 GLU cc_start: 0.8930 (tt0) cc_final: 0.8685 (tt0) REVERT: G 655 GLU cc_start: 0.9169 (tp30) cc_final: 0.8890 (tp30) REVERT: G 660 ARG cc_start: 0.8630 (tpt90) cc_final: 0.8367 (tpt170) REVERT: G 668 ASN cc_start: 0.8775 (t0) cc_final: 0.8211 (t0) REVERT: G 676 SER cc_start: 0.8948 (m) cc_final: 0.8508 (p) REVERT: G 685 SER cc_start: 0.8939 (m) cc_final: 0.8542 (p) REVERT: G 693 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8512 (pm20) outliers start: 50 outliers final: 35 residues processed: 447 average time/residue: 0.5593 time to fit residues: 270.0968 Evaluate side-chains 464 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 422 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 693 GLN Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 537 ILE Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 614 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 693 GLN Chi-restraints excluded: chain F residue 702 SER Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 33 optimal weight: 4.9990 chunk 148 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 ASN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN D 575 ASN ** D 601 GLN ** 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 = 0.3530 r_free = 0.3530 target = 0.126573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.087665 restraints weight = 17653.428| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.80 r_work: 0.2809 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11669 Z= 0.124 Angle : 0.593 9.115 15883 Z= 0.298 Chirality : 0.042 0.195 1967 Planarity : 0.003 0.029 2030 Dihedral : 3.776 16.493 1632 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.83 % Allowed : 26.79 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.23), residues: 1435 helix: 2.83 (0.19), residues: 637 sheet: 0.25 (0.31), residues: 273 loop : 0.29 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 697 TYR 0.013 0.001 TYR F 720 PHE 0.010 0.001 PHE D 567 TRP 0.009 0.001 TRP G 694 HIS 0.002 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00276 (11669) covalent geometry : angle 0.59270 (15883) hydrogen bonds : bond 0.03731 ( 760) hydrogen bonds : angle 3.55116 ( 2208) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 437 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.8225 (m-40) cc_final: 0.7998 (m110) REVERT: A 578 ASP cc_start: 0.8640 (m-30) cc_final: 0.8286 (m-30) REVERT: A 652 GLU cc_start: 0.9043 (tt0) cc_final: 0.8826 (tt0) REVERT: A 655 GLU cc_start: 0.9179 (tp30) cc_final: 0.8925 (tp30) REVERT: A 660 ARG cc_start: 0.8768 (tpt90) cc_final: 0.8492 (tpt170) REVERT: A 664 ILE cc_start: 0.9255 (tp) cc_final: 0.8996 (pp) REVERT: A 668 ASN cc_start: 0.8749 (t0) cc_final: 0.8117 (t0) REVERT: A 676 SER cc_start: 0.8722 (m) cc_final: 0.8254 (p) REVERT: A 685 SER cc_start: 0.8908 (m) cc_final: 0.8417 (p) REVERT: B 560 LYS cc_start: 0.8460 (tttt) cc_final: 0.8094 (pttt) REVERT: B 575 ASN cc_start: 0.8430 (m-40) cc_final: 0.8182 (m-40) REVERT: B 613 SER cc_start: 0.9424 (m) cc_final: 0.9093 (p) REVERT: B 624 ILE cc_start: 0.8632 (pt) cc_final: 0.8423 (pp) REVERT: B 626 SER cc_start: 0.9139 (m) cc_final: 0.8609 (p) REVERT: B 634 ASP cc_start: 0.8897 (t0) cc_final: 0.8656 (t0) REVERT: B 652 GLU cc_start: 0.9076 (tt0) cc_final: 0.8698 (tt0) REVERT: B 658 GLU cc_start: 0.9229 (tp30) cc_final: 0.8956 (mp0) REVERT: B 660 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8514 (tpm170) REVERT: B 668 ASN cc_start: 0.8715 (t0) cc_final: 0.8282 (t0) REVERT: B 676 SER cc_start: 0.8945 (m) cc_final: 0.8436 (p) REVERT: B 685 SER cc_start: 0.8858 (m) cc_final: 0.8488 (p) REVERT: C 560 LYS cc_start: 0.8550 (tttt) cc_final: 0.8240 (pttt) REVERT: C 572 ASN cc_start: 0.9037 (t0) cc_final: 0.8711 (t0) REVERT: C 575 ASN cc_start: 0.8327 (m-40) cc_final: 0.8109 (m110) REVERT: C 578 ASP cc_start: 0.8601 (m-30) cc_final: 0.8353 (m-30) REVERT: C 626 SER cc_start: 0.9007 (m) cc_final: 0.8163 (p) REVERT: C 676 SER cc_start: 0.8905 (m) cc_final: 0.8589 (t) REVERT: C 693 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: D 560 LYS cc_start: 0.8443 (tttt) cc_final: 0.8125 (pttt) REVERT: D 626 SER cc_start: 0.9071 (m) cc_final: 0.8699 (p) REVERT: D 655 GLU cc_start: 0.9204 (tp30) cc_final: 0.8945 (tp30) REVERT: D 660 ARG cc_start: 0.8844 (tpp-160) cc_final: 0.8587 (tpm170) REVERT: D 668 ASN cc_start: 0.8747 (t0) cc_final: 0.8402 (t0) REVERT: D 676 SER cc_start: 0.9047 (m) cc_final: 0.8599 (p) REVERT: D 691 LEU cc_start: 0.9386 (mt) cc_final: 0.9171 (mt) REVERT: D 693 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: D 723 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7625 (tt) REVERT: E 560 LYS cc_start: 0.8458 (tttt) cc_final: 0.8156 (pttt) REVERT: E 575 ASN cc_start: 0.8292 (m-40) cc_final: 0.7483 (m-40) REVERT: E 578 ASP cc_start: 0.8502 (m-30) cc_final: 0.7967 (m-30) REVERT: E 590 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8721 (mt-10) REVERT: E 602 ASP cc_start: 0.8981 (p0) cc_final: 0.8750 (p0) REVERT: E 612 SER cc_start: 0.9579 (p) cc_final: 0.9332 (m) REVERT: E 626 SER cc_start: 0.9017 (m) cc_final: 0.8248 (p) REVERT: E 648 ASP cc_start: 0.9051 (m-30) cc_final: 0.8775 (m-30) REVERT: E 652 GLU cc_start: 0.8745 (tt0) cc_final: 0.8351 (tt0) REVERT: E 655 GLU cc_start: 0.9160 (tp30) cc_final: 0.8867 (tp30) REVERT: E 660 ARG cc_start: 0.8681 (tpt90) cc_final: 0.8350 (tpt170) REVERT: E 666 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9068 (tp30) REVERT: E 668 ASN cc_start: 0.8676 (t0) cc_final: 0.8170 (t0) REVERT: E 676 SER cc_start: 0.8854 (m) cc_final: 0.8396 (p) REVERT: E 685 SER cc_start: 0.9004 (m) cc_final: 0.8660 (p) REVERT: E 720 TYR cc_start: 0.8010 (m-10) cc_final: 0.7648 (m-10) REVERT: F 527 MET cc_start: 0.9252 (mtt) cc_final: 0.9017 (ptp) REVERT: F 572 ASN cc_start: 0.9261 (t0) cc_final: 0.9060 (t0) REVERT: F 578 ASP cc_start: 0.8535 (m-30) cc_final: 0.8198 (m-30) REVERT: F 626 SER cc_start: 0.9074 (m) cc_final: 0.8602 (p) REVERT: F 634 ASP cc_start: 0.8870 (t0) cc_final: 0.8660 (t0) REVERT: F 652 GLU cc_start: 0.8951 (tt0) cc_final: 0.8540 (tt0) REVERT: F 668 ASN cc_start: 0.8747 (t0) cc_final: 0.8458 (t0) REVERT: F 676 SER cc_start: 0.8945 (m) cc_final: 0.8423 (p) REVERT: F 693 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8481 (pm20) REVERT: F 703 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8472 (mm-40) REVERT: G 572 ASN cc_start: 0.8941 (t0) cc_final: 0.8532 (t0) REVERT: G 575 ASN cc_start: 0.8389 (m-40) cc_final: 0.8047 (m110) REVERT: G 578 ASP cc_start: 0.8638 (m-30) cc_final: 0.8283 (m-30) REVERT: G 590 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8723 (mt-10) REVERT: G 612 SER cc_start: 0.9555 (p) cc_final: 0.9186 (m) REVERT: G 622 ARG cc_start: 0.8651 (mmp80) cc_final: 0.8130 (mmp80) REVERT: G 626 SER cc_start: 0.9242 (m) cc_final: 0.8600 (p) REVERT: G 634 ASP cc_start: 0.8860 (t0) cc_final: 0.8641 (t0) REVERT: G 652 GLU cc_start: 0.8942 (tt0) cc_final: 0.8720 (tt0) REVERT: G 655 GLU cc_start: 0.9109 (tp30) cc_final: 0.8882 (tp30) REVERT: G 660 ARG cc_start: 0.8595 (tpt90) cc_final: 0.8271 (tpm170) REVERT: G 668 ASN cc_start: 0.8786 (t0) cc_final: 0.8229 (t0) REVERT: G 676 SER cc_start: 0.8957 (m) cc_final: 0.8511 (p) REVERT: G 685 SER cc_start: 0.8961 (m) cc_final: 0.8566 (p) REVERT: G 693 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8441 (pm20) outliers start: 45 outliers final: 27 residues processed: 457 average time/residue: 0.5319 time to fit residues: 263.4545 Evaluate side-chains 442 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 408 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 693 GLN Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 693 GLN Chi-restraints excluded: chain F residue 703 GLN Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 67 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN C 693 GLN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087812 restraints weight = 17641.428| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.82 r_work: 0.2800 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11669 Z= 0.148 Angle : 0.624 8.594 15883 Z= 0.315 Chirality : 0.042 0.171 1967 Planarity : 0.003 0.038 2030 Dihedral : 3.748 12.814 1631 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.25 % Allowed : 28.06 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.23), residues: 1435 helix: 2.86 (0.19), residues: 637 sheet: 0.34 (0.31), residues: 273 loop : 0.34 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 591 TYR 0.013 0.001 TYR F 720 PHE 0.015 0.001 PHE D 567 TRP 0.009 0.001 TRP D 694 HIS 0.002 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00334 (11669) covalent geometry : angle 0.62354 (15883) hydrogen bonds : bond 0.03779 ( 760) hydrogen bonds : angle 3.55717 ( 2208) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 420 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.8251 (m-40) cc_final: 0.8012 (m110) REVERT: A 578 ASP cc_start: 0.8696 (m-30) cc_final: 0.8326 (m-30) REVERT: A 622 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8487 (mmp80) REVERT: A 652 GLU cc_start: 0.8990 (tt0) cc_final: 0.8789 (tt0) REVERT: A 655 GLU cc_start: 0.9158 (tp30) cc_final: 0.8929 (tp30) REVERT: A 660 ARG cc_start: 0.8771 (tpt90) cc_final: 0.8451 (tpt170) REVERT: A 664 ILE cc_start: 0.9247 (tp) cc_final: 0.8955 (pp) REVERT: A 668 ASN cc_start: 0.8741 (t0) cc_final: 0.8115 (t0) REVERT: A 676 SER cc_start: 0.8720 (m) cc_final: 0.8257 (p) REVERT: A 685 SER cc_start: 0.8943 (m) cc_final: 0.8454 (p) REVERT: B 560 LYS cc_start: 0.8526 (tttt) cc_final: 0.8180 (pttt) REVERT: B 575 ASN cc_start: 0.8394 (m-40) cc_final: 0.8089 (m-40) REVERT: B 613 SER cc_start: 0.9433 (m) cc_final: 0.9111 (p) REVERT: B 626 SER cc_start: 0.9177 (m) cc_final: 0.8682 (p) REVERT: B 652 GLU cc_start: 0.9079 (tt0) cc_final: 0.8732 (tt0) REVERT: B 658 GLU cc_start: 0.9211 (tp30) cc_final: 0.8971 (mp0) REVERT: B 660 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8446 (tpt170) REVERT: B 668 ASN cc_start: 0.8675 (t0) cc_final: 0.8234 (t0) REVERT: B 676 SER cc_start: 0.8950 (m) cc_final: 0.8447 (p) REVERT: B 685 SER cc_start: 0.8857 (m) cc_final: 0.8459 (p) REVERT: C 560 LYS cc_start: 0.8562 (tttt) cc_final: 0.8256 (pttt) REVERT: C 572 ASN cc_start: 0.9061 (t0) cc_final: 0.8736 (t0) REVERT: C 575 ASN cc_start: 0.8281 (m-40) cc_final: 0.8046 (m110) REVERT: C 578 ASP cc_start: 0.8609 (m-30) cc_final: 0.8351 (m-30) REVERT: C 626 SER cc_start: 0.9036 (m) cc_final: 0.8211 (p) REVERT: C 676 SER cc_start: 0.8814 (m) cc_final: 0.8520 (t) REVERT: C 693 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: D 560 LYS cc_start: 0.8451 (tttt) cc_final: 0.8159 (pttt) REVERT: D 626 SER cc_start: 0.9075 (m) cc_final: 0.8689 (p) REVERT: D 655 GLU cc_start: 0.9225 (tp30) cc_final: 0.8971 (tp30) REVERT: D 660 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8583 (tpp-160) REVERT: D 668 ASN cc_start: 0.8726 (t0) cc_final: 0.8394 (t0) REVERT: D 676 SER cc_start: 0.9043 (m) cc_final: 0.8598 (p) REVERT: D 693 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: D 723 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7581 (tt) REVERT: E 560 LYS cc_start: 0.8489 (tttt) cc_final: 0.8187 (pttt) REVERT: E 575 ASN cc_start: 0.8315 (m-40) cc_final: 0.7586 (m-40) REVERT: E 578 ASP cc_start: 0.8519 (m-30) cc_final: 0.7960 (m-30) REVERT: E 590 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8712 (mt-10) REVERT: E 602 ASP cc_start: 0.8983 (p0) cc_final: 0.8759 (p0) REVERT: E 612 SER cc_start: 0.9593 (p) cc_final: 0.9336 (m) REVERT: E 626 SER cc_start: 0.9047 (m) cc_final: 0.8275 (p) REVERT: E 652 GLU cc_start: 0.8771 (tt0) cc_final: 0.8405 (tt0) REVERT: E 655 GLU cc_start: 0.9152 (tp30) cc_final: 0.8870 (tp30) REVERT: E 660 ARG cc_start: 0.8741 (tpt90) cc_final: 0.8426 (tpt170) REVERT: E 666 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9072 (tp30) REVERT: E 668 ASN cc_start: 0.8696 (t0) cc_final: 0.8149 (t0) REVERT: E 676 SER cc_start: 0.8848 (m) cc_final: 0.8396 (p) REVERT: E 685 SER cc_start: 0.9016 (m) cc_final: 0.8672 (p) REVERT: E 720 TYR cc_start: 0.8027 (m-10) cc_final: 0.7682 (m-10) REVERT: F 572 ASN cc_start: 0.9286 (t0) cc_final: 0.8987 (t0) REVERT: F 578 ASP cc_start: 0.8551 (m-30) cc_final: 0.8229 (m-30) REVERT: F 626 SER cc_start: 0.9092 (m) cc_final: 0.8600 (p) REVERT: F 652 GLU cc_start: 0.8957 (tt0) cc_final: 0.8566 (tt0) REVERT: F 660 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8521 (tpm170) REVERT: F 668 ASN cc_start: 0.8768 (t0) cc_final: 0.8461 (t0) REVERT: F 676 SER cc_start: 0.8939 (m) cc_final: 0.8418 (p) REVERT: F 703 GLN cc_start: 0.8747 (tp40) cc_final: 0.8478 (mm-40) REVERT: G 572 ASN cc_start: 0.8967 (t0) cc_final: 0.8687 (t0) REVERT: G 575 ASN cc_start: 0.8377 (m-40) cc_final: 0.8018 (m110) REVERT: G 578 ASP cc_start: 0.8637 (m-30) cc_final: 0.8315 (m-30) REVERT: G 590 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8753 (mt-10) REVERT: G 612 SER cc_start: 0.9534 (p) cc_final: 0.9141 (m) REVERT: G 622 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8416 (mmp80) REVERT: G 626 SER cc_start: 0.9242 (m) cc_final: 0.8621 (p) REVERT: G 652 GLU cc_start: 0.8990 (tt0) cc_final: 0.8721 (tt0) REVERT: G 655 GLU cc_start: 0.9098 (tp30) cc_final: 0.8886 (tp30) REVERT: G 660 ARG cc_start: 0.8702 (tpt90) cc_final: 0.8375 (tpt170) REVERT: G 668 ASN cc_start: 0.8815 (t0) cc_final: 0.8262 (t0) REVERT: G 676 SER cc_start: 0.8952 (m) cc_final: 0.8511 (p) REVERT: G 685 SER cc_start: 0.8968 (m) cc_final: 0.8575 (p) REVERT: G 693 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8495 (pm20) outliers start: 50 outliers final: 32 residues processed: 444 average time/residue: 0.5514 time to fit residues: 264.8524 Evaluate side-chains 453 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 416 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 693 GLN Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 702 SER Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 31 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 0.0030 chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 0.2980 chunk 75 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 556 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN E 572 ASN F 643 ASN G 601 GLN G 630 ASN G 703 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087196 restraints weight = 17643.097| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.72 r_work: 0.2867 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11669 Z= 0.125 Angle : 0.640 8.581 15883 Z= 0.324 Chirality : 0.043 0.188 1967 Planarity : 0.003 0.032 2030 Dihedral : 3.705 13.050 1631 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.49 % Allowed : 29.68 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1435 helix: 2.87 (0.19), residues: 644 sheet: 0.40 (0.31), residues: 273 loop : 0.48 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 697 TYR 0.011 0.001 TYR G 631 PHE 0.016 0.001 PHE D 567 TRP 0.008 0.001 TRP G 694 HIS 0.002 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00278 (11669) covalent geometry : angle 0.64004 (15883) hydrogen bonds : bond 0.03624 ( 760) hydrogen bonds : angle 3.49486 ( 2208) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8135 (pttt) REVERT: A 575 ASN cc_start: 0.8173 (m-40) cc_final: 0.7887 (m110) REVERT: A 578 ASP cc_start: 0.8582 (m-30) cc_final: 0.8108 (m-30) REVERT: A 655 GLU cc_start: 0.9135 (tp30) cc_final: 0.8922 (tp30) REVERT: A 660 ARG cc_start: 0.8736 (tpt90) cc_final: 0.8440 (tpt170) REVERT: A 664 ILE cc_start: 0.9155 (tp) cc_final: 0.8892 (pp) REVERT: A 668 ASN cc_start: 0.8646 (t0) cc_final: 0.8038 (t0) REVERT: A 676 SER cc_start: 0.8655 (m) cc_final: 0.8187 (p) REVERT: A 685 SER cc_start: 0.8874 (m) cc_final: 0.8389 (p) REVERT: B 560 LYS cc_start: 0.8385 (tttt) cc_final: 0.8081 (pttt) REVERT: B 613 SER cc_start: 0.9378 (m) cc_final: 0.9065 (p) REVERT: B 626 SER cc_start: 0.9073 (m) cc_final: 0.8575 (p) REVERT: B 652 GLU cc_start: 0.9072 (tt0) cc_final: 0.8721 (tt0) REVERT: B 655 GLU cc_start: 0.9200 (tp30) cc_final: 0.8947 (tp30) REVERT: B 658 GLU cc_start: 0.9182 (tp30) cc_final: 0.8972 (mp0) REVERT: B 660 ARG cc_start: 0.8694 (tpp-160) cc_final: 0.8431 (tpt170) REVERT: B 668 ASN cc_start: 0.8648 (t0) cc_final: 0.8208 (t0) REVERT: B 676 SER cc_start: 0.8924 (m) cc_final: 0.8407 (p) REVERT: B 685 SER cc_start: 0.8798 (m) cc_final: 0.8399 (p) REVERT: C 560 LYS cc_start: 0.8511 (tttt) cc_final: 0.8227 (pttt) REVERT: C 572 ASN cc_start: 0.9015 (t0) cc_final: 0.8711 (t0) REVERT: C 578 ASP cc_start: 0.8481 (m-30) cc_final: 0.8265 (m-30) REVERT: C 626 SER cc_start: 0.8942 (m) cc_final: 0.8369 (p) REVERT: C 676 SER cc_start: 0.8732 (m) cc_final: 0.8447 (t) REVERT: C 685 SER cc_start: 0.9020 (m) cc_final: 0.8486 (p) REVERT: D 560 LYS cc_start: 0.8373 (tttt) cc_final: 0.8114 (pttt) REVERT: D 626 SER cc_start: 0.9058 (m) cc_final: 0.8669 (p) REVERT: D 652 GLU cc_start: 0.8885 (tt0) cc_final: 0.8362 (tt0) REVERT: D 655 GLU cc_start: 0.9210 (tp30) cc_final: 0.8972 (tp30) REVERT: D 660 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.8569 (tpp-160) REVERT: D 668 ASN cc_start: 0.8684 (t0) cc_final: 0.8376 (t0) REVERT: D 676 SER cc_start: 0.8996 (m) cc_final: 0.8546 (p) REVERT: D 693 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: E 560 LYS cc_start: 0.8411 (tttt) cc_final: 0.8141 (pttt) REVERT: E 575 ASN cc_start: 0.8260 (m-40) cc_final: 0.7478 (m-40) REVERT: E 578 ASP cc_start: 0.8431 (m-30) cc_final: 0.7863 (m-30) REVERT: E 612 SER cc_start: 0.9571 (p) cc_final: 0.9330 (m) REVERT: E 626 SER cc_start: 0.8963 (m) cc_final: 0.8199 (p) REVERT: E 648 ASP cc_start: 0.9018 (m-30) cc_final: 0.8739 (m-30) REVERT: E 652 GLU cc_start: 0.8697 (tt0) cc_final: 0.8312 (tt0) REVERT: E 655 GLU cc_start: 0.9137 (tp30) cc_final: 0.8886 (tp30) REVERT: E 660 ARG cc_start: 0.8633 (tpt90) cc_final: 0.8223 (tpt170) REVERT: E 668 ASN cc_start: 0.8664 (t0) cc_final: 0.8148 (t0) REVERT: E 676 SER cc_start: 0.8770 (m) cc_final: 0.8312 (p) REVERT: E 685 SER cc_start: 0.8963 (m) cc_final: 0.8625 (p) REVERT: E 720 TYR cc_start: 0.7890 (m-10) cc_final: 0.7557 (m-10) REVERT: F 560 LYS cc_start: 0.8407 (tttm) cc_final: 0.7939 (pttt) REVERT: F 572 ASN cc_start: 0.9175 (t0) cc_final: 0.8922 (t0) REVERT: F 578 ASP cc_start: 0.8553 (m-30) cc_final: 0.8221 (m-30) REVERT: F 626 SER cc_start: 0.9027 (m) cc_final: 0.8540 (p) REVERT: F 652 GLU cc_start: 0.8920 (tt0) cc_final: 0.8511 (tt0) REVERT: F 668 ASN cc_start: 0.8738 (t0) cc_final: 0.8443 (t0) REVERT: F 676 SER cc_start: 0.8860 (m) cc_final: 0.8324 (p) REVERT: F 703 GLN cc_start: 0.8590 (tp40) cc_final: 0.8387 (mm-40) REVERT: G 572 ASN cc_start: 0.8897 (t0) cc_final: 0.8639 (t0) REVERT: G 575 ASN cc_start: 0.8314 (m-40) cc_final: 0.7939 (m110) REVERT: G 578 ASP cc_start: 0.8583 (m-30) cc_final: 0.8292 (m-30) REVERT: G 590 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8725 (mt-10) REVERT: G 612 SER cc_start: 0.9506 (p) cc_final: 0.9095 (m) REVERT: G 626 SER cc_start: 0.9122 (m) cc_final: 0.8486 (p) REVERT: G 652 GLU cc_start: 0.8964 (tt0) cc_final: 0.8689 (tt0) REVERT: G 660 ARG cc_start: 0.8629 (tpt90) cc_final: 0.8360 (tpt170) REVERT: G 668 ASN cc_start: 0.8781 (t0) cc_final: 0.8244 (t0) REVERT: G 676 SER cc_start: 0.8917 (m) cc_final: 0.8463 (p) REVERT: G 685 SER cc_start: 0.8901 (m) cc_final: 0.8508 (p) REVERT: G 693 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8403 (pm20) outliers start: 41 outliers final: 27 residues processed: 445 average time/residue: 0.5318 time to fit residues: 256.1712 Evaluate side-chains 433 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 404 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 703 GLN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 526 ILE Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 44 optimal weight: 30.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN E 572 ASN G 630 ASN G 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.086987 restraints weight = 17578.237| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.80 r_work: 0.2816 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11669 Z= 0.148 Angle : 0.676 8.533 15883 Z= 0.344 Chirality : 0.044 0.196 1967 Planarity : 0.004 0.039 2030 Dihedral : 3.744 12.975 1631 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.40 % Allowed : 30.27 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.23), residues: 1435 helix: 2.94 (0.19), residues: 637 sheet: 0.47 (0.31), residues: 273 loop : 0.42 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 660 TYR 0.012 0.001 TYR G 631 PHE 0.019 0.001 PHE C 567 TRP 0.009 0.001 TRP C 694 HIS 0.002 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00333 (11669) covalent geometry : angle 0.67579 (15883) hydrogen bonds : bond 0.03677 ( 760) hydrogen bonds : angle 3.54654 ( 2208) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 409 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.8196 (m-40) cc_final: 0.7902 (m110) REVERT: A 578 ASP cc_start: 0.8565 (m-30) cc_final: 0.8192 (m-30) REVERT: A 660 ARG cc_start: 0.8755 (tpt90) cc_final: 0.8479 (tpt170) REVERT: A 664 ILE cc_start: 0.9186 (tp) cc_final: 0.8915 (pp) REVERT: A 668 ASN cc_start: 0.8667 (t0) cc_final: 0.8056 (t0) REVERT: A 676 SER cc_start: 0.8691 (m) cc_final: 0.8230 (p) REVERT: A 685 SER cc_start: 0.8911 (m) cc_final: 0.8419 (p) REVERT: B 626 SER cc_start: 0.9147 (m) cc_final: 0.8679 (p) REVERT: B 652 GLU cc_start: 0.9060 (tt0) cc_final: 0.8661 (tt0) REVERT: B 655 GLU cc_start: 0.9205 (tp30) cc_final: 0.8869 (tp30) REVERT: B 658 GLU cc_start: 0.9187 (tp30) cc_final: 0.8982 (mp0) REVERT: B 660 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8434 (tpt170) REVERT: B 668 ASN cc_start: 0.8670 (t0) cc_final: 0.8238 (t0) REVERT: B 676 SER cc_start: 0.8944 (m) cc_final: 0.8455 (p) REVERT: B 685 SER cc_start: 0.8832 (m) cc_final: 0.8445 (p) REVERT: C 560 LYS cc_start: 0.8537 (tttt) cc_final: 0.8250 (pttt) REVERT: C 572 ASN cc_start: 0.9062 (t0) cc_final: 0.8732 (t0) REVERT: C 578 ASP cc_start: 0.8491 (m-30) cc_final: 0.8258 (m-30) REVERT: C 626 SER cc_start: 0.9089 (m) cc_final: 0.8505 (p) REVERT: C 676 SER cc_start: 0.8735 (m) cc_final: 0.8462 (t) REVERT: C 685 SER cc_start: 0.9060 (m) cc_final: 0.8513 (p) REVERT: D 560 LYS cc_start: 0.8312 (tttt) cc_final: 0.8070 (pttt) REVERT: D 613 SER cc_start: 0.9415 (t) cc_final: 0.9007 (p) REVERT: D 626 SER cc_start: 0.9062 (m) cc_final: 0.8683 (p) REVERT: D 652 GLU cc_start: 0.8880 (tt0) cc_final: 0.8296 (tt0) REVERT: D 655 GLU cc_start: 0.9216 (tp30) cc_final: 0.8968 (tp30) REVERT: D 660 ARG cc_start: 0.8826 (tpp-160) cc_final: 0.8580 (tpp-160) REVERT: D 668 ASN cc_start: 0.8702 (t0) cc_final: 0.8389 (t0) REVERT: D 676 SER cc_start: 0.9017 (m) cc_final: 0.8565 (p) REVERT: D 693 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8261 (pm20) REVERT: D 723 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7543 (tt) REVERT: E 560 LYS cc_start: 0.8466 (tttt) cc_final: 0.8211 (pttt) REVERT: E 575 ASN cc_start: 0.8227 (m-40) cc_final: 0.7447 (m-40) REVERT: E 578 ASP cc_start: 0.8487 (m-30) cc_final: 0.7934 (m-30) REVERT: E 612 SER cc_start: 0.9591 (p) cc_final: 0.9339 (m) REVERT: E 626 SER cc_start: 0.9038 (m) cc_final: 0.8300 (p) REVERT: E 652 GLU cc_start: 0.8727 (tt0) cc_final: 0.8354 (tt0) REVERT: E 655 GLU cc_start: 0.9142 (tp30) cc_final: 0.8895 (tp30) REVERT: E 660 ARG cc_start: 0.8703 (tpt90) cc_final: 0.8312 (tpt170) REVERT: E 668 ASN cc_start: 0.8744 (t0) cc_final: 0.8095 (t0) REVERT: E 676 SER cc_start: 0.8815 (m) cc_final: 0.8370 (p) REVERT: E 685 SER cc_start: 0.8990 (m) cc_final: 0.8633 (p) REVERT: E 720 TYR cc_start: 0.8001 (m-10) cc_final: 0.7670 (m-10) REVERT: F 572 ASN cc_start: 0.9176 (t0) cc_final: 0.8888 (t0) REVERT: F 578 ASP cc_start: 0.8561 (m-30) cc_final: 0.8202 (m-30) REVERT: F 626 SER cc_start: 0.9014 (m) cc_final: 0.8539 (p) REVERT: F 652 GLU cc_start: 0.8904 (tt0) cc_final: 0.8456 (tt0) REVERT: F 668 ASN cc_start: 0.8808 (t0) cc_final: 0.8502 (t0) REVERT: F 676 SER cc_start: 0.8901 (m) cc_final: 0.8366 (p) REVERT: G 572 ASN cc_start: 0.8969 (t0) cc_final: 0.8710 (t0) REVERT: G 575 ASN cc_start: 0.8350 (m-40) cc_final: 0.8001 (m110) REVERT: G 578 ASP cc_start: 0.8632 (m-30) cc_final: 0.8251 (m-30) REVERT: G 590 GLU cc_start: 0.9058 (tt0) cc_final: 0.8812 (mt-10) REVERT: G 612 SER cc_start: 0.9548 (p) cc_final: 0.9148 (m) REVERT: G 622 ARG cc_start: 0.8702 (mmp80) cc_final: 0.8478 (tpp-160) REVERT: G 626 SER cc_start: 0.9276 (m) cc_final: 0.8679 (p) REVERT: G 652 GLU cc_start: 0.8994 (tt0) cc_final: 0.8707 (tt0) REVERT: G 658 GLU cc_start: 0.9395 (tp30) cc_final: 0.9147 (tp30) REVERT: G 660 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8588 (tpt170) REVERT: G 668 ASN cc_start: 0.8812 (t0) cc_final: 0.8285 (t0) REVERT: G 676 SER cc_start: 0.8924 (m) cc_final: 0.8476 (p) REVERT: G 685 SER cc_start: 0.8908 (m) cc_final: 0.8522 (p) REVERT: G 693 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8473 (pm20) REVERT: G 714 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8447 (mtm-85) outliers start: 40 outliers final: 30 residues processed: 427 average time/residue: 0.5290 time to fit residues: 244.1219 Evaluate side-chains 436 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 703 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 33 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN F 703 GLN G 630 ASN G 703 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.086796 restraints weight = 17716.071| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.73 r_work: 0.2803 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11669 Z= 0.151 Angle : 0.709 12.608 15883 Z= 0.361 Chirality : 0.044 0.209 1967 Planarity : 0.004 0.033 2030 Dihedral : 3.769 13.226 1631 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.89 % Allowed : 31.12 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.23), residues: 1435 helix: 2.88 (0.19), residues: 637 sheet: 0.50 (0.31), residues: 273 loop : 0.44 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 591 TYR 0.011 0.001 TYR G 631 PHE 0.014 0.001 PHE D 567 TRP 0.009 0.001 TRP C 694 HIS 0.002 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00340 (11669) covalent geometry : angle 0.70893 (15883) hydrogen bonds : bond 0.03716 ( 760) hydrogen bonds : angle 3.57256 ( 2208) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2870 Ramachandran restraints generated. 1435 Oldfield, 0 Emsley, 1435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 406 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.8082 (m-40) cc_final: 0.7778 (m110) REVERT: A 578 ASP cc_start: 0.8457 (m-30) cc_final: 0.8061 (m-30) REVERT: A 660 ARG cc_start: 0.8705 (tpt90) cc_final: 0.8419 (tpt170) REVERT: A 664 ILE cc_start: 0.9143 (tp) cc_final: 0.8853 (pp) REVERT: A 668 ASN cc_start: 0.8559 (t0) cc_final: 0.7955 (t0) REVERT: A 676 SER cc_start: 0.8577 (m) cc_final: 0.8120 (p) REVERT: A 685 SER cc_start: 0.8814 (m) cc_final: 0.8332 (p) REVERT: B 560 LYS cc_start: 0.8481 (tttt) cc_final: 0.8194 (pttt) REVERT: B 626 SER cc_start: 0.9089 (m) cc_final: 0.8617 (p) REVERT: B 652 GLU cc_start: 0.9069 (tt0) cc_final: 0.8689 (tt0) REVERT: B 655 GLU cc_start: 0.9228 (tp30) cc_final: 0.8995 (tp30) REVERT: B 658 GLU cc_start: 0.9176 (tp30) cc_final: 0.8951 (mp0) REVERT: B 660 ARG cc_start: 0.8632 (tpp-160) cc_final: 0.8351 (tpt170) REVERT: B 668 ASN cc_start: 0.8595 (t0) cc_final: 0.8151 (t0) REVERT: B 676 SER cc_start: 0.8808 (m) cc_final: 0.8296 (p) REVERT: B 685 SER cc_start: 0.8735 (m) cc_final: 0.8343 (p) REVERT: C 560 LYS cc_start: 0.8514 (tttt) cc_final: 0.8237 (pttt) REVERT: C 572 ASN cc_start: 0.9034 (t0) cc_final: 0.8724 (t0) REVERT: C 575 ASN cc_start: 0.8187 (m-40) cc_final: 0.7962 (m110) REVERT: C 578 ASP cc_start: 0.8407 (m-30) cc_final: 0.8173 (m-30) REVERT: C 626 SER cc_start: 0.9020 (m) cc_final: 0.8439 (p) REVERT: C 668 ASN cc_start: 0.8413 (t0) cc_final: 0.8039 (t0) REVERT: C 676 SER cc_start: 0.8642 (m) cc_final: 0.8381 (t) REVERT: D 560 LYS cc_start: 0.8309 (tttt) cc_final: 0.8040 (pttt) REVERT: D 613 SER cc_start: 0.9398 (t) cc_final: 0.8987 (p) REVERT: D 626 SER cc_start: 0.8992 (m) cc_final: 0.8618 (p) REVERT: D 652 GLU cc_start: 0.8821 (tt0) cc_final: 0.8308 (tt0) REVERT: D 655 GLU cc_start: 0.9217 (tp30) cc_final: 0.8977 (tp30) REVERT: D 660 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8503 (tpp-160) REVERT: D 668 ASN cc_start: 0.8620 (t0) cc_final: 0.8316 (t0) REVERT: D 676 SER cc_start: 0.8920 (m) cc_final: 0.8465 (p) REVERT: D 693 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: D 723 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (tt) REVERT: E 560 LYS cc_start: 0.8444 (tttt) cc_final: 0.8194 (pttt) REVERT: E 575 ASN cc_start: 0.8218 (m-40) cc_final: 0.7423 (m-40) REVERT: E 578 ASP cc_start: 0.8397 (m-30) cc_final: 0.7860 (m-30) REVERT: E 612 SER cc_start: 0.9560 (p) cc_final: 0.9272 (m) REVERT: E 626 SER cc_start: 0.8953 (m) cc_final: 0.8221 (p) REVERT: E 648 ASP cc_start: 0.9005 (m-30) cc_final: 0.8746 (m-30) REVERT: E 652 GLU cc_start: 0.8694 (tt0) cc_final: 0.8336 (tt0) REVERT: E 655 GLU cc_start: 0.9126 (tp30) cc_final: 0.8879 (tp30) REVERT: E 660 ARG cc_start: 0.8623 (tpt90) cc_final: 0.8235 (tpt170) REVERT: E 668 ASN cc_start: 0.8644 (t0) cc_final: 0.7991 (t0) REVERT: E 676 SER cc_start: 0.8716 (m) cc_final: 0.8260 (p) REVERT: E 685 SER cc_start: 0.8883 (m) cc_final: 0.8540 (p) REVERT: E 720 TYR cc_start: 0.7879 (m-10) cc_final: 0.7549 (m-10) REVERT: F 572 ASN cc_start: 0.9067 (t0) cc_final: 0.8843 (t0) REVERT: F 578 ASP cc_start: 0.8478 (m-30) cc_final: 0.8115 (m-30) REVERT: F 626 SER cc_start: 0.8931 (m) cc_final: 0.8456 (p) REVERT: F 652 GLU cc_start: 0.8958 (tt0) cc_final: 0.8613 (tt0) REVERT: F 668 ASN cc_start: 0.8713 (t0) cc_final: 0.8408 (t0) REVERT: F 676 SER cc_start: 0.8787 (m) cc_final: 0.8260 (p) REVERT: G 572 ASN cc_start: 0.8918 (t0) cc_final: 0.8711 (t0) REVERT: G 575 ASN cc_start: 0.8224 (m-40) cc_final: 0.7872 (m110) REVERT: G 578 ASP cc_start: 0.8521 (m-30) cc_final: 0.8181 (m-30) REVERT: G 590 GLU cc_start: 0.9033 (tt0) cc_final: 0.8777 (mt-10) REVERT: G 612 SER cc_start: 0.9491 (p) cc_final: 0.9056 (m) REVERT: G 626 SER cc_start: 0.9217 (m) cc_final: 0.8623 (p) REVERT: G 652 GLU cc_start: 0.8904 (tt0) cc_final: 0.8672 (tt0) REVERT: G 660 ARG cc_start: 0.8596 (tpt90) cc_final: 0.8346 (tpt170) REVERT: G 668 ASN cc_start: 0.8788 (t0) cc_final: 0.8274 (t0) REVERT: G 676 SER cc_start: 0.8838 (m) cc_final: 0.8388 (p) REVERT: G 685 SER cc_start: 0.8834 (m) cc_final: 0.8459 (p) REVERT: G 693 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: G 714 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8341 (mtm-85) outliers start: 34 outliers final: 28 residues processed: 421 average time/residue: 0.5475 time to fit residues: 249.3503 Evaluate side-chains 435 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 404 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 703 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN G 703 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.084799 restraints weight = 17838.168| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.78 r_work: 0.2843 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11669 Z= 0.160 Angle : 0.738 12.740 15883 Z= 0.375 Chirality : 0.044 0.220 1967 Planarity : 0.004 0.044 2030 Dihedral : 3.817 14.863 1631 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.23 % Allowed : 30.27 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.23), residues: 1435 helix: 2.83 (0.19), residues: 637 sheet: 0.53 (0.31), residues: 273 loop : 0.45 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 660 TYR 0.011 0.001 TYR F 720 PHE 0.017 0.001 PHE D 567 TRP 0.009 0.001 TRP C 694 HIS 0.003 0.001 HIS D 607 Details of bonding type rmsd covalent geometry : bond 0.00363 (11669) covalent geometry : angle 0.73775 (15883) hydrogen bonds : bond 0.03788 ( 760) hydrogen bonds : angle 3.63421 ( 2208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.81 seconds wall clock time: 84 minutes 20.83 seconds (5060.83 seconds total)