Starting phenix.real_space_refine on Tue Jul 29 21:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a46_11629/07_2025/7a46_11629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a46_11629/07_2025/7a46_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_11629/07_2025/7a46_11629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a46_11629/07_2025/7a46_11629.map" model { file = "/net/cci-nas-00/data/ceres_data/7a46_11629/07_2025/7a46_11629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a46_11629/07_2025/7a46_11629.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.094 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D, G, F Time building chain proxies: 4.21, per 1000 atoms: 0.37 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: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.64 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: 3.37 Time building geometry restraints manager: 3.75 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.180 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.720 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 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:50.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP C 694 HIS 0.004 0.001 HIS A 707 PHE 0.008 0.001 PHE G 680 TYR 0.009 0.001 TYR B 606 ARG 0.002 0.000 ARG A 714 Details of bonding type rmsd hydrogen bonds : bond 0.15464 ( 760) hydrogen bonds : angle 5.81730 ( 2208) covalent geometry : bond 0.00657 (11669) covalent geometry : angle 0.60979 (15883) *********************** 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 : 1.244 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: 0.8557 (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: 0.8459 (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: 0.8970 (m) cc_final: 0.8475 (p) REVERT: B 685 SER cc_start: 0.8779 (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: 0.8905 (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: 0.9150 (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: 1.0755 time to fit residues: 637.2154 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 : 1.178 ------------------------------------------------------------------------------- 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 130 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 0.0060 chunk 78 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 89 optimal weight: 20.0000 chunk 139 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.124745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086052 restraints weight = 17450.104| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.67 r_work: 0.2776 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2294 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= 0.125 Angle : 0.588 8.458 15883 Z= 0.299 Chirality : 0.042 0.190 1967 Planarity : 0.003 0.028 2030 Dihedral : 6.001 41.624 1686 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.68 % Allowed : 20.75 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1435 helix: 1.44 (0.18), residues: 644 sheet: -0.62 (0.31), residues: 273 loop : -0.24 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 694 HIS 0.002 0.001 HIS G 607 PHE 0.008 0.001 PHE E 680 TYR 0.010 0.001 TYR E 606 ARG 0.006 0.001 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 760) hydrogen bonds : angle 4.02658 ( 2208) covalent geometry : bond 0.00262 (11669) covalent geometry : angle 0.58785 (15883) *********************** 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: 55 poor density : 462 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.8985 (t0) cc_final: 0.8732 (t0) REVERT: A 575 ASN cc_start: 0.8559 (m-40) cc_final: 0.8145 (m-40) REVERT: A 578 ASP cc_start: 0.8684 (m-30) cc_final: 0.8381 (m-30) REVERT: A 613 SER cc_start: 0.9504 (t) cc_final: 0.9050 (p) REVERT: A 647 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8035 (mttm) REVERT: A 654 MET cc_start: 0.9122 (mmm) cc_final: 0.8900 (mmm) REVERT: A 656 ASN cc_start: 0.7967 (t0) cc_final: 0.7727 (t0) REVERT: A 659 ILE cc_start: 0.8998 (mm) cc_final: 0.8760 (mp) REVERT: A 660 ARG cc_start: 0.8671 (tpt90) cc_final: 0.8436 (tpp-160) REVERT: A 668 ASN cc_start: 0.8880 (t0) cc_final: 0.8292 (t0) REVERT: A 676 SER cc_start: 0.8672 (m) cc_final: 0.8214 (p) REVERT: A 681 THR cc_start: 0.8513 (m) cc_final: 0.8136 (p) REVERT: A 685 SER cc_start: 0.8890 (m) cc_final: 0.8390 (p) REVERT: A 703 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8480 (tp40) REVERT: B 572 ASN cc_start: 0.9171 (t0) cc_final: 0.8850 (t0) REVERT: B 578 ASP cc_start: 0.8523 (m-30) cc_final: 0.8030 (m-30) REVERT: B 613 SER cc_start: 0.9500 (m) cc_final: 0.9183 (p) REVERT: B 626 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8820 (p) REVERT: B 634 ASP cc_start: 0.8845 (t0) cc_final: 0.8631 (t0) REVERT: B 660 ARG cc_start: 0.8797 (tpp-160) cc_final: 0.8420 (tpm170) REVERT: B 668 ASN cc_start: 0.8514 (t0) cc_final: 0.8062 (t0) REVERT: B 676 SER cc_start: 0.9105 (m) cc_final: 0.8595 (p) REVERT: B 685 SER cc_start: 0.8802 (m) cc_final: 0.8464 (p) REVERT: C 572 ASN cc_start: 0.9083 (t0) cc_final: 0.8632 (t0) REVERT: C 596 SER cc_start: 0.9499 (p) cc_final: 0.8826 (p) REVERT: C 626 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8502 (p) REVERT: C 654 MET cc_start: 0.8873 (mmm) cc_final: 0.8648 (mmm) REVERT: C 655 GLU cc_start: 0.9108 (tp30) cc_final: 0.8860 (tp30) REVERT: C 658 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8965 (mp0) REVERT: C 660 ARG cc_start: 0.8454 (tpt90) cc_final: 0.8161 (tpp-160) REVERT: C 676 SER cc_start: 0.9119 (m) cc_final: 0.8654 (p) REVERT: C 685 SER cc_start: 0.8910 (m) cc_final: 0.8523 (p) REVERT: D 613 SER cc_start: 0.9447 (t) cc_final: 0.9201 (p) REVERT: D 624 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (pp) REVERT: D 626 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8682 (p) REVERT: D 652 GLU cc_start: 0.9121 (tt0) cc_final: 0.8629 (tt0) REVERT: D 655 GLU cc_start: 0.9205 (tp30) cc_final: 0.8866 (tp30) REVERT: D 660 ARG cc_start: 0.8988 (tpp-160) cc_final: 0.8784 (tpm170) REVERT: D 666 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9067 (mm-30) REVERT: D 668 ASN cc_start: 0.8718 (t0) cc_final: 0.8315 (t0) REVERT: D 676 SER cc_start: 0.9260 (m) cc_final: 0.8908 (p) REVERT: E 574 MET cc_start: 0.9348 (ttm) cc_final: 0.9111 (mtm) REVERT: E 575 ASN cc_start: 0.8473 (m-40) cc_final: 0.8225 (m110) REVERT: E 578 ASP cc_start: 0.8672 (m-30) cc_final: 0.8243 (m-30) REVERT: E 612 SER cc_start: 0.9565 (p) cc_final: 0.9345 (m) REVERT: E 613 SER cc_start: 0.9450 (m) cc_final: 0.9113 (p) REVERT: E 626 SER cc_start: 0.9154 (m) cc_final: 0.8560 (p) REVERT: E 648 ASP cc_start: 0.8895 (m-30) cc_final: 0.8606 (m-30) REVERT: E 652 GLU cc_start: 0.8987 (tt0) cc_final: 0.8598 (tt0) REVERT: E 655 GLU cc_start: 0.9195 (tp30) cc_final: 0.8903 (tp30) REVERT: E 660 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8454 (tpt170) REVERT: E 666 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9051 (tp30) REVERT: E 668 ASN cc_start: 0.8632 (t0) cc_final: 0.7929 (t0) REVERT: E 676 SER cc_start: 0.8938 (m) cc_final: 0.8482 (p) REVERT: E 681 THR cc_start: 0.8462 (m) cc_final: 0.8238 (p) REVERT: E 685 SER cc_start: 0.8980 (m) cc_final: 0.8648 (p) REVERT: E 720 TYR cc_start: 0.8004 (m-10) cc_final: 0.7683 (m-10) REVERT: F 572 ASN cc_start: 0.9271 (t0) cc_final: 0.8920 (t0) REVERT: F 575 ASN cc_start: 0.8134 (m-40) cc_final: 0.7672 (m-40) REVERT: F 578 ASP cc_start: 0.8524 (m-30) cc_final: 0.7953 (m-30) REVERT: F 590 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8847 (mt-10) REVERT: F 626 SER cc_start: 0.9078 (m) cc_final: 0.8555 (p) REVERT: F 634 ASP cc_start: 0.8959 (t0) cc_final: 0.8741 (t0) REVERT: F 652 GLU cc_start: 0.8988 (tt0) cc_final: 0.8525 (tt0) REVERT: F 655 GLU cc_start: 0.9083 (tp30) cc_final: 0.8810 (tp30) REVERT: F 660 ARG cc_start: 0.9012 (tpp-160) cc_final: 0.8789 (tpm170) REVERT: F 668 ASN cc_start: 0.8508 (t0) cc_final: 0.8003 (t0) REVERT: F 676 SER cc_start: 0.9012 (m) cc_final: 0.8485 (p) REVERT: F 685 SER cc_start: 0.8984 (m) cc_final: 0.8705 (p) REVERT: F 723 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7934 (tt) REVERT: G 572 ASN cc_start: 0.9242 (t0) cc_final: 0.9036 (t0) REVERT: G 578 ASP cc_start: 0.8707 (m-30) cc_final: 0.8476 (m-30) REVERT: G 590 GLU cc_start: 0.9044 (tt0) cc_final: 0.8808 (mt-10) REVERT: G 612 SER cc_start: 0.9516 (p) cc_final: 0.9225 (m) REVERT: G 626 SER cc_start: 0.9153 (m) cc_final: 0.8566 (p) REVERT: G 634 ASP cc_start: 0.8716 (t0) cc_final: 0.8472 (t0) REVERT: G 652 GLU cc_start: 0.9019 (tt0) cc_final: 0.8622 (tt0) REVERT: G 655 GLU cc_start: 0.9203 (tp30) cc_final: 0.8901 (tp30) REVERT: G 660 ARG cc_start: 0.8691 (tpt90) cc_final: 0.8348 (tpt170) REVERT: G 668 ASN cc_start: 0.8773 (t0) cc_final: 0.8166 (t0) REVERT: G 676 SER cc_start: 0.8989 (m) cc_final: 0.8573 (p) REVERT: G 685 SER cc_start: 0.8983 (m) cc_final: 0.8592 (p) REVERT: G 713 VAL cc_start: 0.9527 (t) cc_final: 0.9201 (p) outliers start: 55 outliers final: 26 residues processed: 485 average time/residue: 1.0091 time to fit residues: 533.9103 Evaluate side-chains 445 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 412 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 624 ILE 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 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 38 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 ASN A 644 GLN A 703 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085852 restraints weight = 17632.877| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.78 r_work: 0.2789 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2661 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= 0.141 Angle : 0.571 8.705 15883 Z= 0.287 Chirality : 0.042 0.187 1967 Planarity : 0.003 0.037 2030 Dihedral : 4.405 40.165 1645 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.66 % Allowed : 23.38 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1435 helix: 2.37 (0.19), residues: 644 sheet: -0.22 (0.30), residues: 273 loop : 0.07 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 694 HIS 0.003 0.001 HIS A 707 PHE 0.009 0.001 PHE E 680 TYR 0.011 0.001 TYR E 606 ARG 0.006 0.001 ARG D 591 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 760) hydrogen bonds : angle 3.75025 ( 2208) covalent geometry : bond 0.00316 (11669) covalent geometry : angle 0.57092 (15883) *********************** 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 478 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 435 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9094 (t0) cc_final: 0.8834 (t0) REVERT: A 575 ASN cc_start: 0.8423 (m-40) cc_final: 0.8051 (m-40) REVERT: A 578 ASP cc_start: 0.8704 (m-30) cc_final: 0.8371 (m-30) REVERT: A 634 ASP cc_start: 0.8730 (t0) cc_final: 0.8518 (t0) REVERT: A 647 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8022 (mttm) REVERT: A 668 ASN cc_start: 0.8829 (t0) cc_final: 0.8191 (t0) REVERT: A 676 SER cc_start: 0.8656 (m) cc_final: 0.8182 (p) REVERT: A 681 THR cc_start: 0.8543 (m) cc_final: 0.8191 (p) REVERT: A 685 SER cc_start: 0.8879 (m) cc_final: 0.8389 (p) REVERT: B 572 ASN cc_start: 0.9080 (t0) cc_final: 0.8872 (t0) REVERT: B 578 ASP cc_start: 0.8635 (m-30) cc_final: 0.8385 (m-30) REVERT: B 613 SER cc_start: 0.9510 (m) cc_final: 0.9246 (p) REVERT: B 624 ILE cc_start: 0.8788 (pt) cc_final: 0.8568 (pp) REVERT: B 626 SER cc_start: 0.9245 (m) cc_final: 0.8709 (p) REVERT: B 634 ASP cc_start: 0.8806 (t0) cc_final: 0.8563 (t0) REVERT: B 641 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8636 (ttpp) REVERT: B 660 ARG cc_start: 0.8837 (tpp-160) cc_final: 0.8516 (tpt170) REVERT: B 668 ASN cc_start: 0.8607 (t0) cc_final: 0.8145 (t0) REVERT: B 676 SER cc_start: 0.9063 (m) cc_final: 0.8560 (p) REVERT: B 685 SER cc_start: 0.8800 (m) cc_final: 0.8441 (p) REVERT: C 572 ASN cc_start: 0.9031 (t0) cc_final: 0.8507 (t0) REVERT: C 626 SER cc_start: 0.9143 (m) cc_final: 0.8604 (p) REVERT: C 655 GLU cc_start: 0.9094 (tp30) cc_final: 0.8825 (tp30) REVERT: C 676 SER cc_start: 0.9045 (m) cc_final: 0.8596 (p) REVERT: C 685 SER cc_start: 0.9045 (m) cc_final: 0.8590 (p) REVERT: C 703 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8477 (mm110) REVERT: D 560 LYS cc_start: 0.8528 (tttt) cc_final: 0.8078 (pttt) REVERT: D 590 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8886 (mt-10) REVERT: D 613 SER cc_start: 0.9387 (t) cc_final: 0.9065 (p) REVERT: D 626 SER cc_start: 0.9151 (m) cc_final: 0.8795 (p) REVERT: D 648 ASP cc_start: 0.8941 (m-30) cc_final: 0.8737 (m-30) REVERT: D 652 GLU cc_start: 0.8973 (tt0) cc_final: 0.8314 (tt0) REVERT: D 655 GLU cc_start: 0.9238 (tp30) cc_final: 0.8906 (tp30) REVERT: D 660 ARG cc_start: 0.8981 (tpp-160) cc_final: 0.8731 (tpm170) REVERT: D 666 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9158 (mm-30) REVERT: D 668 ASN cc_start: 0.8742 (t0) cc_final: 0.8364 (t0) REVERT: D 676 SER cc_start: 0.9137 (m) cc_final: 0.8706 (p) REVERT: D 693 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8316 (pm20) REVERT: D 723 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7679 (tt) REVERT: E 560 LYS cc_start: 0.8378 (tttt) cc_final: 0.8066 (pttt) REVERT: E 575 ASN cc_start: 0.8379 (m-40) cc_final: 0.7939 (m110) REVERT: E 578 ASP cc_start: 0.8522 (m-30) cc_final: 0.8056 (m-30) REVERT: E 602 ASP cc_start: 0.9092 (p0) cc_final: 0.8846 (p0) REVERT: E 612 SER cc_start: 0.9610 (p) cc_final: 0.9406 (m) REVERT: E 613 SER cc_start: 0.9508 (m) cc_final: 0.9192 (p) REVERT: E 626 SER cc_start: 0.9076 (m) cc_final: 0.8370 (p) REVERT: E 648 ASP cc_start: 0.8981 (m-30) cc_final: 0.8719 (m-30) REVERT: E 652 GLU cc_start: 0.8942 (tt0) cc_final: 0.8567 (tt0) REVERT: E 655 GLU cc_start: 0.9164 (tp30) cc_final: 0.8742 (tp30) REVERT: E 660 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8593 (tpp-160) REVERT: E 668 ASN cc_start: 0.8667 (t0) cc_final: 0.8133 (t0) REVERT: E 676 SER cc_start: 0.8855 (m) cc_final: 0.8407 (p) REVERT: E 681 THR cc_start: 0.8605 (m) cc_final: 0.8289 (p) REVERT: E 685 SER cc_start: 0.8990 (m) cc_final: 0.8645 (p) REVERT: E 703 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8362 (mm110) REVERT: E 720 TYR cc_start: 0.8032 (m-10) cc_final: 0.7747 (m-10) REVERT: F 572 ASN cc_start: 0.9274 (t0) cc_final: 0.8996 (t0) REVERT: F 575 ASN cc_start: 0.8177 (m-40) cc_final: 0.7733 (m-40) REVERT: F 578 ASP cc_start: 0.8534 (m-30) cc_final: 0.8068 (m-30) REVERT: F 626 SER cc_start: 0.9087 (m) cc_final: 0.8552 (p) REVERT: F 634 ASP cc_start: 0.8933 (t0) cc_final: 0.8695 (t0) REVERT: F 652 GLU cc_start: 0.9060 (tt0) cc_final: 0.8613 (tt0) REVERT: F 655 GLU cc_start: 0.9051 (tp30) cc_final: 0.8805 (tp30) REVERT: F 660 ARG cc_start: 0.8919 (tpp-160) cc_final: 0.8688 (tpm170) REVERT: F 668 ASN cc_start: 0.8614 (t0) cc_final: 0.8079 (t0) REVERT: F 676 SER cc_start: 0.8958 (m) cc_final: 0.8440 (p) REVERT: F 685 SER cc_start: 0.8945 (m) cc_final: 0.8623 (p) REVERT: F 703 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (mm-40) REVERT: G 572 ASN cc_start: 0.9109 (t0) cc_final: 0.8796 (t0) REVERT: G 575 ASN cc_start: 0.8495 (m-40) cc_final: 0.8156 (m-40) REVERT: G 578 ASP cc_start: 0.8620 (m-30) cc_final: 0.8350 (m-30) REVERT: G 612 SER cc_start: 0.9580 (p) cc_final: 0.9325 (m) REVERT: G 622 ARG cc_start: 0.8745 (mmp80) cc_final: 0.8200 (mmt90) REVERT: G 626 SER cc_start: 0.9225 (m) cc_final: 0.8714 (p) REVERT: G 652 GLU cc_start: 0.8969 (tt0) cc_final: 0.8687 (tt0) REVERT: G 655 GLU cc_start: 0.9175 (tp30) cc_final: 0.8928 (tp30) REVERT: G 668 ASN cc_start: 0.8789 (t0) cc_final: 0.8212 (t0) REVERT: G 676 SER cc_start: 0.8950 (m) cc_final: 0.8516 (p) REVERT: G 685 SER cc_start: 0.8954 (m) cc_final: 0.8539 (p) REVERT: G 693 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8519 (pm20) outliers start: 43 outliers final: 25 residues processed: 459 average time/residue: 1.0906 time to fit residues: 543.8768 Evaluate side-chains 441 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 411 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 647 LYS 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 C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL 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 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 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 570 PHE Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 702 SER Chi-restraints excluded: chain F residue 703 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN A 703 GLN B 556 GLN B 703 GLN C 575 ASN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.087223 restraints weight = 17424.909| |-----------------------------------------------------------------------------| r_work (start): 0.3000 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: 0.7617 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11669 Z= 0.123 Angle : 0.566 9.086 15883 Z= 0.281 Chirality : 0.042 0.176 1967 Planarity : 0.003 0.029 2030 Dihedral : 3.911 35.396 1637 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.57 % Allowed : 26.19 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1435 helix: 2.67 (0.19), residues: 644 sheet: -0.00 (0.30), residues: 273 loop : 0.24 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 694 HIS 0.003 0.001 HIS D 607 PHE 0.010 0.001 PHE A 567 TYR 0.010 0.001 TYR F 720 ARG 0.006 0.001 ARG B 697 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 760) hydrogen bonds : angle 3.59860 ( 2208) covalent geometry : bond 0.00273 (11669) covalent geometry : angle 0.56584 (15883) *********************** 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 473 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 431 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8078 (pttt) REVERT: A 575 ASN cc_start: 0.8359 (m-40) cc_final: 0.7961 (m-40) REVERT: A 578 ASP cc_start: 0.8669 (m-30) cc_final: 0.8350 (m-30) REVERT: A 634 ASP cc_start: 0.8653 (t0) cc_final: 0.8389 (t0) REVERT: A 647 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8003 (mttm) REVERT: A 652 GLU cc_start: 0.9081 (tt0) cc_final: 0.8774 (tt0) REVERT: A 664 ILE cc_start: 0.9181 (tp) cc_final: 0.8968 (pp) REVERT: A 668 ASN cc_start: 0.8772 (t0) cc_final: 0.8128 (t0) REVERT: A 676 SER cc_start: 0.8619 (m) cc_final: 0.8132 (p) REVERT: A 685 SER cc_start: 0.8878 (m) cc_final: 0.8387 (p) REVERT: B 560 LYS cc_start: 0.8449 (tttt) cc_final: 0.8054 (pttt) REVERT: B 578 ASP cc_start: 0.8560 (m-30) cc_final: 0.8243 (m-30) REVERT: B 613 SER cc_start: 0.9456 (m) cc_final: 0.9129 (p) REVERT: B 626 SER cc_start: 0.9208 (m) cc_final: 0.8709 (p) REVERT: B 641 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8628 (ttpp) REVERT: B 652 GLU cc_start: 0.9110 (tt0) cc_final: 0.8699 (tt0) REVERT: B 658 GLU cc_start: 0.9214 (tp30) cc_final: 0.8912 (mp0) REVERT: B 660 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8505 (tpt170) REVERT: B 668 ASN cc_start: 0.8627 (t0) cc_final: 0.8167 (t0) REVERT: B 676 SER cc_start: 0.9002 (m) cc_final: 0.8473 (p) REVERT: B 685 SER cc_start: 0.8861 (m) cc_final: 0.8499 (p) REVERT: C 560 LYS cc_start: 0.8392 (tppp) cc_final: 0.8139 (pttt) REVERT: C 572 ASN cc_start: 0.8995 (t0) cc_final: 0.8714 (t0) REVERT: C 575 ASN cc_start: 0.8294 (m-40) cc_final: 0.8084 (m110) REVERT: C 578 ASP cc_start: 0.8648 (m-30) cc_final: 0.8430 (m-30) REVERT: C 626 SER cc_start: 0.9090 (m) cc_final: 0.8543 (p) REVERT: C 655 GLU cc_start: 0.9076 (tp30) cc_final: 0.8800 (tp30) REVERT: C 660 ARG cc_start: 0.8420 (tpt90) cc_final: 0.8172 (tpt170) REVERT: C 676 SER cc_start: 0.9018 (m) cc_final: 0.8576 (p) REVERT: C 685 SER cc_start: 0.9063 (m) cc_final: 0.8589 (p) REVERT: D 560 LYS cc_start: 0.8416 (tttt) cc_final: 0.8135 (pttt) REVERT: D 575 ASN cc_start: 0.8577 (m-40) cc_final: 0.8360 (m110) REVERT: D 578 ASP cc_start: 0.8654 (m-30) cc_final: 0.8452 (m-30) REVERT: D 613 SER cc_start: 0.9388 (t) cc_final: 0.9039 (p) REVERT: D 626 SER cc_start: 0.9101 (m) cc_final: 0.8715 (p) REVERT: D 634 ASP cc_start: 0.8768 (t0) cc_final: 0.8559 (t0) REVERT: D 655 GLU cc_start: 0.9208 (tp30) cc_final: 0.8933 (tp30) REVERT: D 660 ARG cc_start: 0.8934 (tpp-160) cc_final: 0.8637 (tpm170) REVERT: D 666 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9135 (mm-30) REVERT: D 668 ASN cc_start: 0.8727 (t0) cc_final: 0.8368 (t0) REVERT: D 676 SER cc_start: 0.9106 (m) cc_final: 0.8670 (p) REVERT: D 693 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: D 723 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7650 (tt) REVERT: E 560 LYS cc_start: 0.8372 (tttt) cc_final: 0.8068 (pttt) REVERT: E 575 ASN cc_start: 0.8310 (m-40) cc_final: 0.7950 (m110) REVERT: E 578 ASP cc_start: 0.8434 (m-30) cc_final: 0.7965 (m-30) REVERT: E 596 SER cc_start: 0.9503 (p) cc_final: 0.9023 (m) REVERT: E 602 ASP cc_start: 0.9003 (p0) cc_final: 0.8756 (p0) REVERT: E 613 SER cc_start: 0.9498 (m) cc_final: 0.9208 (p) REVERT: E 626 SER cc_start: 0.9013 (m) cc_final: 0.8304 (p) REVERT: E 648 ASP cc_start: 0.8977 (m-30) cc_final: 0.8709 (m-30) REVERT: E 652 GLU cc_start: 0.8938 (tt0) cc_final: 0.8590 (tt0) REVERT: E 655 GLU cc_start: 0.9141 (tp30) cc_final: 0.8781 (tp30) REVERT: E 668 ASN cc_start: 0.8676 (t0) cc_final: 0.7992 (t0) REVERT: E 676 SER cc_start: 0.8863 (m) cc_final: 0.8418 (p) REVERT: E 685 SER cc_start: 0.8972 (m) cc_final: 0.8612 (p) REVERT: E 720 TYR cc_start: 0.8006 (m-10) cc_final: 0.7679 (m-10) REVERT: F 527 MET cc_start: 0.9253 (mtt) cc_final: 0.9045 (ptp) REVERT: F 572 ASN cc_start: 0.9244 (t0) cc_final: 0.8924 (t0) REVERT: F 575 ASN cc_start: 0.8210 (m-40) cc_final: 0.7736 (m-40) REVERT: F 578 ASP cc_start: 0.8549 (m-30) cc_final: 0.8141 (m-30) REVERT: F 626 SER cc_start: 0.9025 (m) cc_final: 0.8524 (p) REVERT: F 634 ASP cc_start: 0.8861 (t0) cc_final: 0.8640 (t0) REVERT: F 652 GLU cc_start: 0.8992 (tt0) cc_final: 0.8512 (tt0) REVERT: F 660 ARG cc_start: 0.8891 (tpp-160) cc_final: 0.8662 (tpm170) REVERT: F 668 ASN cc_start: 0.8622 (t0) cc_final: 0.8415 (t0) REVERT: F 676 SER cc_start: 0.8989 (m) cc_final: 0.8445 (p) REVERT: F 703 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: G 572 ASN cc_start: 0.8956 (t0) cc_final: 0.8546 (t0) REVERT: G 575 ASN cc_start: 0.8435 (m-40) cc_final: 0.8144 (m-40) REVERT: G 578 ASP cc_start: 0.8622 (m-30) cc_final: 0.8341 (m-30) REVERT: G 590 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8647 (mt-10) REVERT: G 612 SER cc_start: 0.9590 (p) cc_final: 0.9326 (m) REVERT: G 622 ARG cc_start: 0.8608 (mmp80) cc_final: 0.8228 (mmt-90) REVERT: G 626 SER cc_start: 0.9206 (m) cc_final: 0.8678 (p) REVERT: G 634 ASP cc_start: 0.8677 (t0) cc_final: 0.8435 (t0) REVERT: G 652 GLU cc_start: 0.8948 (tt0) cc_final: 0.8675 (tt0) REVERT: G 655 GLU cc_start: 0.9174 (tp30) cc_final: 0.8875 (tp30) REVERT: G 660 ARG cc_start: 0.8749 (tpt90) cc_final: 0.8427 (tpt170) REVERT: G 668 ASN cc_start: 0.8771 (t0) cc_final: 0.8213 (t0) REVERT: G 676 SER cc_start: 0.8932 (m) cc_final: 0.8492 (p) REVERT: G 685 SER cc_start: 0.8924 (m) cc_final: 0.8505 (p) REVERT: G 693 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8492 (pm20) outliers start: 42 outliers final: 24 residues processed: 450 average time/residue: 1.1264 time to fit residues: 550.2265 Evaluate side-chains 446 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 416 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 647 LYS 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 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 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 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 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 128 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 693 GLN A 703 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089743 restraints weight = 17442.207| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.80 r_work: 0.2810 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11669 Z= 0.134 Angle : 0.579 8.936 15883 Z= 0.289 Chirality : 0.041 0.162 1967 Planarity : 0.003 0.028 2030 Dihedral : 3.687 12.473 1631 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.83 % Allowed : 27.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1435 helix: 2.87 (0.19), residues: 637 sheet: 0.16 (0.31), residues: 273 loop : 0.25 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 694 HIS 0.003 0.001 HIS D 607 PHE 0.008 0.001 PHE E 680 TYR 0.012 0.001 TYR F 720 ARG 0.006 0.001 ARG D 591 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 760) hydrogen bonds : angle 3.54417 ( 2208) covalent geometry : bond 0.00301 (11669) covalent geometry : angle 0.57864 (15883) *********************** 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 468 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 423 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8055 (pttt) REVERT: A 575 ASN cc_start: 0.8305 (m-40) cc_final: 0.7875 (m-40) REVERT: A 578 ASP cc_start: 0.8603 (m-30) cc_final: 0.8288 (m-30) REVERT: A 634 ASP cc_start: 0.8694 (t0) cc_final: 0.8438 (t0) REVERT: A 647 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7989 (mttm) REVERT: A 652 GLU cc_start: 0.9150 (tt0) cc_final: 0.8866 (tt0) REVERT: A 655 GLU cc_start: 0.9206 (tp30) cc_final: 0.8881 (tp30) REVERT: A 660 ARG cc_start: 0.8735 (tpt90) cc_final: 0.8389 (tpt170) REVERT: A 664 ILE cc_start: 0.9185 (tp) cc_final: 0.8964 (pp) REVERT: A 668 ASN cc_start: 0.8753 (t0) cc_final: 0.8127 (t0) REVERT: A 676 SER cc_start: 0.8664 (m) cc_final: 0.8184 (p) REVERT: A 685 SER cc_start: 0.8921 (m) cc_final: 0.8426 (p) REVERT: B 560 LYS cc_start: 0.8481 (tttt) cc_final: 0.8104 (pttt) REVERT: B 578 ASP cc_start: 0.8571 (m-30) cc_final: 0.8246 (m-30) REVERT: B 613 SER cc_start: 0.9450 (m) cc_final: 0.9106 (p) REVERT: B 626 SER cc_start: 0.9194 (m) cc_final: 0.8688 (p) REVERT: B 641 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8653 (ttpp) REVERT: B 652 GLU cc_start: 0.9050 (tt0) cc_final: 0.8643 (tt0) REVERT: B 658 GLU cc_start: 0.9212 (tp30) cc_final: 0.8929 (mp0) REVERT: B 660 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8550 (tpt170) REVERT: B 668 ASN cc_start: 0.8618 (t0) cc_final: 0.8170 (t0) REVERT: B 676 SER cc_start: 0.8982 (m) cc_final: 0.8432 (p) REVERT: B 685 SER cc_start: 0.8841 (m) cc_final: 0.8468 (p) REVERT: C 560 LYS cc_start: 0.8440 (tppp) cc_final: 0.8161 (pttt) REVERT: C 572 ASN cc_start: 0.9018 (t0) cc_final: 0.8733 (t0) REVERT: C 575 ASN cc_start: 0.8241 (m-40) cc_final: 0.8031 (m110) REVERT: C 578 ASP cc_start: 0.8605 (m-30) cc_final: 0.8369 (m-30) REVERT: C 626 SER cc_start: 0.9103 (m) cc_final: 0.8458 (p) REVERT: C 634 ASP cc_start: 0.8866 (t0) cc_final: 0.8649 (t0) REVERT: C 660 ARG cc_start: 0.8369 (tpt90) cc_final: 0.7953 (tpp-160) REVERT: C 676 SER cc_start: 0.8930 (m) cc_final: 0.8449 (p) REVERT: C 685 SER cc_start: 0.9051 (m) cc_final: 0.8605 (p) REVERT: D 560 LYS cc_start: 0.8409 (tttt) cc_final: 0.8135 (pttt) REVERT: D 575 ASN cc_start: 0.8524 (m-40) cc_final: 0.8280 (m110) REVERT: D 578 ASP cc_start: 0.8640 (m-30) cc_final: 0.8409 (m-30) REVERT: D 613 SER cc_start: 0.9394 (t) cc_final: 0.9040 (p) REVERT: D 626 SER cc_start: 0.9110 (m) cc_final: 0.8740 (p) REVERT: D 655 GLU cc_start: 0.9197 (tp30) cc_final: 0.8921 (tp30) REVERT: D 660 ARG cc_start: 0.8930 (tpp-160) cc_final: 0.8672 (tpm170) REVERT: D 668 ASN cc_start: 0.8733 (t0) cc_final: 0.8379 (t0) REVERT: D 676 SER cc_start: 0.9078 (m) cc_final: 0.8641 (p) REVERT: D 693 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: D 723 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7597 (tt) REVERT: E 560 LYS cc_start: 0.8464 (tttt) cc_final: 0.8191 (pttt) REVERT: E 575 ASN cc_start: 0.8235 (m-40) cc_final: 0.7862 (m110) REVERT: E 578 ASP cc_start: 0.8510 (m-30) cc_final: 0.8030 (m-30) REVERT: E 602 ASP cc_start: 0.9003 (p0) cc_final: 0.8758 (p0) REVERT: E 613 SER cc_start: 0.9480 (m) cc_final: 0.9210 (p) REVERT: E 626 SER cc_start: 0.9049 (m) cc_final: 0.8346 (p) REVERT: E 648 ASP cc_start: 0.8981 (m-30) cc_final: 0.8742 (m-30) REVERT: E 652 GLU cc_start: 0.8836 (tt0) cc_final: 0.8476 (tt0) REVERT: E 655 GLU cc_start: 0.9153 (tp30) cc_final: 0.8808 (tp30) REVERT: E 660 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8440 (tpp-160) REVERT: E 668 ASN cc_start: 0.8679 (t0) cc_final: 0.8025 (t0) REVERT: E 676 SER cc_start: 0.8846 (m) cc_final: 0.8390 (p) REVERT: E 685 SER cc_start: 0.8999 (m) cc_final: 0.8637 (p) REVERT: E 720 TYR cc_start: 0.8012 (m-10) cc_final: 0.7669 (m-10) REVERT: F 572 ASN cc_start: 0.9249 (t0) cc_final: 0.9030 (t0) REVERT: F 578 ASP cc_start: 0.8535 (m-30) cc_final: 0.8175 (m-30) REVERT: F 626 SER cc_start: 0.9082 (m) cc_final: 0.8634 (p) REVERT: F 652 GLU cc_start: 0.8960 (tt0) cc_final: 0.8463 (tt0) REVERT: F 660 ARG cc_start: 0.8905 (tpp-160) cc_final: 0.8672 (tpm170) REVERT: F 668 ASN cc_start: 0.8703 (t0) cc_final: 0.8428 (t0) REVERT: F 676 SER cc_start: 0.8948 (m) cc_final: 0.8402 (p) REVERT: F 693 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: F 703 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8438 (mm-40) REVERT: G 575 ASN cc_start: 0.8419 (m-40) cc_final: 0.8131 (m-40) REVERT: G 578 ASP cc_start: 0.8644 (m-30) cc_final: 0.8336 (m-30) REVERT: G 590 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8676 (mt-10) REVERT: G 612 SER cc_start: 0.9564 (p) cc_final: 0.9259 (m) REVERT: G 626 SER cc_start: 0.9233 (m) cc_final: 0.8683 (p) REVERT: G 652 GLU cc_start: 0.8938 (tt0) cc_final: 0.8683 (tt0) REVERT: G 655 GLU cc_start: 0.9161 (tp30) cc_final: 0.8882 (tp30) REVERT: G 660 ARG cc_start: 0.8741 (tpt90) cc_final: 0.8431 (tpt170) REVERT: G 668 ASN cc_start: 0.8788 (t0) cc_final: 0.8246 (t0) REVERT: G 676 SER cc_start: 0.8926 (m) cc_final: 0.8481 (p) REVERT: G 685 SER cc_start: 0.8933 (m) cc_final: 0.8525 (p) REVERT: G 693 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: G 714 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8509 (mtm-85) outliers start: 45 outliers final: 31 residues processed: 444 average time/residue: 1.5017 time to fit residues: 724.8688 Evaluate side-chains 443 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 405 time to evaluate : 2.907 ------------------------------------------------------------------------------- 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 647 LYS 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 663 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 SER 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 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 537 ILE 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 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 693 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 556 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090422 restraints weight = 17573.280| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.82 r_work: 0.2838 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3391 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= 0.115 Angle : 0.586 8.819 15883 Z= 0.292 Chirality : 0.041 0.159 1967 Planarity : 0.003 0.030 2030 Dihedral : 3.616 12.524 1631 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.57 % Allowed : 27.38 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.23), residues: 1435 helix: 3.06 (0.19), residues: 637 sheet: 0.32 (0.31), residues: 273 loop : 0.31 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 694 HIS 0.002 0.001 HIS D 607 PHE 0.012 0.001 PHE D 567 TYR 0.010 0.001 TYR F 720 ARG 0.007 0.001 ARG D 697 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 760) hydrogen bonds : angle 3.45058 ( 2208) covalent geometry : bond 0.00254 (11669) covalent geometry : angle 0.58627 (15883) *********************** 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 471 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 429 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8059 (pttt) REVERT: A 575 ASN cc_start: 0.8267 (m-40) cc_final: 0.7977 (m110) REVERT: A 578 ASP cc_start: 0.8602 (m-30) cc_final: 0.8185 (m-30) REVERT: A 634 ASP cc_start: 0.8608 (t0) cc_final: 0.8363 (t0) REVERT: A 652 GLU cc_start: 0.9159 (tt0) cc_final: 0.8706 (tt0) REVERT: A 655 GLU cc_start: 0.9179 (tp30) cc_final: 0.8882 (tp30) REVERT: A 660 ARG cc_start: 0.8751 (tpt90) cc_final: 0.8490 (tpt170) REVERT: A 664 ILE cc_start: 0.9158 (tp) cc_final: 0.8947 (pp) REVERT: A 668 ASN cc_start: 0.8737 (t0) cc_final: 0.8132 (t0) REVERT: A 676 SER cc_start: 0.8640 (m) cc_final: 0.8150 (p) REVERT: A 685 SER cc_start: 0.8894 (m) cc_final: 0.8396 (p) REVERT: B 560 LYS cc_start: 0.8395 (tttt) cc_final: 0.8066 (pttt) REVERT: B 578 ASP cc_start: 0.8566 (m-30) cc_final: 0.8131 (m-30) REVERT: B 589 VAL cc_start: 0.9443 (t) cc_final: 0.9149 (p) REVERT: B 626 SER cc_start: 0.9140 (m) cc_final: 0.8605 (p) REVERT: B 641 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8646 (ttpp) REVERT: B 652 GLU cc_start: 0.9053 (tt0) cc_final: 0.8678 (tt0) REVERT: B 655 GLU cc_start: 0.9176 (tp30) cc_final: 0.8884 (tp30) REVERT: B 660 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8468 (tpp-160) REVERT: B 668 ASN cc_start: 0.8680 (t0) cc_final: 0.8246 (t0) REVERT: B 676 SER cc_start: 0.9015 (m) cc_final: 0.8454 (p) REVERT: B 685 SER cc_start: 0.8834 (m) cc_final: 0.8443 (p) REVERT: C 560 LYS cc_start: 0.8371 (tppp) cc_final: 0.8119 (pttt) REVERT: C 572 ASN cc_start: 0.9059 (t0) cc_final: 0.8750 (t0) REVERT: C 578 ASP cc_start: 0.8478 (m-30) cc_final: 0.8278 (m-30) REVERT: C 626 SER cc_start: 0.9021 (m) cc_final: 0.8565 (p) REVERT: C 634 ASP cc_start: 0.8852 (t0) cc_final: 0.8602 (t0) REVERT: C 676 SER cc_start: 0.9007 (m) cc_final: 0.8520 (p) REVERT: C 685 SER cc_start: 0.9038 (m) cc_final: 0.8597 (p) REVERT: C 693 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8404 (pm20) REVERT: D 560 LYS cc_start: 0.8299 (tttt) cc_final: 0.8020 (pttt) REVERT: D 575 ASN cc_start: 0.8474 (m-40) cc_final: 0.8196 (m110) REVERT: D 578 ASP cc_start: 0.8638 (m-30) cc_final: 0.8319 (m-30) REVERT: D 613 SER cc_start: 0.9391 (t) cc_final: 0.9034 (p) REVERT: D 626 SER cc_start: 0.9065 (m) cc_final: 0.8690 (p) REVERT: D 655 GLU cc_start: 0.9211 (tp30) cc_final: 0.8960 (tp30) REVERT: D 660 ARG cc_start: 0.8898 (tpp-160) cc_final: 0.8666 (tpm170) REVERT: D 668 ASN cc_start: 0.8710 (t0) cc_final: 0.8386 (t0) REVERT: D 676 SER cc_start: 0.9034 (m) cc_final: 0.8582 (p) REVERT: D 693 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: D 723 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7607 (tt) REVERT: E 560 LYS cc_start: 0.8425 (tttt) cc_final: 0.8169 (pttt) REVERT: E 575 ASN cc_start: 0.8142 (m-40) cc_final: 0.7810 (m110) REVERT: E 578 ASP cc_start: 0.8511 (m-30) cc_final: 0.8010 (m-30) REVERT: E 613 SER cc_start: 0.9449 (m) cc_final: 0.9191 (p) REVERT: E 626 SER cc_start: 0.8985 (m) cc_final: 0.8243 (p) REVERT: E 652 GLU cc_start: 0.8762 (tt0) cc_final: 0.8388 (tt0) REVERT: E 655 GLU cc_start: 0.9142 (tp30) cc_final: 0.8871 (tp30) REVERT: E 660 ARG cc_start: 0.8650 (tpt90) cc_final: 0.8314 (tpp-160) REVERT: E 668 ASN cc_start: 0.8711 (t0) cc_final: 0.8044 (t0) REVERT: E 676 SER cc_start: 0.8825 (m) cc_final: 0.8375 (p) REVERT: E 685 SER cc_start: 0.8974 (m) cc_final: 0.8614 (p) REVERT: E 720 TYR cc_start: 0.8008 (m-10) cc_final: 0.7697 (m-10) REVERT: F 572 ASN cc_start: 0.9212 (t0) cc_final: 0.8965 (t0) REVERT: F 575 ASN cc_start: 0.8148 (m-40) cc_final: 0.7860 (m110) REVERT: F 578 ASP cc_start: 0.8575 (m-30) cc_final: 0.8265 (m-30) REVERT: F 626 SER cc_start: 0.9077 (m) cc_final: 0.8599 (p) REVERT: F 652 GLU cc_start: 0.8951 (tt0) cc_final: 0.8535 (tt0) REVERT: F 668 ASN cc_start: 0.8688 (t0) cc_final: 0.8428 (t0) REVERT: F 676 SER cc_start: 0.8935 (m) cc_final: 0.8394 (p) REVERT: F 693 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: F 703 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8445 (mm-40) REVERT: G 572 ASN cc_start: 0.9030 (t0) cc_final: 0.8828 (t0) REVERT: G 575 ASN cc_start: 0.8432 (m-40) cc_final: 0.8067 (m110) REVERT: G 578 ASP cc_start: 0.8638 (m-30) cc_final: 0.8341 (m-30) REVERT: G 590 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8702 (mt-10) REVERT: G 612 SER cc_start: 0.9573 (p) cc_final: 0.9252 (m) REVERT: G 622 ARG cc_start: 0.8749 (mmp80) cc_final: 0.8150 (mmt90) REVERT: G 626 SER cc_start: 0.9182 (m) cc_final: 0.8643 (p) REVERT: G 652 GLU cc_start: 0.8934 (tt0) cc_final: 0.8696 (tt0) REVERT: G 655 GLU cc_start: 0.9142 (tp30) cc_final: 0.8902 (tp30) REVERT: G 660 ARG cc_start: 0.8726 (tpt90) cc_final: 0.8410 (tpm170) REVERT: G 668 ASN cc_start: 0.8834 (t0) cc_final: 0.8300 (t0) REVERT: G 676 SER cc_start: 0.8907 (m) cc_final: 0.8461 (p) REVERT: G 685 SER cc_start: 0.8921 (m) cc_final: 0.8515 (p) REVERT: G 693 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: G 714 ARG cc_start: 0.8711 (mtp85) cc_final: 0.8453 (mtm-85) outliers start: 42 outliers final: 23 residues processed: 447 average time/residue: 1.2802 time to fit residues: 619.0408 Evaluate side-chains 437 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 408 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 663 ILE 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 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 616 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 693 GLN Chi-restraints excluded: chain F residue 703 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 10 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 148 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN C 575 ASN C 693 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN 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 = 0.3550 r_free = 0.3550 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088422 restraints weight = 17834.152| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.87 r_work: 0.2835 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3531 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= 0.123 Angle : 0.610 8.191 15883 Z= 0.306 Chirality : 0.041 0.172 1967 Planarity : 0.003 0.035 2030 Dihedral : 3.573 12.649 1631 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.25 % Allowed : 27.81 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.23), residues: 1435 helix: 3.09 (0.19), residues: 637 sheet: 0.39 (0.31), residues: 273 loop : 0.36 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 694 HIS 0.002 0.001 HIS D 607 PHE 0.015 0.001 PHE D 567 TYR 0.010 0.001 TYR F 720 ARG 0.007 0.001 ARG D 600 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 760) hydrogen bonds : angle 3.42429 ( 2208) covalent geometry : bond 0.00276 (11669) covalent geometry : angle 0.60983 (15883) *********************** 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 : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8166 (pttt) REVERT: A 575 ASN cc_start: 0.8259 (m-40) cc_final: 0.7968 (m110) REVERT: A 578 ASP cc_start: 0.8542 (m-30) cc_final: 0.8229 (m-30) REVERT: A 634 ASP cc_start: 0.8674 (t0) cc_final: 0.8408 (t0) REVERT: A 652 GLU cc_start: 0.9167 (tt0) cc_final: 0.8761 (tt0) REVERT: A 655 GLU cc_start: 0.9149 (tp30) cc_final: 0.8930 (tp30) REVERT: A 660 ARG cc_start: 0.8738 (tpt90) cc_final: 0.8406 (tpt170) REVERT: A 664 ILE cc_start: 0.9133 (tp) cc_final: 0.8919 (pp) REVERT: A 668 ASN cc_start: 0.8759 (t0) cc_final: 0.8178 (t0) REVERT: A 676 SER cc_start: 0.8696 (m) cc_final: 0.8212 (p) REVERT: A 685 SER cc_start: 0.8913 (m) cc_final: 0.8420 (p) REVERT: B 560 LYS cc_start: 0.8392 (tttt) cc_final: 0.8081 (pttt) REVERT: B 578 ASP cc_start: 0.8588 (m-30) cc_final: 0.8120 (m-30) REVERT: B 589 VAL cc_start: 0.9454 (t) cc_final: 0.9166 (p) REVERT: B 626 SER cc_start: 0.9143 (m) cc_final: 0.8663 (p) REVERT: B 652 GLU cc_start: 0.9070 (tt0) cc_final: 0.8710 (tt0) REVERT: B 655 GLU cc_start: 0.9180 (tp30) cc_final: 0.8873 (tp30) REVERT: B 660 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8501 (tpp-160) REVERT: B 668 ASN cc_start: 0.8722 (t0) cc_final: 0.8278 (t0) REVERT: B 676 SER cc_start: 0.9014 (m) cc_final: 0.8456 (p) REVERT: B 685 SER cc_start: 0.8858 (m) cc_final: 0.8467 (p) REVERT: C 560 LYS cc_start: 0.8387 (tppp) cc_final: 0.8149 (pttt) REVERT: C 572 ASN cc_start: 0.9073 (t0) cc_final: 0.8793 (t0) REVERT: C 575 ASN cc_start: 0.8277 (m-40) cc_final: 0.8076 (m110) REVERT: C 578 ASP cc_start: 0.8546 (m-30) cc_final: 0.8332 (m-30) REVERT: C 626 SER cc_start: 0.9084 (m) cc_final: 0.8389 (p) REVERT: C 634 ASP cc_start: 0.8891 (t0) cc_final: 0.8666 (t0) REVERT: C 676 SER cc_start: 0.8839 (m) cc_final: 0.8361 (p) REVERT: C 685 SER cc_start: 0.9047 (m) cc_final: 0.8642 (p) REVERT: D 560 LYS cc_start: 0.8339 (tttt) cc_final: 0.8065 (pttt) REVERT: D 575 ASN cc_start: 0.8428 (m-40) cc_final: 0.8174 (m110) REVERT: D 578 ASP cc_start: 0.8601 (m-30) cc_final: 0.8296 (m-30) REVERT: D 591 ARG cc_start: 0.8724 (ptm-80) cc_final: 0.8491 (ptm-80) REVERT: D 613 SER cc_start: 0.9391 (t) cc_final: 0.9040 (p) REVERT: D 622 ARG cc_start: 0.8940 (tpp-160) cc_final: 0.8480 (tpp80) REVERT: D 626 SER cc_start: 0.9088 (m) cc_final: 0.8714 (p) REVERT: D 652 GLU cc_start: 0.8919 (tt0) cc_final: 0.8321 (tt0) REVERT: D 655 GLU cc_start: 0.9214 (tp30) cc_final: 0.8976 (tp30) REVERT: D 660 ARG cc_start: 0.8879 (tpp-160) cc_final: 0.8580 (tpp-160) REVERT: D 668 ASN cc_start: 0.8717 (t0) cc_final: 0.8395 (t0) REVERT: D 676 SER cc_start: 0.9038 (m) cc_final: 0.8586 (p) REVERT: D 693 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: E 560 LYS cc_start: 0.8447 (tttt) cc_final: 0.8214 (pttt) REVERT: E 575 ASN cc_start: 0.8170 (m-40) cc_final: 0.7758 (m110) REVERT: E 578 ASP cc_start: 0.8515 (m-30) cc_final: 0.7985 (m-30) REVERT: E 613 SER cc_start: 0.9454 (m) cc_final: 0.9200 (p) REVERT: E 626 SER cc_start: 0.9008 (m) cc_final: 0.8271 (p) REVERT: E 648 ASP cc_start: 0.9029 (m-30) cc_final: 0.8745 (m-30) REVERT: E 652 GLU cc_start: 0.8747 (tt0) cc_final: 0.8338 (tt0) REVERT: E 655 GLU cc_start: 0.9188 (tp30) cc_final: 0.8920 (tp30) REVERT: E 660 ARG cc_start: 0.8696 (tpt90) cc_final: 0.8247 (tpt170) REVERT: E 668 ASN cc_start: 0.8740 (t0) cc_final: 0.8086 (t0) REVERT: E 676 SER cc_start: 0.8837 (m) cc_final: 0.8387 (p) REVERT: E 685 SER cc_start: 0.8989 (m) cc_final: 0.8630 (p) REVERT: E 720 TYR cc_start: 0.8029 (m-10) cc_final: 0.7732 (m-10) REVERT: F 578 ASP cc_start: 0.8600 (m-30) cc_final: 0.8285 (m-30) REVERT: F 626 SER cc_start: 0.9079 (m) cc_final: 0.8638 (p) REVERT: F 652 GLU cc_start: 0.8957 (tt0) cc_final: 0.8562 (tt0) REVERT: F 668 ASN cc_start: 0.8709 (t0) cc_final: 0.8434 (t0) REVERT: F 676 SER cc_start: 0.8920 (m) cc_final: 0.8383 (p) REVERT: F 693 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: F 703 GLN cc_start: 0.8712 (tp40) cc_final: 0.8449 (mm-40) REVERT: G 572 ASN cc_start: 0.9089 (t0) cc_final: 0.8833 (t0) REVERT: G 575 ASN cc_start: 0.8400 (m-40) cc_final: 0.8014 (m110) REVERT: G 578 ASP cc_start: 0.8672 (m-30) cc_final: 0.8351 (m-30) REVERT: G 590 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8688 (mt-10) REVERT: G 612 SER cc_start: 0.9547 (p) cc_final: 0.9190 (m) REVERT: G 622 ARG cc_start: 0.8733 (mmp80) cc_final: 0.8116 (mmt90) REVERT: G 626 SER cc_start: 0.9181 (m) cc_final: 0.8637 (p) REVERT: G 652 GLU cc_start: 0.9022 (tt0) cc_final: 0.8700 (tt0) REVERT: G 655 GLU cc_start: 0.9138 (tp30) cc_final: 0.8929 (tp30) REVERT: G 660 ARG cc_start: 0.8684 (tpt90) cc_final: 0.8417 (tpt170) REVERT: G 668 ASN cc_start: 0.8815 (t0) cc_final: 0.8282 (t0) REVERT: G 676 SER cc_start: 0.8917 (m) cc_final: 0.8473 (p) REVERT: G 685 SER cc_start: 0.8967 (m) cc_final: 0.8562 (p) REVERT: G 693 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: G 714 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8438 (mtm-85) outliers start: 50 outliers final: 28 residues processed: 441 average time/residue: 1.4521 time to fit residues: 694.9403 Evaluate side-chains 440 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 408 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 559 VAL 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 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 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 693 GLN 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 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 44 optimal weight: 30.0000 chunk 145 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN C 644 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 572 ASN G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084500 restraints weight = 17886.784| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.71 r_work: 0.2826 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11669 Z= 0.194 Angle : 0.654 9.339 15883 Z= 0.333 Chirality : 0.043 0.186 1967 Planarity : 0.003 0.034 2030 Dihedral : 3.747 12.862 1631 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.91 % Allowed : 28.57 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.23), residues: 1435 helix: 2.89 (0.19), residues: 637 sheet: 0.42 (0.31), residues: 273 loop : 0.49 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 611 HIS 0.003 0.001 HIS D 607 PHE 0.018 0.001 PHE D 567 TYR 0.015 0.001 TYR F 720 ARG 0.007 0.001 ARG D 697 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 760) hydrogen bonds : angle 3.58275 ( 2208) covalent geometry : bond 0.00441 (11669) covalent geometry : angle 0.65422 (15883) *********************** 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 456 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 410 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8154 (pttt) REVERT: A 575 ASN cc_start: 0.8198 (m-40) cc_final: 0.7901 (m110) REVERT: A 578 ASP cc_start: 0.8613 (m-30) cc_final: 0.8235 (m-30) REVERT: A 634 ASP cc_start: 0.8803 (t0) cc_final: 0.8531 (t0) REVERT: A 652 GLU cc_start: 0.9124 (tt0) cc_final: 0.8729 (tt0) REVERT: A 655 GLU cc_start: 0.9139 (tp30) cc_final: 0.8928 (tp30) REVERT: A 660 ARG cc_start: 0.8761 (tpt90) cc_final: 0.8465 (tpt170) REVERT: A 664 ILE cc_start: 0.9217 (tp) cc_final: 0.8917 (pp) REVERT: A 668 ASN cc_start: 0.8657 (t0) cc_final: 0.8043 (t0) REVERT: A 676 SER cc_start: 0.8665 (m) cc_final: 0.8193 (p) REVERT: A 685 SER cc_start: 0.8897 (m) cc_final: 0.8437 (p) REVERT: B 578 ASP cc_start: 0.8541 (m-30) cc_final: 0.8265 (m-30) REVERT: B 626 SER cc_start: 0.9195 (m) cc_final: 0.8735 (p) REVERT: B 652 GLU cc_start: 0.9035 (tt0) cc_final: 0.8644 (tt0) REVERT: B 655 GLU cc_start: 0.9234 (tp30) cc_final: 0.8944 (tp30) REVERT: B 660 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8428 (tpt170) REVERT: B 668 ASN cc_start: 0.8697 (t0) cc_final: 0.8276 (t0) REVERT: B 676 SER cc_start: 0.8856 (m) cc_final: 0.8359 (p) REVERT: B 685 SER cc_start: 0.8809 (m) cc_final: 0.8433 (p) REVERT: C 572 ASN cc_start: 0.9089 (t0) cc_final: 0.8746 (t0) REVERT: C 626 SER cc_start: 0.9066 (m) cc_final: 0.8371 (p) REVERT: C 676 SER cc_start: 0.8734 (m) cc_final: 0.8449 (t) REVERT: C 685 SER cc_start: 0.9018 (m) cc_final: 0.8552 (p) REVERT: C 693 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: D 560 LYS cc_start: 0.8372 (tttt) cc_final: 0.8052 (pttt) REVERT: D 572 ASN cc_start: 0.9187 (t0) cc_final: 0.8928 (t0) REVERT: D 575 ASN cc_start: 0.8303 (m-40) cc_final: 0.8087 (m110) REVERT: D 578 ASP cc_start: 0.8551 (m-30) cc_final: 0.8285 (m-30) REVERT: D 591 ARG cc_start: 0.8794 (ptm-80) cc_final: 0.8526 (ptm-80) REVERT: D 626 SER cc_start: 0.9108 (m) cc_final: 0.8730 (p) REVERT: D 655 GLU cc_start: 0.9220 (tp30) cc_final: 0.8955 (tp30) REVERT: D 660 ARG cc_start: 0.8883 (tpp-160) cc_final: 0.8566 (tpp-160) REVERT: D 664 ILE cc_start: 0.9169 (tp) cc_final: 0.8920 (pp) REVERT: D 668 ASN cc_start: 0.8674 (t0) cc_final: 0.8346 (t0) REVERT: D 676 SER cc_start: 0.8978 (m) cc_final: 0.8535 (p) REVERT: D 693 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: D 723 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7230 (tt) REVERT: E 560 LYS cc_start: 0.8490 (tttt) cc_final: 0.8250 (pttt) REVERT: E 575 ASN cc_start: 0.8043 (m-40) cc_final: 0.7629 (m110) REVERT: E 578 ASP cc_start: 0.8521 (m-30) cc_final: 0.7977 (m-30) REVERT: E 590 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8602 (mt-10) REVERT: E 613 SER cc_start: 0.9466 (m) cc_final: 0.9204 (p) REVERT: E 626 SER cc_start: 0.9055 (m) cc_final: 0.8318 (p) REVERT: E 648 ASP cc_start: 0.9028 (m-30) cc_final: 0.8760 (m-30) REVERT: E 652 GLU cc_start: 0.8764 (tt0) cc_final: 0.8402 (tt0) REVERT: E 655 GLU cc_start: 0.9153 (tp30) cc_final: 0.8879 (tp30) REVERT: E 658 GLU cc_start: 0.9341 (tp30) cc_final: 0.9098 (tp30) REVERT: E 660 ARG cc_start: 0.8689 (tpt90) cc_final: 0.8292 (tpt170) REVERT: E 668 ASN cc_start: 0.8707 (t0) cc_final: 0.8058 (t0) REVERT: E 676 SER cc_start: 0.8775 (m) cc_final: 0.8324 (p) REVERT: E 685 SER cc_start: 0.8949 (m) cc_final: 0.8587 (p) REVERT: E 720 TYR cc_start: 0.7937 (m-10) cc_final: 0.7588 (m-10) REVERT: F 578 ASP cc_start: 0.8495 (m-30) cc_final: 0.8164 (m-30) REVERT: F 626 SER cc_start: 0.9121 (m) cc_final: 0.8668 (p) REVERT: F 652 GLU cc_start: 0.8859 (tt0) cc_final: 0.8473 (tt0) REVERT: F 668 ASN cc_start: 0.8679 (t0) cc_final: 0.8362 (t0) REVERT: F 676 SER cc_start: 0.8869 (m) cc_final: 0.8348 (p) REVERT: F 703 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: G 572 ASN cc_start: 0.9066 (t0) cc_final: 0.8803 (t0) REVERT: G 575 ASN cc_start: 0.8286 (m-40) cc_final: 0.7875 (m110) REVERT: G 578 ASP cc_start: 0.8569 (m-30) cc_final: 0.8161 (m-30) REVERT: G 590 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8712 (mt-10) REVERT: G 612 SER cc_start: 0.9510 (p) cc_final: 0.9126 (m) REVERT: G 626 SER cc_start: 0.9290 (m) cc_final: 0.8726 (p) REVERT: G 652 GLU cc_start: 0.8927 (tt0) cc_final: 0.8670 (tt0) REVERT: G 655 GLU cc_start: 0.9120 (tp30) cc_final: 0.8906 (tp30) REVERT: G 658 GLU cc_start: 0.9365 (tp30) cc_final: 0.9139 (tp30) REVERT: G 660 ARG cc_start: 0.8665 (tpt90) cc_final: 0.8387 (tpt170) REVERT: G 668 ASN cc_start: 0.8761 (t0) cc_final: 0.8227 (t0) REVERT: G 676 SER cc_start: 0.8907 (m) cc_final: 0.8434 (p) REVERT: G 685 SER cc_start: 0.8885 (m) cc_final: 0.8491 (p) REVERT: G 693 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: G 714 ARG cc_start: 0.8644 (mtp85) cc_final: 0.8377 (mtm-85) outliers start: 46 outliers final: 30 residues processed: 433 average time/residue: 1.4907 time to fit residues: 699.1681 Evaluate side-chains 436 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 400 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 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 B residue 703 GLN Chi-restraints excluded: chain C residue 562 ILE 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 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 537 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 30 optimal weight: 0.0040 chunk 122 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN C 575 ASN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.087841 restraints weight = 17573.115| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.81 r_work: 0.2825 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11669 Z= 0.130 Angle : 0.665 9.157 15883 Z= 0.334 Chirality : 0.043 0.201 1967 Planarity : 0.003 0.036 2030 Dihedral : 3.700 13.112 1631 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.06 % Allowed : 30.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.23), residues: 1435 helix: 2.99 (0.19), residues: 637 sheet: 0.45 (0.31), residues: 273 loop : 0.55 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 694 HIS 0.003 0.001 HIS D 607 PHE 0.009 0.001 PHE A 567 TYR 0.012 0.001 TYR G 631 ARG 0.007 0.001 ARG D 697 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 760) hydrogen bonds : angle 3.49333 ( 2208) covalent geometry : bond 0.00291 (11669) covalent geometry : angle 0.66531 (15883) *********************** 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 447 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 411 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8229 (pttt) REVERT: A 575 ASN cc_start: 0.8226 (m-40) cc_final: 0.7930 (m110) REVERT: A 578 ASP cc_start: 0.8539 (m-30) cc_final: 0.8206 (m-30) REVERT: A 634 ASP cc_start: 0.8782 (t0) cc_final: 0.8514 (t0) REVERT: A 652 GLU cc_start: 0.9132 (tt0) cc_final: 0.8823 (tt0) REVERT: A 660 ARG cc_start: 0.8760 (tpt90) cc_final: 0.8480 (tpt170) REVERT: A 664 ILE cc_start: 0.9199 (tp) cc_final: 0.8910 (pp) REVERT: A 668 ASN cc_start: 0.8691 (t0) cc_final: 0.8061 (t0) REVERT: A 676 SER cc_start: 0.8715 (m) cc_final: 0.8245 (p) REVERT: A 685 SER cc_start: 0.8919 (m) cc_final: 0.8423 (p) REVERT: B 560 LYS cc_start: 0.8429 (tttt) cc_final: 0.8127 (pttt) REVERT: B 578 ASP cc_start: 0.8541 (m-30) cc_final: 0.8059 (m-30) REVERT: B 589 VAL cc_start: 0.9453 (t) cc_final: 0.9145 (p) REVERT: B 626 SER cc_start: 0.9150 (m) cc_final: 0.8670 (p) REVERT: B 652 GLU cc_start: 0.9047 (tt0) cc_final: 0.8656 (tt0) REVERT: B 655 GLU cc_start: 0.9216 (tp30) cc_final: 0.8859 (tp30) REVERT: B 660 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (tpt170) REVERT: B 664 ILE cc_start: 0.9205 (tp) cc_final: 0.8936 (pp) REVERT: B 668 ASN cc_start: 0.8677 (t0) cc_final: 0.8208 (t0) REVERT: B 676 SER cc_start: 0.8958 (m) cc_final: 0.8425 (p) REVERT: B 685 SER cc_start: 0.8822 (m) cc_final: 0.8420 (p) REVERT: C 560 LYS cc_start: 0.8537 (tppp) cc_final: 0.8222 (pttt) REVERT: C 572 ASN cc_start: 0.9091 (t0) cc_final: 0.8805 (t0) REVERT: C 578 ASP cc_start: 0.8510 (m-30) cc_final: 0.8302 (m-30) REVERT: C 626 SER cc_start: 0.9032 (m) cc_final: 0.8439 (p) REVERT: C 668 ASN cc_start: 0.8452 (t0) cc_final: 0.8085 (t0) REVERT: C 676 SER cc_start: 0.8764 (m) cc_final: 0.8490 (t) REVERT: D 560 LYS cc_start: 0.8404 (tttt) cc_final: 0.8127 (pttt) REVERT: D 575 ASN cc_start: 0.8419 (m-40) cc_final: 0.8204 (m110) REVERT: D 578 ASP cc_start: 0.8588 (m-30) cc_final: 0.8332 (m-30) REVERT: D 591 ARG cc_start: 0.8837 (ptm-80) cc_final: 0.8561 (ptm-80) REVERT: D 613 SER cc_start: 0.9429 (t) cc_final: 0.9031 (p) REVERT: D 626 SER cc_start: 0.9099 (m) cc_final: 0.8691 (p) REVERT: D 652 GLU cc_start: 0.8882 (tt0) cc_final: 0.8310 (tt0) REVERT: D 660 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.8598 (tpp-160) REVERT: D 668 ASN cc_start: 0.8695 (t0) cc_final: 0.8378 (t0) REVERT: D 676 SER cc_start: 0.9023 (m) cc_final: 0.8576 (p) REVERT: D 693 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: E 560 LYS cc_start: 0.8486 (tttt) cc_final: 0.8246 (pttt) REVERT: E 575 ASN cc_start: 0.8072 (m-40) cc_final: 0.7658 (m110) REVERT: E 578 ASP cc_start: 0.8515 (m-30) cc_final: 0.8007 (m-30) REVERT: E 613 SER cc_start: 0.9465 (m) cc_final: 0.9198 (p) REVERT: E 626 SER cc_start: 0.8988 (m) cc_final: 0.8260 (p) REVERT: E 648 ASP cc_start: 0.9040 (m-30) cc_final: 0.8768 (m-30) REVERT: E 652 GLU cc_start: 0.8745 (tt0) cc_final: 0.8517 (tt0) REVERT: E 655 GLU cc_start: 0.9188 (tp30) cc_final: 0.8935 (tp30) REVERT: E 658 GLU cc_start: 0.9346 (tp30) cc_final: 0.9072 (tp30) REVERT: E 660 ARG cc_start: 0.8683 (tpt90) cc_final: 0.8300 (tpt170) REVERT: E 668 ASN cc_start: 0.8737 (t0) cc_final: 0.8084 (t0) REVERT: E 676 SER cc_start: 0.8805 (m) cc_final: 0.8360 (p) REVERT: E 685 SER cc_start: 0.8987 (m) cc_final: 0.8628 (p) REVERT: E 720 TYR cc_start: 0.8017 (m-10) cc_final: 0.7682 (m-10) REVERT: F 578 ASP cc_start: 0.8534 (m-30) cc_final: 0.8206 (m-30) REVERT: F 626 SER cc_start: 0.9049 (m) cc_final: 0.8583 (p) REVERT: F 652 GLU cc_start: 0.8973 (tt0) cc_final: 0.8570 (tt0) REVERT: F 660 ARG cc_start: 0.8804 (tpp-160) cc_final: 0.8572 (tpm170) REVERT: F 668 ASN cc_start: 0.8689 (t0) cc_final: 0.8397 (t0) REVERT: F 676 SER cc_start: 0.8927 (m) cc_final: 0.8389 (p) REVERT: G 572 ASN cc_start: 0.9100 (t0) cc_final: 0.8860 (t0) REVERT: G 575 ASN cc_start: 0.8377 (m-40) cc_final: 0.8002 (m110) REVERT: G 578 ASP cc_start: 0.8593 (m-30) cc_final: 0.8291 (m-30) REVERT: G 590 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8642 (mt-10) REVERT: G 612 SER cc_start: 0.9526 (p) cc_final: 0.9140 (m) REVERT: G 626 SER cc_start: 0.9197 (m) cc_final: 0.8610 (p) REVERT: G 652 GLU cc_start: 0.8964 (tt0) cc_final: 0.8686 (tt0) REVERT: G 660 ARG cc_start: 0.8853 (tpt90) cc_final: 0.8629 (tpt170) REVERT: G 668 ASN cc_start: 0.8813 (t0) cc_final: 0.8297 (t0) REVERT: G 676 SER cc_start: 0.8937 (m) cc_final: 0.8492 (p) REVERT: G 685 SER cc_start: 0.8923 (m) cc_final: 0.8522 (p) REVERT: G 693 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: G 714 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8398 (mtm-85) outliers start: 36 outliers final: 24 residues processed: 430 average time/residue: 1.5007 time to fit residues: 698.8787 Evaluate side-chains 423 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 396 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 693 GLN 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 688 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN C 693 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 703 GLN G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089472 restraints weight = 17569.221| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.73 r_work: 0.2872 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11669 Z= 0.130 Angle : 0.706 11.200 15883 Z= 0.356 Chirality : 0.044 0.214 1967 Planarity : 0.003 0.038 2030 Dihedral : 3.658 13.072 1631 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.55 % Allowed : 30.87 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.23), residues: 1435 helix: 3.08 (0.19), residues: 637 sheet: 0.50 (0.31), residues: 273 loop : 0.47 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 694 HIS 0.003 0.001 HIS D 607 PHE 0.009 0.001 PHE A 567 TYR 0.010 0.001 TYR G 631 ARG 0.007 0.001 ARG E 591 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 760) hydrogen bonds : angle 3.46148 ( 2208) covalent geometry : bond 0.00290 (11669) covalent geometry : angle 0.70573 (15883) ********************** 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 442 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 412 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8220 (pttt) REVERT: A 575 ASN cc_start: 0.8146 (m-40) cc_final: 0.7877 (m110) REVERT: A 578 ASP cc_start: 0.8467 (m-30) cc_final: 0.8144 (m-30) REVERT: A 634 ASP cc_start: 0.8701 (t0) cc_final: 0.8441 (t0) REVERT: A 652 GLU cc_start: 0.9072 (tt0) cc_final: 0.8785 (tt0) REVERT: A 660 ARG cc_start: 0.8700 (tpt90) cc_final: 0.8448 (tpt170) REVERT: A 664 ILE cc_start: 0.9141 (tp) cc_final: 0.8881 (pp) REVERT: A 668 ASN cc_start: 0.8604 (t0) cc_final: 0.7993 (t0) REVERT: A 676 SER cc_start: 0.8642 (m) cc_final: 0.8173 (p) REVERT: A 685 SER cc_start: 0.8847 (m) cc_final: 0.8366 (p) REVERT: B 560 LYS cc_start: 0.8378 (tttt) cc_final: 0.8098 (pttt) REVERT: B 578 ASP cc_start: 0.8467 (m-30) cc_final: 0.7973 (m-30) REVERT: B 589 VAL cc_start: 0.9437 (t) cc_final: 0.9175 (p) REVERT: B 626 SER cc_start: 0.9119 (m) cc_final: 0.8643 (p) REVERT: B 652 GLU cc_start: 0.9023 (tt0) cc_final: 0.8682 (tt0) REVERT: B 655 GLU cc_start: 0.9212 (tp30) cc_final: 0.8881 (tp30) REVERT: B 660 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8393 (tpt170) REVERT: B 664 ILE cc_start: 0.9135 (tp) cc_final: 0.8895 (pp) REVERT: B 668 ASN cc_start: 0.8673 (t0) cc_final: 0.8233 (t0) REVERT: B 676 SER cc_start: 0.8865 (m) cc_final: 0.8322 (p) REVERT: B 685 SER cc_start: 0.8772 (m) cc_final: 0.8374 (p) REVERT: C 560 LYS cc_start: 0.8513 (tppp) cc_final: 0.8224 (pttt) REVERT: C 578 ASP cc_start: 0.8464 (m-30) cc_final: 0.8207 (m-30) REVERT: C 626 SER cc_start: 0.9038 (m) cc_final: 0.8478 (p) REVERT: C 664 ILE cc_start: 0.9067 (mt) cc_final: 0.8786 (mp) REVERT: C 668 ASN cc_start: 0.8405 (t0) cc_final: 0.7700 (t0) REVERT: C 676 SER cc_start: 0.8671 (m) cc_final: 0.8416 (t) REVERT: C 685 SER cc_start: 0.9001 (m) cc_final: 0.8461 (p) REVERT: D 560 LYS cc_start: 0.8336 (tttt) cc_final: 0.8096 (pttt) REVERT: D 578 ASP cc_start: 0.8511 (m-30) cc_final: 0.8249 (m-30) REVERT: D 591 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8475 (ptm-80) REVERT: D 613 SER cc_start: 0.9407 (t) cc_final: 0.9007 (p) REVERT: D 622 ARG cc_start: 0.8802 (tpp-160) cc_final: 0.8571 (tpp-160) REVERT: D 626 SER cc_start: 0.9030 (m) cc_final: 0.8622 (p) REVERT: D 652 GLU cc_start: 0.8812 (tt0) cc_final: 0.8274 (tt0) REVERT: D 660 ARG cc_start: 0.8784 (tpp-160) cc_final: 0.8466 (tpp-160) REVERT: D 668 ASN cc_start: 0.8638 (t0) cc_final: 0.8334 (t0) REVERT: D 676 SER cc_start: 0.8964 (m) cc_final: 0.8517 (p) REVERT: D 693 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: E 560 LYS cc_start: 0.8406 (tttt) cc_final: 0.8185 (pttt) REVERT: E 575 ASN cc_start: 0.8029 (m-40) cc_final: 0.7555 (m110) REVERT: E 578 ASP cc_start: 0.8412 (m-30) cc_final: 0.7912 (m-30) REVERT: E 613 SER cc_start: 0.9413 (m) cc_final: 0.9136 (p) REVERT: E 626 SER cc_start: 0.8943 (m) cc_final: 0.8236 (p) REVERT: E 648 ASP cc_start: 0.8992 (m-30) cc_final: 0.8724 (m-30) REVERT: E 652 GLU cc_start: 0.8745 (tt0) cc_final: 0.8318 (tt0) REVERT: E 655 GLU cc_start: 0.9183 (tp30) cc_final: 0.8921 (tp30) REVERT: E 658 GLU cc_start: 0.9324 (tp30) cc_final: 0.9056 (tp30) REVERT: E 660 ARG cc_start: 0.8608 (tpt90) cc_final: 0.8192 (tpt170) REVERT: E 668 ASN cc_start: 0.8667 (t0) cc_final: 0.8028 (t0) REVERT: E 676 SER cc_start: 0.8743 (m) cc_final: 0.8290 (p) REVERT: E 685 SER cc_start: 0.8881 (m) cc_final: 0.8540 (p) REVERT: E 706 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8002 (tmmt) REVERT: E 720 TYR cc_start: 0.7904 (m-10) cc_final: 0.7573 (m-10) REVERT: F 578 ASP cc_start: 0.8532 (m-30) cc_final: 0.8145 (m-30) REVERT: F 626 SER cc_start: 0.8958 (m) cc_final: 0.8487 (p) REVERT: F 652 GLU cc_start: 0.8786 (tt0) cc_final: 0.8262 (tt0) REVERT: F 668 ASN cc_start: 0.8610 (t0) cc_final: 0.8352 (t0) REVERT: F 676 SER cc_start: 0.8829 (m) cc_final: 0.8304 (p) REVERT: G 575 ASN cc_start: 0.8290 (m-40) cc_final: 0.7926 (m110) REVERT: G 578 ASP cc_start: 0.8529 (m-30) cc_final: 0.8229 (m-30) REVERT: G 590 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8653 (mt-10) REVERT: G 612 SER cc_start: 0.9503 (p) cc_final: 0.9100 (m) REVERT: G 626 SER cc_start: 0.9137 (m) cc_final: 0.8551 (p) REVERT: G 652 GLU cc_start: 0.8914 (tt0) cc_final: 0.8647 (tt0) REVERT: G 660 ARG cc_start: 0.8812 (tpt90) cc_final: 0.8532 (tpm170) REVERT: G 668 ASN cc_start: 0.8738 (t0) cc_final: 0.8236 (t0) REVERT: G 676 SER cc_start: 0.8856 (m) cc_final: 0.8407 (p) REVERT: G 685 SER cc_start: 0.8882 (m) cc_final: 0.8484 (p) REVERT: G 693 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: G 714 ARG cc_start: 0.8620 (mtp85) cc_final: 0.8338 (mtm-85) outliers start: 30 outliers final: 25 residues processed: 428 average time/residue: 1.1249 time to fit residues: 522.0062 Evaluate side-chains 432 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 404 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 537 ILE 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 702 SER 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 723 LEU Chi-restraints excluded: chain D residue 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 693 GLN 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 688 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.0980 chunk 94 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.0070 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 GLN C 575 ASN C 693 GLN D 556 GLN D 575 ASN E 572 ASN F 556 GLN F 703 GLN G 630 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091422 restraints weight = 17451.480| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.81 r_work: 0.2866 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11669 Z= 0.127 Angle : 0.745 13.196 15883 Z= 0.376 Chirality : 0.044 0.231 1967 Planarity : 0.003 0.032 2030 Dihedral : 3.630 14.682 1631 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.64 % Allowed : 31.12 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.23), residues: 1435 helix: 3.16 (0.19), residues: 637 sheet: 0.84 (0.31), residues: 259 loop : 0.42 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 694 HIS 0.002 0.001 HIS D 607 PHE 0.009 0.001 PHE A 567 TYR 0.009 0.001 TYR G 631 ARG 0.008 0.001 ARG D 697 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 760) hydrogen bonds : angle 3.44091 ( 2208) covalent geometry : bond 0.00282 (11669) covalent geometry : angle 0.74464 (15883) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11436.18 seconds wall clock time: 204 minutes 55.81 seconds (12295.81 seconds total)