Starting phenix.real_space_refine on Thu Sep 26 01:16:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_11629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_11629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_11629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_11629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a46_11629/09_2024/7a46_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.20, 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 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: 1.23 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: 3.48 Time building geometry restraints manager: 3.22 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.030 Find NCS groups from input model: 0.390 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:15.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.840 ------------------------------------------------------------------------------- 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= 0.429 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 *********************** 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 fitting. rotamer outliers: 70 poor density : 496 time to evaluate : 1.268 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: 0.9527 time to fit residues: 566.0298 Evaluate side-chains 434 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 398 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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= 0.171 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 *********************** 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 fitting. rotamer outliers: 55 poor density : 462 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9050 (t0) cc_final: 0.8749 (t0) REVERT: A 575 ASN cc_start: 0.8632 (m-40) cc_final: 0.8179 (m-40) REVERT: A 578 ASP cc_start: 0.8521 (m-30) cc_final: 0.8192 (m-30) REVERT: A 613 SER cc_start: 0.9471 (t) cc_final: 0.8991 (p) REVERT: A 647 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8136 (mttm) REVERT: A 654 MET cc_start: 0.9051 (mmm) cc_final: 0.8702 (mmm) REVERT: A 656 ASN cc_start: 0.8137 (t0) cc_final: 0.7823 (t0) REVERT: A 659 ILE cc_start: 0.9042 (mm) cc_final: 0.8817 (mp) REVERT: A 660 ARG cc_start: 0.8715 (tpt90) cc_final: 0.8462 (tpp-160) REVERT: A 668 ASN cc_start: 0.9011 (t0) cc_final: 0.8404 (t0) REVERT: A 676 SER cc_start: 0.8863 (m) cc_final: 0.8406 (p) REVERT: A 681 THR cc_start: 0.8668 (m) cc_final: 0.8270 (p) REVERT: A 685 SER cc_start: 0.8961 (m) cc_final: 0.8446 (p) REVERT: A 703 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8550 (tp40) REVERT: B 572 ASN cc_start: 0.9224 (t0) cc_final: 0.8841 (t0) REVERT: B 578 ASP cc_start: 0.8379 (m-30) cc_final: 0.7885 (m-30) REVERT: B 613 SER cc_start: 0.9508 (m) cc_final: 0.9184 (p) REVERT: B 626 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.8858 (p) REVERT: B 634 ASP cc_start: 0.8807 (t0) cc_final: 0.8599 (t0) REVERT: B 660 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8403 (tpm170) REVERT: B 668 ASN cc_start: 0.8650 (t0) cc_final: 0.8202 (t0) REVERT: B 676 SER cc_start: 0.9201 (m) cc_final: 0.8688 (p) REVERT: B 685 SER cc_start: 0.8829 (m) cc_final: 0.8506 (p) REVERT: C 572 ASN cc_start: 0.9224 (t0) cc_final: 0.8703 (t0) REVERT: C 596 SER cc_start: 0.9387 (p) cc_final: 0.8445 (p) REVERT: C 626 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 654 MET cc_start: 0.8820 (mmm) cc_final: 0.8452 (mmm) REVERT: C 655 GLU cc_start: 0.8903 (tp30) cc_final: 0.8582 (tp30) REVERT: C 660 ARG cc_start: 0.8592 (tpt90) cc_final: 0.8263 (tpp-160) REVERT: C 676 SER cc_start: 0.9244 (m) cc_final: 0.8770 (p) REVERT: C 681 THR cc_start: 0.8649 (m) cc_final: 0.8415 (p) REVERT: C 685 SER cc_start: 0.9008 (m) cc_final: 0.8628 (p) REVERT: D 572 ASN cc_start: 0.9343 (t0) cc_final: 0.9102 (t0) REVERT: D 612 SER cc_start: 0.9561 (p) cc_final: 0.9344 (m) REVERT: D 613 SER cc_start: 0.9384 (t) cc_final: 0.9172 (p) REVERT: D 626 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8717 (p) REVERT: D 648 ASP cc_start: 0.8846 (m-30) cc_final: 0.8587 (m-30) REVERT: D 652 GLU cc_start: 0.9042 (tt0) cc_final: 0.8532 (tt0) REVERT: D 655 GLU cc_start: 0.9023 (tp30) cc_final: 0.8636 (tp30) REVERT: D 660 ARG cc_start: 0.9006 (tpp-160) cc_final: 0.8793 (tpm170) REVERT: D 666 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8929 (mm-30) REVERT: D 668 ASN cc_start: 0.8855 (t0) cc_final: 0.8438 (t0) REVERT: D 676 SER cc_start: 0.9334 (m) cc_final: 0.8990 (p) REVERT: D 703 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8369 (mm-40) REVERT: E 574 MET cc_start: 0.9158 (ttm) cc_final: 0.8954 (mtm) REVERT: E 575 ASN cc_start: 0.8534 (m-40) cc_final: 0.8243 (m110) REVERT: E 578 ASP cc_start: 0.8449 (m-30) cc_final: 0.7994 (m-30) REVERT: E 612 SER cc_start: 0.9583 (p) cc_final: 0.9346 (m) REVERT: E 613 SER cc_start: 0.9470 (m) cc_final: 0.9114 (p) REVERT: E 626 SER cc_start: 0.9214 (m) cc_final: 0.8610 (p) REVERT: E 648 ASP cc_start: 0.8781 (m-30) cc_final: 0.8406 (m-30) REVERT: E 652 GLU cc_start: 0.8912 (tt0) cc_final: 0.8479 (tt0) REVERT: E 655 GLU cc_start: 0.8989 (tp30) cc_final: 0.8640 (tp30) REVERT: E 660 ARG cc_start: 0.8862 (tpt90) cc_final: 0.8518 (tpt170) REVERT: E 666 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8887 (tp30) REVERT: E 668 ASN cc_start: 0.8748 (t0) cc_final: 0.8032 (t0) REVERT: E 676 SER cc_start: 0.9075 (m) cc_final: 0.8605 (p) REVERT: E 681 THR cc_start: 0.8653 (m) cc_final: 0.8384 (p) REVERT: E 685 SER cc_start: 0.9059 (m) cc_final: 0.8735 (p) REVERT: E 720 TYR cc_start: 0.7525 (m-10) cc_final: 0.7150 (m-10) REVERT: F 572 ASN cc_start: 0.9316 (t0) cc_final: 0.8900 (t0) REVERT: F 575 ASN cc_start: 0.8188 (m-40) cc_final: 0.7684 (m-40) REVERT: F 578 ASP cc_start: 0.8401 (m-30) cc_final: 0.7797 (m-30) REVERT: F 590 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8576 (mt-10) REVERT: F 626 SER cc_start: 0.9149 (m) cc_final: 0.8641 (p) REVERT: F 634 ASP cc_start: 0.8905 (t0) cc_final: 0.8672 (t0) REVERT: F 652 GLU cc_start: 0.8908 (tt0) cc_final: 0.8364 (tt0) REVERT: F 655 GLU cc_start: 0.8910 (tp30) cc_final: 0.8592 (tp30) REVERT: F 660 ARG cc_start: 0.9011 (tpp-160) cc_final: 0.8781 (tpm170) REVERT: F 668 ASN cc_start: 0.8628 (t0) cc_final: 0.8099 (t0) REVERT: F 676 SER cc_start: 0.9155 (m) cc_final: 0.8616 (p) REVERT: F 685 SER cc_start: 0.9037 (m) cc_final: 0.8753 (p) REVERT: F 703 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8536 (tp40) REVERT: F 723 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7979 (tt) REVERT: G 572 ASN cc_start: 0.9334 (t0) cc_final: 0.9062 (t0) REVERT: G 578 ASP cc_start: 0.8439 (m-30) cc_final: 0.8186 (m-30) REVERT: G 590 GLU cc_start: 0.8704 (tt0) cc_final: 0.8425 (mt-10) REVERT: G 612 SER cc_start: 0.9494 (p) cc_final: 0.9177 (m) REVERT: G 626 SER cc_start: 0.9182 (m) cc_final: 0.8590 (p) REVERT: G 634 ASP cc_start: 0.8671 (t0) cc_final: 0.8413 (t0) REVERT: G 652 GLU cc_start: 0.8972 (tt0) cc_final: 0.8510 (tt0) REVERT: G 655 GLU cc_start: 0.8987 (tp30) cc_final: 0.8598 (tp30) REVERT: G 660 ARG cc_start: 0.8753 (tpt90) cc_final: 0.8381 (tpt170) REVERT: G 668 ASN cc_start: 0.8903 (t0) cc_final: 0.8281 (t0) REVERT: G 676 SER cc_start: 0.9121 (m) cc_final: 0.8725 (p) REVERT: G 685 SER cc_start: 0.9063 (m) cc_final: 0.8670 (p) REVERT: G 713 VAL cc_start: 0.9504 (t) cc_final: 0.9173 (p) outliers start: 55 outliers final: 26 residues processed: 485 average time/residue: 0.9910 time to fit residues: 525.4306 Evaluate side-chains 448 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 415 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 703 GLN 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 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 B 556 GLN C 668 ASN D 575 ASN D 630 ASN E 630 ASN G 575 ASN G 630 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2718 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= 0.176 Angle : 0.565 8.971 15883 Z= 0.283 Chirality : 0.042 0.185 1967 Planarity : 0.003 0.032 2030 Dihedral : 4.336 40.612 1645 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.06 % Allowed : 23.72 % Favored : 73.21 % 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: 2.39 (0.19), residues: 644 sheet: -0.28 (0.30), residues: 273 loop : 0.08 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 694 HIS 0.002 0.001 HIS D 607 PHE 0.008 0.001 PHE E 680 TYR 0.009 0.001 TYR E 606 ARG 0.006 0.001 ARG D 591 *********************** 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 464 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 428 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 572 ASN cc_start: 0.9150 (t0) cc_final: 0.8875 (t0) REVERT: A 575 ASN cc_start: 0.8522 (m-40) cc_final: 0.8112 (m-40) REVERT: A 578 ASP cc_start: 0.8508 (m-30) cc_final: 0.8169 (m-30) REVERT: A 622 ARG cc_start: 0.8785 (mmp80) cc_final: 0.8559 (mmp80) REVERT: A 644 GLN cc_start: 0.8297 (tp40) cc_final: 0.7939 (tp40) REVERT: A 647 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8111 (mttm) REVERT: A 652 GLU cc_start: 0.8998 (tt0) cc_final: 0.8794 (tt0) REVERT: A 668 ASN cc_start: 0.8927 (t0) cc_final: 0.8285 (t0) REVERT: A 676 SER cc_start: 0.8794 (m) cc_final: 0.8315 (p) REVERT: A 681 THR cc_start: 0.8684 (m) cc_final: 0.8267 (p) REVERT: A 685 SER cc_start: 0.8981 (m) cc_final: 0.8449 (p) REVERT: B 572 ASN cc_start: 0.9112 (t0) cc_final: 0.8889 (t0) REVERT: B 578 ASP cc_start: 0.8481 (m-30) cc_final: 0.8150 (m-30) REVERT: B 613 SER cc_start: 0.9452 (m) cc_final: 0.9184 (p) REVERT: B 626 SER cc_start: 0.9233 (m) cc_final: 0.8698 (p) REVERT: B 641 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8681 (ttpp) REVERT: B 660 ARG cc_start: 0.8818 (tpp-160) cc_final: 0.8512 (tpt170) REVERT: B 668 ASN cc_start: 0.8707 (t0) cc_final: 0.8245 (t0) REVERT: B 676 SER cc_start: 0.9198 (m) cc_final: 0.8684 (p) REVERT: B 685 SER cc_start: 0.8884 (m) cc_final: 0.8525 (p) REVERT: C 572 ASN cc_start: 0.9127 (t0) cc_final: 0.8522 (t0) REVERT: C 626 SER cc_start: 0.9151 (m) cc_final: 0.8614 (p) REVERT: C 655 GLU cc_start: 0.8865 (tp30) cc_final: 0.8608 (tp30) REVERT: C 676 SER cc_start: 0.9186 (m) cc_final: 0.8740 (p) REVERT: C 681 THR cc_start: 0.8723 (m) cc_final: 0.8431 (p) REVERT: C 685 SER cc_start: 0.9069 (m) cc_final: 0.8648 (p) REVERT: C 703 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8406 (mm110) REVERT: D 560 LYS cc_start: 0.8669 (tttt) cc_final: 0.8183 (pttt) REVERT: D 570 PHE cc_start: 0.8880 (t80) cc_final: 0.8618 (m-80) REVERT: D 572 ASN cc_start: 0.9292 (t0) cc_final: 0.8991 (t0) REVERT: D 612 SER cc_start: 0.9541 (p) cc_final: 0.9319 (m) REVERT: D 613 SER cc_start: 0.9472 (t) cc_final: 0.9200 (p) REVERT: D 626 SER cc_start: 0.9123 (m) cc_final: 0.8771 (p) REVERT: D 648 ASP cc_start: 0.8867 (m-30) cc_final: 0.8601 (m-30) REVERT: D 655 GLU cc_start: 0.9058 (tp30) cc_final: 0.8703 (tp30) REVERT: D 660 ARG cc_start: 0.9016 (tpp-160) cc_final: 0.8784 (tpm170) REVERT: D 666 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8953 (mm-30) REVERT: D 668 ASN cc_start: 0.8857 (t0) cc_final: 0.8459 (t0) REVERT: D 676 SER cc_start: 0.9256 (m) cc_final: 0.8831 (p) REVERT: D 693 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8189 (pm20) REVERT: D 723 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7779 (tt) REVERT: E 560 LYS cc_start: 0.8415 (tttt) cc_final: 0.8130 (pttt) REVERT: E 575 ASN cc_start: 0.8409 (m-40) cc_final: 0.8050 (m110) REVERT: E 578 ASP cc_start: 0.8313 (m-30) cc_final: 0.7842 (m-30) REVERT: E 612 SER cc_start: 0.9602 (p) cc_final: 0.9392 (m) REVERT: E 613 SER cc_start: 0.9501 (m) cc_final: 0.9159 (p) REVERT: E 626 SER cc_start: 0.9145 (m) cc_final: 0.8438 (p) REVERT: E 648 ASP cc_start: 0.8851 (m-30) cc_final: 0.8490 (m-30) REVERT: E 652 GLU cc_start: 0.8882 (tt0) cc_final: 0.8472 (tt0) REVERT: E 655 GLU cc_start: 0.8978 (tp30) cc_final: 0.8522 (tp30) REVERT: E 660 ARG cc_start: 0.8897 (tpt90) cc_final: 0.8601 (tpp-160) REVERT: E 666 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8886 (tp30) REVERT: E 668 ASN cc_start: 0.8763 (t0) cc_final: 0.8020 (t0) REVERT: E 676 SER cc_start: 0.9018 (m) cc_final: 0.8554 (p) REVERT: E 685 SER cc_start: 0.9054 (m) cc_final: 0.8702 (p) REVERT: E 720 TYR cc_start: 0.7583 (m-10) cc_final: 0.7170 (m-10) REVERT: F 572 ASN cc_start: 0.9279 (t0) cc_final: 0.8977 (t0) REVERT: F 575 ASN cc_start: 0.8245 (m-40) cc_final: 0.7780 (m-40) REVERT: F 578 ASP cc_start: 0.8421 (m-30) cc_final: 0.7940 (m-30) REVERT: F 626 SER cc_start: 0.9100 (m) cc_final: 0.8574 (p) REVERT: F 634 ASP cc_start: 0.8828 (t0) cc_final: 0.8573 (t0) REVERT: F 652 GLU cc_start: 0.8900 (tt0) cc_final: 0.8433 (tt0) REVERT: F 655 GLU cc_start: 0.8897 (tp30) cc_final: 0.8695 (tp30) REVERT: F 668 ASN cc_start: 0.8676 (t0) cc_final: 0.8107 (t0) REVERT: F 676 SER cc_start: 0.9119 (m) cc_final: 0.8593 (p) REVERT: F 685 SER cc_start: 0.8986 (m) cc_final: 0.8665 (p) REVERT: G 572 ASN cc_start: 0.9215 (t0) cc_final: 0.8948 (t0) REVERT: G 575 ASN cc_start: 0.8513 (m-40) cc_final: 0.8246 (m-40) REVERT: G 578 ASP cc_start: 0.8396 (m-30) cc_final: 0.8145 (m-30) REVERT: G 590 GLU cc_start: 0.8698 (tt0) cc_final: 0.8428 (mt-10) REVERT: G 612 SER cc_start: 0.9529 (p) cc_final: 0.9243 (m) REVERT: G 626 SER cc_start: 0.9197 (m) cc_final: 0.8664 (p) REVERT: G 652 GLU cc_start: 0.8935 (tt0) cc_final: 0.8600 (tt0) REVERT: G 655 GLU cc_start: 0.8974 (tp30) cc_final: 0.8658 (tp30) REVERT: G 668 ASN cc_start: 0.8891 (t0) cc_final: 0.8294 (t0) REVERT: G 676 SER cc_start: 0.9084 (m) cc_final: 0.8673 (p) REVERT: G 685 SER cc_start: 0.9062 (m) cc_final: 0.8647 (p) REVERT: G 693 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8425 (pm20) outliers start: 36 outliers final: 18 residues processed: 445 average time/residue: 1.0757 time to fit residues: 520.7798 Evaluate side-chains 431 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 409 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 A residue 723 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain C residue 616 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 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 F residue 570 PHE Chi-restraints excluded: chain F residue 688 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 94 optimal weight: 0.0770 chunk 140 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN C 575 ASN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN F 703 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2968 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= 0.188 Angle : 0.566 9.079 15883 Z= 0.283 Chirality : 0.042 0.180 1967 Planarity : 0.003 0.031 2030 Dihedral : 3.841 35.429 1634 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.23 % Allowed : 26.36 % Favored : 70.41 % 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: 1.98 (0.22), residues: 1435 helix: 2.67 (0.19), residues: 644 sheet: 0.19 (0.31), residues: 259 loop : 0.27 (0.29), residues: 532 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 0.019 0.001 PHE A 567 TYR 0.010 0.001 TYR F 720 ARG 0.006 0.001 ARG B 697 *********************** 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 468 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 430 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8132 (pttt) REVERT: A 572 ASN cc_start: 0.9101 (t0) cc_final: 0.8724 (t0) REVERT: A 575 ASN cc_start: 0.8439 (m-40) cc_final: 0.7976 (m-40) REVERT: A 578 ASP cc_start: 0.8470 (m-30) cc_final: 0.8051 (m-30) REVERT: A 590 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 647 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8102 (mttm) REVERT: A 660 ARG cc_start: 0.8791 (tpt90) cc_final: 0.8315 (tpt170) REVERT: A 668 ASN cc_start: 0.8896 (t0) cc_final: 0.8229 (t0) REVERT: A 676 SER cc_start: 0.8793 (m) cc_final: 0.8303 (p) REVERT: A 685 SER cc_start: 0.8965 (m) cc_final: 0.8447 (p) REVERT: B 560 LYS cc_start: 0.8575 (tttt) cc_final: 0.8158 (pttt) REVERT: B 578 ASP cc_start: 0.8419 (m-30) cc_final: 0.8069 (m-30) REVERT: B 613 SER cc_start: 0.9439 (m) cc_final: 0.9100 (p) REVERT: B 626 SER cc_start: 0.9204 (m) cc_final: 0.8722 (p) REVERT: B 634 ASP cc_start: 0.8790 (t0) cc_final: 0.8473 (t0) REVERT: B 641 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8668 (ttpp) REVERT: B 660 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8506 (tpt170) REVERT: B 668 ASN cc_start: 0.8736 (t0) cc_final: 0.8297 (t0) REVERT: B 676 SER cc_start: 0.9189 (m) cc_final: 0.8676 (p) REVERT: B 685 SER cc_start: 0.8900 (m) cc_final: 0.8544 (p) REVERT: C 560 LYS cc_start: 0.8550 (tppp) cc_final: 0.8247 (pttt) REVERT: C 572 ASN cc_start: 0.9134 (t0) cc_final: 0.8754 (t0) REVERT: C 575 ASN cc_start: 0.8392 (m-40) cc_final: 0.8153 (m110) REVERT: C 578 ASP cc_start: 0.8446 (m-30) cc_final: 0.8213 (m-30) REVERT: C 626 SER cc_start: 0.9149 (m) cc_final: 0.8570 (p) REVERT: C 655 GLU cc_start: 0.8873 (tp30) cc_final: 0.8559 (tp30) REVERT: C 660 ARG cc_start: 0.8542 (tpt90) cc_final: 0.8209 (tpt170) REVERT: C 676 SER cc_start: 0.9051 (m) cc_final: 0.8591 (p) REVERT: C 685 SER cc_start: 0.9091 (m) cc_final: 0.8639 (p) REVERT: D 560 LYS cc_start: 0.8520 (tttt) cc_final: 0.8184 (pttt) REVERT: D 570 PHE cc_start: 0.8916 (t80) cc_final: 0.8528 (m-10) REVERT: D 572 ASN cc_start: 0.9294 (t0) cc_final: 0.9017 (t0) REVERT: D 612 SER cc_start: 0.9516 (p) cc_final: 0.9280 (m) REVERT: D 613 SER cc_start: 0.9474 (t) cc_final: 0.9098 (p) REVERT: D 626 SER cc_start: 0.9132 (m) cc_final: 0.8793 (p) REVERT: D 634 ASP cc_start: 0.8747 (t0) cc_final: 0.8531 (t0) REVERT: D 648 ASP cc_start: 0.8901 (m-30) cc_final: 0.8635 (m-30) REVERT: D 652 GLU cc_start: 0.8966 (tt0) cc_final: 0.8314 (tt0) REVERT: D 655 GLU cc_start: 0.9029 (tp30) cc_final: 0.8726 (tp30) REVERT: D 658 GLU cc_start: 0.9057 (tp30) cc_final: 0.8853 (tp30) REVERT: D 660 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8660 (tpm170) REVERT: D 666 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8949 (mm-30) REVERT: D 668 ASN cc_start: 0.8846 (t0) cc_final: 0.8467 (t0) REVERT: D 676 SER cc_start: 0.9215 (m) cc_final: 0.8787 (p) REVERT: D 693 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: D 723 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7725 (tt) REVERT: E 560 LYS cc_start: 0.8450 (tttt) cc_final: 0.8150 (pttt) REVERT: E 575 ASN cc_start: 0.8387 (m-40) cc_final: 0.7992 (m110) REVERT: E 578 ASP cc_start: 0.8236 (m-30) cc_final: 0.7721 (m-30) REVERT: E 596 SER cc_start: 0.9393 (p) cc_final: 0.8958 (m) REVERT: E 612 SER cc_start: 0.9590 (p) cc_final: 0.9377 (m) REVERT: E 613 SER cc_start: 0.9498 (m) cc_final: 0.9196 (p) REVERT: E 626 SER cc_start: 0.9135 (m) cc_final: 0.8455 (p) REVERT: E 648 ASP cc_start: 0.8869 (m-30) cc_final: 0.8521 (m-30) REVERT: E 652 GLU cc_start: 0.8894 (tt0) cc_final: 0.8535 (tt0) REVERT: E 655 GLU cc_start: 0.8946 (tp30) cc_final: 0.8562 (tp30) REVERT: E 660 ARG cc_start: 0.8900 (tpt90) cc_final: 0.8533 (tpp-160) REVERT: E 666 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8893 (tp30) REVERT: E 668 ASN cc_start: 0.8767 (t0) cc_final: 0.8121 (t0) REVERT: E 676 SER cc_start: 0.9019 (m) cc_final: 0.8552 (p) REVERT: E 685 SER cc_start: 0.9059 (m) cc_final: 0.8715 (p) REVERT: E 703 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8336 (mm110) REVERT: E 720 TYR cc_start: 0.7603 (m-10) cc_final: 0.7236 (m-10) REVERT: F 527 MET cc_start: 0.9240 (mtt) cc_final: 0.9029 (ptp) REVERT: F 572 ASN cc_start: 0.9281 (t0) cc_final: 0.8927 (t0) REVERT: F 575 ASN cc_start: 0.8272 (m-40) cc_final: 0.7761 (m-40) REVERT: F 578 ASP cc_start: 0.8420 (m-30) cc_final: 0.7929 (m-30) REVERT: F 626 SER cc_start: 0.9092 (m) cc_final: 0.8601 (p) REVERT: F 652 GLU cc_start: 0.8940 (tt0) cc_final: 0.8487 (tt0) REVERT: F 655 GLU cc_start: 0.8919 (tp30) cc_final: 0.8701 (tp30) REVERT: F 658 GLU cc_start: 0.9123 (tp30) cc_final: 0.8872 (tp30) REVERT: F 668 ASN cc_start: 0.8677 (t0) cc_final: 0.8465 (t0) REVERT: F 676 SER cc_start: 0.9118 (m) cc_final: 0.8562 (p) REVERT: F 703 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8488 (mm-40) REVERT: G 572 ASN cc_start: 0.9145 (t0) cc_final: 0.8895 (t0) REVERT: G 575 ASN cc_start: 0.8467 (m-40) cc_final: 0.8211 (m-40) REVERT: G 578 ASP cc_start: 0.8368 (m-30) cc_final: 0.8080 (m-30) REVERT: G 590 GLU cc_start: 0.8742 (tt0) cc_final: 0.8504 (mt-10) REVERT: G 612 SER cc_start: 0.9565 (p) cc_final: 0.9273 (m) REVERT: G 626 SER cc_start: 0.9192 (m) cc_final: 0.8608 (p) REVERT: G 652 GLU cc_start: 0.8873 (tt0) cc_final: 0.8574 (tt0) REVERT: G 654 MET cc_start: 0.9057 (mmm) cc_final: 0.8852 (mmm) REVERT: G 655 GLU cc_start: 0.8944 (tp30) cc_final: 0.8592 (tp30) REVERT: G 660 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8451 (tpt170) REVERT: G 668 ASN cc_start: 0.8895 (t0) cc_final: 0.8313 (t0) REVERT: G 676 SER cc_start: 0.9069 (m) cc_final: 0.8647 (p) REVERT: G 685 SER cc_start: 0.9072 (m) cc_final: 0.8643 (p) REVERT: G 693 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8430 (pm20) outliers start: 38 outliers final: 24 residues processed: 448 average time/residue: 1.0669 time to fit residues: 520.4052 Evaluate side-chains 440 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 411 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 616 THR Chi-restraints excluded: chain A residue 647 LYS 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 61 optimal weight: 0.0970 chunk 127 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11669 Z= 0.232 Angle : 0.584 8.834 15883 Z= 0.292 Chirality : 0.041 0.165 1967 Planarity : 0.003 0.030 2030 Dihedral : 3.738 12.503 1631 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.74 % Allowed : 27.21 % 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: 2.13 (0.23), residues: 1435 helix: 2.81 (0.19), residues: 637 sheet: 0.39 (0.32), residues: 259 loop : 0.28 (0.29), residues: 539 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 0.012 0.001 PHE A 567 TYR 0.013 0.001 TYR F 720 ARG 0.006 0.001 ARG A 697 *********************** 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 467 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 423 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8106 (pttt) REVERT: A 572 ASN cc_start: 0.9130 (t0) cc_final: 0.8837 (t0) REVERT: A 575 ASN cc_start: 0.8360 (m-40) cc_final: 0.7865 (m-40) REVERT: A 578 ASP cc_start: 0.8438 (m-30) cc_final: 0.8117 (m-30) REVERT: A 622 ARG cc_start: 0.8941 (tpp-160) cc_final: 0.8344 (mmp80) REVERT: A 647 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8094 (mttm) REVERT: A 652 GLU cc_start: 0.8966 (tt0) cc_final: 0.8704 (tt0) REVERT: A 660 ARG cc_start: 0.8820 (tpt90) cc_final: 0.8452 (tpt170) REVERT: A 668 ASN cc_start: 0.8861 (t0) cc_final: 0.8194 (t0) REVERT: A 676 SER cc_start: 0.8827 (m) cc_final: 0.8350 (p) REVERT: A 685 SER cc_start: 0.8980 (m) cc_final: 0.8472 (p) REVERT: B 578 ASP cc_start: 0.8410 (m-30) cc_final: 0.8021 (m-30) REVERT: B 613 SER cc_start: 0.9467 (m) cc_final: 0.9138 (p) REVERT: B 626 SER cc_start: 0.9227 (m) cc_final: 0.8743 (p) REVERT: B 634 ASP cc_start: 0.8820 (t0) cc_final: 0.8541 (t0) REVERT: B 641 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8684 (ttpp) REVERT: B 652 GLU cc_start: 0.9038 (tt0) cc_final: 0.8648 (tt0) REVERT: B 660 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8406 (tpp-160) REVERT: B 668 ASN cc_start: 0.8775 (t0) cc_final: 0.8346 (t0) REVERT: B 676 SER cc_start: 0.9035 (m) cc_final: 0.8523 (p) REVERT: B 685 SER cc_start: 0.8895 (m) cc_final: 0.8541 (p) REVERT: C 572 ASN cc_start: 0.9164 (t0) cc_final: 0.8759 (t0) REVERT: C 626 SER cc_start: 0.9182 (m) cc_final: 0.8600 (p) REVERT: C 634 ASP cc_start: 0.8885 (t0) cc_final: 0.8662 (t0) REVERT: C 660 ARG cc_start: 0.8569 (tpt90) cc_final: 0.8124 (tpp-160) REVERT: C 676 SER cc_start: 0.9003 (m) cc_final: 0.8553 (p) REVERT: C 685 SER cc_start: 0.9120 (m) cc_final: 0.8649 (p) REVERT: D 560 LYS cc_start: 0.8520 (tttt) cc_final: 0.8177 (pttt) REVERT: D 572 ASN cc_start: 0.9311 (t0) cc_final: 0.8989 (t0) REVERT: D 612 SER cc_start: 0.9535 (p) cc_final: 0.9284 (m) REVERT: D 626 SER cc_start: 0.9135 (m) cc_final: 0.8743 (p) REVERT: D 655 GLU cc_start: 0.9033 (tp30) cc_final: 0.8748 (tp30) REVERT: D 658 GLU cc_start: 0.9095 (tp30) cc_final: 0.8794 (tp30) REVERT: D 660 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8681 (tpm170) REVERT: D 668 ASN cc_start: 0.8844 (t0) cc_final: 0.8467 (t0) REVERT: D 676 SER cc_start: 0.9180 (m) cc_final: 0.8754 (p) REVERT: D 693 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: D 723 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7703 (tt) REVERT: E 560 LYS cc_start: 0.8467 (tttt) cc_final: 0.8159 (pttt) REVERT: E 575 ASN cc_start: 0.8367 (m-40) cc_final: 0.7738 (m110) REVERT: E 578 ASP cc_start: 0.8256 (m-30) cc_final: 0.7743 (m-30) REVERT: E 590 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 612 SER cc_start: 0.9597 (p) cc_final: 0.9370 (m) REVERT: E 626 SER cc_start: 0.9165 (m) cc_final: 0.8468 (p) REVERT: E 652 GLU cc_start: 0.8862 (tt0) cc_final: 0.8492 (tt0) REVERT: E 655 GLU cc_start: 0.8963 (tp30) cc_final: 0.8608 (tp30) REVERT: E 660 ARG cc_start: 0.8874 (tpt90) cc_final: 0.8495 (tpt170) REVERT: E 666 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8905 (tp30) REVERT: E 668 ASN cc_start: 0.8797 (t0) cc_final: 0.8280 (t0) REVERT: E 676 SER cc_start: 0.8988 (m) cc_final: 0.8531 (p) REVERT: E 685 SER cc_start: 0.9071 (m) cc_final: 0.8737 (p) REVERT: E 703 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8443 (mm110) REVERT: E 720 TYR cc_start: 0.7604 (m-10) cc_final: 0.7215 (m-10) REVERT: F 572 ASN cc_start: 0.9301 (t0) cc_final: 0.9048 (t0) REVERT: F 575 ASN cc_start: 0.8296 (m-40) cc_final: 0.8046 (m110) REVERT: F 578 ASP cc_start: 0.8403 (m-30) cc_final: 0.7986 (m-30) REVERT: F 626 SER cc_start: 0.9172 (m) cc_final: 0.8730 (p) REVERT: F 652 GLU cc_start: 0.8881 (tt0) cc_final: 0.8570 (tt0) REVERT: F 658 GLU cc_start: 0.9194 (tp30) cc_final: 0.8946 (tp30) REVERT: F 668 ASN cc_start: 0.8755 (t0) cc_final: 0.8478 (t0) REVERT: F 676 SER cc_start: 0.9053 (m) cc_final: 0.8527 (p) REVERT: F 693 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: G 572 ASN cc_start: 0.9191 (t0) cc_final: 0.8791 (t0) REVERT: G 575 ASN cc_start: 0.8484 (m-40) cc_final: 0.8167 (m-40) REVERT: G 578 ASP cc_start: 0.8377 (m-30) cc_final: 0.8059 (m-30) REVERT: G 590 GLU cc_start: 0.8770 (tt0) cc_final: 0.8548 (mt-10) REVERT: G 601 GLN cc_start: 0.8865 (tt0) cc_final: 0.8658 (tt0) REVERT: G 612 SER cc_start: 0.9557 (p) cc_final: 0.9222 (m) REVERT: G 622 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8263 (mmp80) REVERT: G 626 SER cc_start: 0.9310 (m) cc_final: 0.8695 (p) REVERT: G 652 GLU cc_start: 0.8850 (tt0) cc_final: 0.8588 (tt0) REVERT: G 654 MET cc_start: 0.9045 (mmm) cc_final: 0.8824 (mmm) REVERT: G 655 GLU cc_start: 0.8968 (tp30) cc_final: 0.8657 (tp30) REVERT: G 660 ARG cc_start: 0.8644 (tpt90) cc_final: 0.8282 (tpt170) REVERT: G 668 ASN cc_start: 0.8905 (t0) cc_final: 0.8349 (t0) REVERT: G 676 SER cc_start: 0.9061 (m) cc_final: 0.8631 (p) REVERT: G 685 SER cc_start: 0.9028 (m) cc_final: 0.8614 (p) REVERT: G 693 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8439 (pm20) outliers start: 44 outliers final: 32 residues processed: 444 average time/residue: 1.0818 time to fit residues: 521.6948 Evaluate side-chains 448 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 410 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 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 703 GLN Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 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 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain E residue 702 SER Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain F residue 693 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 50 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN C 693 GLN D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3183 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= 0.228 Angle : 0.602 8.730 15883 Z= 0.302 Chirality : 0.042 0.162 1967 Planarity : 0.003 0.029 2030 Dihedral : 3.730 12.605 1631 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.51 % Allowed : 26.96 % Favored : 68.54 % 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: 2.29 (0.23), residues: 1435 helix: 2.90 (0.19), residues: 637 sheet: 0.53 (0.32), residues: 259 loop : 0.40 (0.29), residues: 539 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 0.013 0.001 PHE D 567 TYR 0.014 0.001 TYR F 720 ARG 0.006 0.001 ARG D 697 *********************** 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 475 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 422 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8103 (pttt) REVERT: A 572 ASN cc_start: 0.9129 (t0) cc_final: 0.8688 (t0) REVERT: A 575 ASN cc_start: 0.8311 (m-40) cc_final: 0.7835 (m110) REVERT: A 578 ASP cc_start: 0.8453 (m-30) cc_final: 0.8054 (m-30) REVERT: A 652 GLU cc_start: 0.8969 (tt0) cc_final: 0.8710 (tt0) REVERT: A 655 GLU cc_start: 0.8992 (tp30) cc_final: 0.8644 (tp30) REVERT: A 660 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8543 (tpt170) REVERT: A 668 ASN cc_start: 0.8807 (t0) cc_final: 0.8142 (t0) REVERT: A 676 SER cc_start: 0.8841 (m) cc_final: 0.8358 (p) REVERT: A 685 SER cc_start: 0.8976 (m) cc_final: 0.8467 (p) REVERT: B 560 LYS cc_start: 0.8606 (tttt) cc_final: 0.8189 (pttt) REVERT: B 578 ASP cc_start: 0.8371 (m-30) cc_final: 0.8027 (m-30) REVERT: B 613 SER cc_start: 0.9451 (m) cc_final: 0.9113 (p) REVERT: B 626 SER cc_start: 0.9231 (m) cc_final: 0.8744 (p) REVERT: B 634 ASP cc_start: 0.8836 (t0) cc_final: 0.8595 (t0) REVERT: B 641 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8676 (ttpp) REVERT: B 652 GLU cc_start: 0.9024 (tt0) cc_final: 0.8589 (tt0) REVERT: B 655 GLU cc_start: 0.8956 (tp30) cc_final: 0.8600 (tp30) REVERT: B 660 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8487 (tpp-160) REVERT: B 668 ASN cc_start: 0.8782 (t0) cc_final: 0.8346 (t0) REVERT: B 676 SER cc_start: 0.9017 (m) cc_final: 0.8504 (p) REVERT: B 685 SER cc_start: 0.8902 (m) cc_final: 0.8520 (p) REVERT: C 560 LYS cc_start: 0.8585 (tppp) cc_final: 0.8248 (pttt) REVERT: C 572 ASN cc_start: 0.9196 (t0) cc_final: 0.8836 (t0) REVERT: C 575 ASN cc_start: 0.8463 (m-40) cc_final: 0.8214 (m110) REVERT: C 578 ASP cc_start: 0.8405 (m-30) cc_final: 0.8160 (m-30) REVERT: C 626 SER cc_start: 0.9152 (m) cc_final: 0.8545 (p) REVERT: C 634 ASP cc_start: 0.8895 (t0) cc_final: 0.8680 (t0) REVERT: C 652 GLU cc_start: 0.8874 (tt0) cc_final: 0.8671 (tt0) REVERT: C 676 SER cc_start: 0.9003 (m) cc_final: 0.8545 (p) REVERT: C 685 SER cc_start: 0.9123 (m) cc_final: 0.8648 (p) REVERT: D 560 LYS cc_start: 0.8540 (tttt) cc_final: 0.8205 (pttt) REVERT: D 572 ASN cc_start: 0.9308 (t0) cc_final: 0.8973 (t0) REVERT: D 612 SER cc_start: 0.9523 (p) cc_final: 0.9236 (m) REVERT: D 626 SER cc_start: 0.9135 (m) cc_final: 0.8740 (p) REVERT: D 652 GLU cc_start: 0.8905 (tt0) cc_final: 0.8257 (tt0) REVERT: D 655 GLU cc_start: 0.9037 (tp30) cc_final: 0.8754 (tp30) REVERT: D 658 GLU cc_start: 0.9140 (tp30) cc_final: 0.8895 (tp30) REVERT: D 668 ASN cc_start: 0.8842 (t0) cc_final: 0.8477 (t0) REVERT: D 676 SER cc_start: 0.9151 (m) cc_final: 0.8716 (p) REVERT: D 693 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: D 723 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7635 (tt) REVERT: E 560 LYS cc_start: 0.8535 (tttt) cc_final: 0.8226 (pttt) REVERT: E 572 ASN cc_start: 0.9217 (t0) cc_final: 0.8980 (t0) REVERT: E 578 ASP cc_start: 0.8284 (m-30) cc_final: 0.7737 (m-30) REVERT: E 590 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8405 (mt-10) REVERT: E 612 SER cc_start: 0.9580 (p) cc_final: 0.9342 (m) REVERT: E 626 SER cc_start: 0.9149 (m) cc_final: 0.8423 (p) REVERT: E 652 GLU cc_start: 0.8857 (tt0) cc_final: 0.8484 (tt0) REVERT: E 655 GLU cc_start: 0.8961 (tp30) cc_final: 0.8698 (tp30) REVERT: E 660 ARG cc_start: 0.8801 (tpt90) cc_final: 0.8338 (tpt170) REVERT: E 666 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8893 (tp30) REVERT: E 668 ASN cc_start: 0.8800 (t0) cc_final: 0.8290 (t0) REVERT: E 676 SER cc_start: 0.8988 (m) cc_final: 0.8528 (p) REVERT: E 685 SER cc_start: 0.9067 (m) cc_final: 0.8736 (p) REVERT: E 703 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8496 (mm110) REVERT: E 720 TYR cc_start: 0.7614 (m-10) cc_final: 0.7234 (m-10) REVERT: F 572 ASN cc_start: 0.9311 (t0) cc_final: 0.8890 (t0) REVERT: F 578 ASP cc_start: 0.8411 (m-30) cc_final: 0.8021 (m-30) REVERT: F 622 ARG cc_start: 0.9024 (tpp-160) cc_final: 0.8785 (tpp-160) REVERT: F 626 SER cc_start: 0.9168 (m) cc_final: 0.8731 (p) REVERT: F 652 GLU cc_start: 0.8917 (tt0) cc_final: 0.8458 (tt0) REVERT: F 658 GLU cc_start: 0.9167 (tp30) cc_final: 0.8881 (tp30) REVERT: F 668 ASN cc_start: 0.8750 (t0) cc_final: 0.8460 (t0) REVERT: F 676 SER cc_start: 0.9075 (m) cc_final: 0.8537 (p) REVERT: F 693 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: G 572 ASN cc_start: 0.9202 (t0) cc_final: 0.8848 (t0) REVERT: G 575 ASN cc_start: 0.8415 (m-40) cc_final: 0.8031 (m-40) REVERT: G 578 ASP cc_start: 0.8398 (m-30) cc_final: 0.8059 (m-30) REVERT: G 590 GLU cc_start: 0.8751 (tt0) cc_final: 0.8491 (mt-10) REVERT: G 601 GLN cc_start: 0.8887 (tt0) cc_final: 0.8664 (tt0) REVERT: G 612 SER cc_start: 0.9534 (p) cc_final: 0.9127 (m) REVERT: G 622 ARG cc_start: 0.8685 (mmp80) cc_final: 0.8187 (mmt90) REVERT: G 626 SER cc_start: 0.9305 (m) cc_final: 0.8697 (p) REVERT: G 652 GLU cc_start: 0.8865 (tt0) cc_final: 0.8606 (tt0) REVERT: G 654 MET cc_start: 0.9041 (mmm) cc_final: 0.8774 (mmm) REVERT: G 655 GLU cc_start: 0.8973 (tp30) cc_final: 0.8670 (tp30) REVERT: G 660 ARG cc_start: 0.8632 (tpt90) cc_final: 0.8243 (tpt170) REVERT: G 668 ASN cc_start: 0.8926 (t0) cc_final: 0.8367 (t0) REVERT: G 676 SER cc_start: 0.9069 (m) cc_final: 0.8600 (p) REVERT: G 685 SER cc_start: 0.9024 (m) cc_final: 0.8618 (p) REVERT: G 693 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8429 (pm20) outliers start: 53 outliers final: 34 residues processed: 449 average time/residue: 0.9171 time to fit residues: 446.9189 Evaluate side-chains 448 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 408 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 560 LYS 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 C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 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 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 616 THR Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN F 703 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11669 Z= 0.194 Angle : 0.614 8.299 15883 Z= 0.306 Chirality : 0.042 0.166 1967 Planarity : 0.003 0.030 2030 Dihedral : 3.659 12.661 1631 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.91 % Allowed : 27.81 % Favored : 68.28 % 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: 2.41 (0.23), residues: 1435 helix: 3.02 (0.19), residues: 637 sheet: 0.60 (0.32), residues: 259 loop : 0.43 (0.29), residues: 539 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 0.013 0.001 PHE D 567 TYR 0.011 0.001 TYR F 720 ARG 0.007 0.001 ARG D 697 *********************** 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 473 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 427 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8255 (pttt) REVERT: A 575 ASN cc_start: 0.8298 (m-40) cc_final: 0.7998 (m110) REVERT: A 578 ASP cc_start: 0.8405 (m-30) cc_final: 0.8022 (m-30) REVERT: A 652 GLU cc_start: 0.8950 (tt0) cc_final: 0.8713 (tt0) REVERT: A 655 GLU cc_start: 0.8973 (tp30) cc_final: 0.8663 (tp30) REVERT: A 660 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8500 (tpt170) REVERT: A 668 ASN cc_start: 0.8823 (t0) cc_final: 0.8165 (t0) REVERT: A 676 SER cc_start: 0.8859 (m) cc_final: 0.8390 (p) REVERT: A 685 SER cc_start: 0.8973 (m) cc_final: 0.8458 (p) REVERT: B 560 LYS cc_start: 0.8526 (tttt) cc_final: 0.8148 (pttt) REVERT: B 578 ASP cc_start: 0.8397 (m-30) cc_final: 0.8025 (m-30) REVERT: B 626 SER cc_start: 0.9181 (m) cc_final: 0.8699 (p) REVERT: B 634 ASP cc_start: 0.8762 (t0) cc_final: 0.8542 (t0) REVERT: B 641 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8718 (ttpp) REVERT: B 652 GLU cc_start: 0.9044 (tt0) cc_final: 0.8600 (tt0) REVERT: B 655 GLU cc_start: 0.9016 (tp30) cc_final: 0.8661 (tp30) REVERT: B 668 ASN cc_start: 0.8796 (t0) cc_final: 0.8336 (t0) REVERT: B 676 SER cc_start: 0.9078 (m) cc_final: 0.8534 (p) REVERT: B 685 SER cc_start: 0.8905 (m) cc_final: 0.8519 (p) REVERT: C 572 ASN cc_start: 0.9211 (t0) cc_final: 0.8837 (t0) REVERT: C 575 ASN cc_start: 0.8427 (m-40) cc_final: 0.8188 (m110) REVERT: C 578 ASP cc_start: 0.8321 (m-30) cc_final: 0.8104 (m-30) REVERT: C 626 SER cc_start: 0.9091 (m) cc_final: 0.8624 (p) REVERT: C 634 ASP cc_start: 0.8893 (t0) cc_final: 0.8666 (t0) REVERT: C 676 SER cc_start: 0.9017 (m) cc_final: 0.8528 (p) REVERT: C 685 SER cc_start: 0.9110 (m) cc_final: 0.8692 (p) REVERT: D 560 LYS cc_start: 0.8460 (tttt) cc_final: 0.8100 (pttt) REVERT: D 572 ASN cc_start: 0.9237 (t0) cc_final: 0.8816 (t0) REVERT: D 612 SER cc_start: 0.9523 (p) cc_final: 0.9242 (m) REVERT: D 622 ARG cc_start: 0.8706 (mmp80) cc_final: 0.8462 (mmt-90) REVERT: D 626 SER cc_start: 0.9105 (m) cc_final: 0.8700 (p) REVERT: D 652 GLU cc_start: 0.8829 (tt0) cc_final: 0.8171 (tt0) REVERT: D 658 GLU cc_start: 0.9111 (tp30) cc_final: 0.8901 (tp30) REVERT: D 660 ARG cc_start: 0.8768 (tpm170) cc_final: 0.8521 (tpm170) REVERT: D 668 ASN cc_start: 0.8828 (t0) cc_final: 0.8481 (t0) REVERT: D 676 SER cc_start: 0.9149 (m) cc_final: 0.8705 (p) REVERT: D 693 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: E 560 LYS cc_start: 0.8514 (tttt) cc_final: 0.8218 (pttt) REVERT: E 575 ASN cc_start: 0.8313 (m-40) cc_final: 0.7686 (m110) REVERT: E 578 ASP cc_start: 0.8281 (m-30) cc_final: 0.7694 (m-30) REVERT: E 612 SER cc_start: 0.9579 (p) cc_final: 0.9334 (m) REVERT: E 626 SER cc_start: 0.9116 (m) cc_final: 0.8381 (p) REVERT: E 648 ASP cc_start: 0.8972 (m-30) cc_final: 0.8602 (m-30) REVERT: E 652 GLU cc_start: 0.8836 (tt0) cc_final: 0.8485 (tt0) REVERT: E 655 GLU cc_start: 0.8953 (tp30) cc_final: 0.8708 (tp30) REVERT: E 660 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8281 (tpt170) REVERT: E 666 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8887 (tp30) REVERT: E 668 ASN cc_start: 0.8800 (t0) cc_final: 0.8188 (t0) REVERT: E 676 SER cc_start: 0.8982 (m) cc_final: 0.8526 (p) REVERT: E 685 SER cc_start: 0.9071 (m) cc_final: 0.8736 (p) REVERT: E 703 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8483 (mm110) REVERT: E 720 TYR cc_start: 0.7590 (m-10) cc_final: 0.7146 (m-10) REVERT: F 572 ASN cc_start: 0.9266 (t0) cc_final: 0.9039 (t0) REVERT: F 578 ASP cc_start: 0.8409 (m-30) cc_final: 0.8048 (m-30) REVERT: F 626 SER cc_start: 0.9140 (m) cc_final: 0.8692 (p) REVERT: F 652 GLU cc_start: 0.8943 (tt0) cc_final: 0.8397 (tt0) REVERT: F 658 GLU cc_start: 0.9120 (tp30) cc_final: 0.8807 (tp30) REVERT: F 660 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8568 (tpm170) REVERT: F 668 ASN cc_start: 0.8739 (t0) cc_final: 0.8457 (t0) REVERT: F 676 SER cc_start: 0.9061 (m) cc_final: 0.8503 (p) REVERT: G 572 ASN cc_start: 0.9200 (t0) cc_final: 0.8873 (t0) REVERT: G 575 ASN cc_start: 0.8415 (m-40) cc_final: 0.8034 (m-40) REVERT: G 578 ASP cc_start: 0.8396 (m-30) cc_final: 0.8034 (m-30) REVERT: G 590 GLU cc_start: 0.8747 (tt0) cc_final: 0.8450 (mt-10) REVERT: G 601 GLN cc_start: 0.8890 (tt0) cc_final: 0.8680 (tt0) REVERT: G 612 SER cc_start: 0.9534 (p) cc_final: 0.9130 (m) REVERT: G 622 ARG cc_start: 0.8702 (mmp80) cc_final: 0.8174 (mmt90) REVERT: G 626 SER cc_start: 0.9211 (m) cc_final: 0.8565 (p) REVERT: G 652 GLU cc_start: 0.8865 (tt0) cc_final: 0.8596 (tt0) REVERT: G 655 GLU cc_start: 0.8972 (tp30) cc_final: 0.8681 (tp30) REVERT: G 668 ASN cc_start: 0.8940 (t0) cc_final: 0.8383 (t0) REVERT: G 676 SER cc_start: 0.9068 (m) cc_final: 0.8628 (p) REVERT: G 685 SER cc_start: 0.9020 (m) cc_final: 0.8613 (p) REVERT: G 693 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: G 714 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8364 (mtm-85) outliers start: 46 outliers final: 25 residues processed: 447 average time/residue: 1.0965 time to fit residues: 531.7695 Evaluate side-chains 436 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 409 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 PHE 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 688 THR 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 570 PHE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain E residue 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 E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain G residue 570 PHE Chi-restraints excluded: chain G residue 586 THR Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 THR Chi-restraints excluded: chain G residue 693 GLN Chi-restraints excluded: chain G residue 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 556 GLN G 630 ASN G 703 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3588 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= 0.184 Angle : 0.637 8.553 15883 Z= 0.323 Chirality : 0.043 0.184 1967 Planarity : 0.003 0.030 2030 Dihedral : 3.632 12.919 1631 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.89 % Allowed : 29.68 % Favored : 67.43 % 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: 2.49 (0.23), residues: 1435 helix: 3.05 (0.19), residues: 637 sheet: 0.67 (0.32), residues: 259 loop : 0.49 (0.30), residues: 539 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 0.011 0.001 PHE A 567 TYR 0.010 0.001 TYR G 631 ARG 0.007 0.001 ARG D 697 *********************** 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 458 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 424 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8263 (pttt) REVERT: A 574 MET cc_start: 0.9339 (mtp) cc_final: 0.9039 (mtt) REVERT: A 575 ASN cc_start: 0.8327 (m-40) cc_final: 0.8006 (m110) REVERT: A 578 ASP cc_start: 0.8352 (m-30) cc_final: 0.7994 (m-30) REVERT: A 652 GLU cc_start: 0.8948 (tt0) cc_final: 0.8696 (tt0) REVERT: A 655 GLU cc_start: 0.8953 (tp30) cc_final: 0.8727 (tp30) REVERT: A 660 ARG cc_start: 0.8795 (tpt90) cc_final: 0.8502 (tpt170) REVERT: A 668 ASN cc_start: 0.8813 (t0) cc_final: 0.8190 (t0) REVERT: A 676 SER cc_start: 0.8858 (m) cc_final: 0.8360 (p) REVERT: A 685 SER cc_start: 0.8961 (m) cc_final: 0.8452 (p) REVERT: B 560 LYS cc_start: 0.8527 (tttt) cc_final: 0.8159 (pttt) REVERT: B 578 ASP cc_start: 0.8402 (m-30) cc_final: 0.8017 (m-30) REVERT: B 626 SER cc_start: 0.9148 (m) cc_final: 0.8664 (p) REVERT: B 634 ASP cc_start: 0.8671 (t0) cc_final: 0.8455 (t0) REVERT: B 641 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8661 (ttpp) REVERT: B 652 GLU cc_start: 0.9031 (tt0) cc_final: 0.8594 (tt0) REVERT: B 655 GLU cc_start: 0.9008 (tp30) cc_final: 0.8578 (tp30) REVERT: B 668 ASN cc_start: 0.8814 (t0) cc_final: 0.8361 (t0) REVERT: B 676 SER cc_start: 0.9074 (m) cc_final: 0.8529 (p) REVERT: B 685 SER cc_start: 0.8906 (m) cc_final: 0.8513 (p) REVERT: C 572 ASN cc_start: 0.9215 (t0) cc_final: 0.8885 (t0) REVERT: C 575 ASN cc_start: 0.8382 (m-40) cc_final: 0.8127 (m110) REVERT: C 578 ASP cc_start: 0.8329 (m-30) cc_final: 0.8095 (m-30) REVERT: C 596 SER cc_start: 0.9390 (p) cc_final: 0.9049 (t) REVERT: C 626 SER cc_start: 0.9171 (m) cc_final: 0.8604 (p) REVERT: C 634 ASP cc_start: 0.8837 (t0) cc_final: 0.8614 (t0) REVERT: C 658 GLU cc_start: 0.8276 (mp0) cc_final: 0.8029 (mp0) REVERT: C 668 ASN cc_start: 0.8590 (t0) cc_final: 0.7859 (t0) REVERT: C 676 SER cc_start: 0.8911 (m) cc_final: 0.8443 (p) REVERT: C 685 SER cc_start: 0.9110 (m) cc_final: 0.8676 (p) REVERT: D 560 LYS cc_start: 0.8444 (tttt) cc_final: 0.8100 (pttt) REVERT: D 572 ASN cc_start: 0.9274 (t0) cc_final: 0.8844 (t0) REVERT: D 612 SER cc_start: 0.9516 (p) cc_final: 0.9226 (m) REVERT: D 622 ARG cc_start: 0.8668 (mmp80) cc_final: 0.8403 (mmt-90) REVERT: D 626 SER cc_start: 0.9083 (m) cc_final: 0.8666 (p) REVERT: D 652 GLU cc_start: 0.8813 (tt0) cc_final: 0.8166 (tt0) REVERT: D 658 GLU cc_start: 0.9071 (tp30) cc_final: 0.8865 (tp30) REVERT: D 668 ASN cc_start: 0.8821 (t0) cc_final: 0.8481 (t0) REVERT: D 676 SER cc_start: 0.9141 (m) cc_final: 0.8697 (p) REVERT: D 693 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: E 560 LYS cc_start: 0.8517 (tttt) cc_final: 0.8259 (pttt) REVERT: E 575 ASN cc_start: 0.8375 (m-40) cc_final: 0.7766 (m110) REVERT: E 578 ASP cc_start: 0.8239 (m-30) cc_final: 0.7673 (m-30) REVERT: E 612 SER cc_start: 0.9587 (p) cc_final: 0.9332 (m) REVERT: E 626 SER cc_start: 0.9085 (m) cc_final: 0.8358 (p) REVERT: E 652 GLU cc_start: 0.8829 (tt0) cc_final: 0.8491 (tt0) REVERT: E 655 GLU cc_start: 0.8988 (tp30) cc_final: 0.8744 (tp30) REVERT: E 660 ARG cc_start: 0.8719 (tpt90) cc_final: 0.8285 (tpt170) REVERT: E 666 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8911 (tp30) REVERT: E 668 ASN cc_start: 0.8799 (t0) cc_final: 0.8215 (t0) REVERT: E 676 SER cc_start: 0.8973 (m) cc_final: 0.8520 (p) REVERT: E 685 SER cc_start: 0.9064 (m) cc_final: 0.8729 (p) REVERT: E 703 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8490 (mm110) REVERT: E 720 TYR cc_start: 0.7588 (m-10) cc_final: 0.7155 (m-10) REVERT: F 572 ASN cc_start: 0.9233 (t0) cc_final: 0.8964 (t0) REVERT: F 575 ASN cc_start: 0.8194 (m-40) cc_final: 0.7902 (m110) REVERT: F 578 ASP cc_start: 0.8465 (m-30) cc_final: 0.8122 (m-30) REVERT: F 626 SER cc_start: 0.9140 (m) cc_final: 0.8688 (p) REVERT: F 658 GLU cc_start: 0.9029 (tp30) cc_final: 0.8820 (tp30) REVERT: F 668 ASN cc_start: 0.8749 (t0) cc_final: 0.8453 (t0) REVERT: F 676 SER cc_start: 0.9055 (m) cc_final: 0.8501 (p) REVERT: G 572 ASN cc_start: 0.9189 (t0) cc_final: 0.8829 (t0) REVERT: G 575 ASN cc_start: 0.8411 (m-40) cc_final: 0.8073 (m-40) REVERT: G 578 ASP cc_start: 0.8345 (m-30) cc_final: 0.7968 (m-30) REVERT: G 590 GLU cc_start: 0.8745 (tt0) cc_final: 0.8462 (mt-10) REVERT: G 612 SER cc_start: 0.9547 (p) cc_final: 0.9120 (m) REVERT: G 626 SER cc_start: 0.9193 (m) cc_final: 0.8532 (p) REVERT: G 652 GLU cc_start: 0.8946 (tt0) cc_final: 0.8574 (tt0) REVERT: G 655 GLU cc_start: 0.8933 (tp30) cc_final: 0.8707 (tp30) REVERT: G 658 GLU cc_start: 0.9212 (tp30) cc_final: 0.8933 (tp30) REVERT: G 660 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8283 (tpm170) REVERT: G 668 ASN cc_start: 0.8942 (t0) cc_final: 0.8387 (t0) REVERT: G 676 SER cc_start: 0.9053 (m) cc_final: 0.8615 (p) REVERT: G 685 SER cc_start: 0.9030 (m) cc_final: 0.8619 (p) REVERT: G 693 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: G 714 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8348 (mtm-85) outliers start: 34 outliers final: 26 residues processed: 438 average time/residue: 1.0999 time to fit residues: 523.2980 Evaluate side-chains 435 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 407 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 PHE 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 688 THR 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 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 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN E 572 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11669 Z= 0.205 Angle : 0.666 9.638 15883 Z= 0.334 Chirality : 0.043 0.202 1967 Planarity : 0.003 0.037 2030 Dihedral : 3.655 12.873 1631 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.06 % Allowed : 29.34 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.49 (0.23), residues: 1435 helix: 3.01 (0.19), residues: 637 sheet: 0.74 (0.32), residues: 259 loop : 0.52 (0.30), residues: 539 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 0.012 0.001 PHE A 567 TYR 0.010 0.001 TYR F 720 ARG 0.011 0.001 ARG F 660 *********************** 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 454 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 418 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 560 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8309 (pttt) REVERT: A 575 ASN cc_start: 0.8330 (m-40) cc_final: 0.7977 (m110) REVERT: A 578 ASP cc_start: 0.8360 (m-30) cc_final: 0.7990 (m-30) REVERT: A 652 GLU cc_start: 0.8944 (tt0) cc_final: 0.8681 (tt0) REVERT: A 655 GLU cc_start: 0.8956 (tp30) cc_final: 0.8755 (tp30) REVERT: A 660 ARG cc_start: 0.8799 (tpt90) cc_final: 0.8472 (tpt170) REVERT: A 668 ASN cc_start: 0.8800 (t0) cc_final: 0.8171 (t0) REVERT: A 676 SER cc_start: 0.8858 (m) cc_final: 0.8389 (p) REVERT: A 685 SER cc_start: 0.8947 (m) cc_final: 0.8438 (p) REVERT: B 560 LYS cc_start: 0.8540 (tttt) cc_final: 0.8173 (pttt) REVERT: B 578 ASP cc_start: 0.8388 (m-30) cc_final: 0.8005 (m-30) REVERT: B 626 SER cc_start: 0.9169 (m) cc_final: 0.8665 (p) REVERT: B 634 ASP cc_start: 0.8731 (t0) cc_final: 0.8526 (t0) REVERT: B 641 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8644 (ttpp) REVERT: B 652 GLU cc_start: 0.9030 (tt0) cc_final: 0.8541 (tt0) REVERT: B 655 GLU cc_start: 0.8967 (tp30) cc_final: 0.8621 (tp30) REVERT: B 668 ASN cc_start: 0.8815 (t0) cc_final: 0.8367 (t0) REVERT: B 676 SER cc_start: 0.9066 (m) cc_final: 0.8527 (p) REVERT: B 685 SER cc_start: 0.8923 (m) cc_final: 0.8512 (p) REVERT: C 572 ASN cc_start: 0.9216 (t0) cc_final: 0.8891 (t0) REVERT: C 575 ASN cc_start: 0.8372 (m-40) cc_final: 0.8137 (m110) REVERT: C 578 ASP cc_start: 0.8329 (m-30) cc_final: 0.8104 (m-30) REVERT: C 626 SER cc_start: 0.9212 (m) cc_final: 0.8650 (p) REVERT: C 634 ASP cc_start: 0.8885 (t0) cc_final: 0.8679 (t0) REVERT: C 668 ASN cc_start: 0.8580 (t0) cc_final: 0.8185 (t0) REVERT: C 676 SER cc_start: 0.8852 (m) cc_final: 0.8590 (t) REVERT: D 560 LYS cc_start: 0.8467 (tttt) cc_final: 0.8116 (pttt) REVERT: D 572 ASN cc_start: 0.9279 (t0) cc_final: 0.9017 (t0) REVERT: D 591 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8286 (ptm-80) REVERT: D 612 SER cc_start: 0.9507 (p) cc_final: 0.9227 (m) REVERT: D 626 SER cc_start: 0.9107 (m) cc_final: 0.8667 (p) REVERT: D 652 GLU cc_start: 0.8817 (tt0) cc_final: 0.8212 (tt0) REVERT: D 668 ASN cc_start: 0.8812 (t0) cc_final: 0.8483 (t0) REVERT: D 676 SER cc_start: 0.9135 (m) cc_final: 0.8690 (p) REVERT: D 693 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8168 (pm20) REVERT: E 560 LYS cc_start: 0.8557 (tttt) cc_final: 0.8304 (pttt) REVERT: E 575 ASN cc_start: 0.8372 (m-40) cc_final: 0.7536 (m-40) REVERT: E 578 ASP cc_start: 0.8269 (m-30) cc_final: 0.7698 (m-30) REVERT: E 590 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8402 (mt-10) REVERT: E 612 SER cc_start: 0.9603 (p) cc_final: 0.9326 (m) REVERT: E 626 SER cc_start: 0.9123 (m) cc_final: 0.8390 (p) REVERT: E 648 ASP cc_start: 0.8977 (m-30) cc_final: 0.8605 (m-30) REVERT: E 652 GLU cc_start: 0.8822 (tt0) cc_final: 0.8488 (tt0) REVERT: E 655 GLU cc_start: 0.8984 (tp30) cc_final: 0.8747 (tp30) REVERT: E 658 GLU cc_start: 0.9211 (tp30) cc_final: 0.8980 (tp30) REVERT: E 660 ARG cc_start: 0.8742 (tpt90) cc_final: 0.8304 (tpt170) REVERT: E 668 ASN cc_start: 0.8802 (t0) cc_final: 0.8127 (t0) REVERT: E 676 SER cc_start: 0.8969 (m) cc_final: 0.8518 (p) REVERT: E 685 SER cc_start: 0.9063 (m) cc_final: 0.8726 (p) REVERT: E 703 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8485 (mm110) REVERT: E 720 TYR cc_start: 0.7587 (m-10) cc_final: 0.7183 (m-10) REVERT: F 572 ASN cc_start: 0.9203 (t0) cc_final: 0.8970 (t0) REVERT: F 578 ASP cc_start: 0.8455 (m-30) cc_final: 0.8112 (m-30) REVERT: F 626 SER cc_start: 0.9163 (m) cc_final: 0.8718 (p) REVERT: F 668 ASN cc_start: 0.8750 (t0) cc_final: 0.8474 (t0) REVERT: F 676 SER cc_start: 0.9045 (m) cc_final: 0.8490 (p) REVERT: G 572 ASN cc_start: 0.9079 (t0) cc_final: 0.8852 (t0) REVERT: G 575 ASN cc_start: 0.8414 (m-40) cc_final: 0.8033 (m-40) REVERT: G 578 ASP cc_start: 0.8342 (m-30) cc_final: 0.7990 (m-30) REVERT: G 590 GLU cc_start: 0.8760 (tt0) cc_final: 0.8482 (mt-10) REVERT: G 612 SER cc_start: 0.9531 (p) cc_final: 0.9068 (m) REVERT: G 626 SER cc_start: 0.9223 (m) cc_final: 0.8592 (p) REVERT: G 652 GLU cc_start: 0.8880 (tt0) cc_final: 0.8571 (tt0) REVERT: G 658 GLU cc_start: 0.9245 (tp30) cc_final: 0.9014 (tp30) REVERT: G 660 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8378 (tpt170) REVERT: G 668 ASN cc_start: 0.8951 (t0) cc_final: 0.8400 (t0) REVERT: G 676 SER cc_start: 0.9046 (m) cc_final: 0.8608 (p) REVERT: G 685 SER cc_start: 0.9006 (m) cc_final: 0.8606 (p) REVERT: G 693 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: G 714 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8340 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 436 average time/residue: 1.0923 time to fit residues: 517.3343 Evaluate side-chains 441 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 409 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain D residue 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 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR Chi-restraints excluded: chain G residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN E 572 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3707 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= 0.218 Angle : 0.689 12.271 15883 Z= 0.347 Chirality : 0.043 0.201 1967 Planarity : 0.004 0.031 2030 Dihedral : 3.709 14.784 1631 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.81 % Allowed : 30.61 % 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: 2.48 (0.23), residues: 1435 helix: 2.97 (0.19), residues: 637 sheet: 0.78 (0.32), residues: 259 loop : 0.51 (0.30), residues: 539 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 0.012 0.001 PHE A 567 TYR 0.011 0.001 TYR G 631 ARG 0.009 0.001 ARG F 660 ********************** 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 445 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 412 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 537 ILE cc_start: 0.8931 (pt) cc_final: 0.8708 (pt) REVERT: A 560 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8313 (pttt) REVERT: A 575 ASN cc_start: 0.8322 (m-40) cc_final: 0.7969 (m110) REVERT: A 578 ASP cc_start: 0.8418 (m-30) cc_final: 0.8009 (m-30) REVERT: A 652 GLU cc_start: 0.8934 (tt0) cc_final: 0.8731 (tt0) REVERT: A 660 ARG cc_start: 0.8827 (tpt90) cc_final: 0.8476 (tpm170) REVERT: A 668 ASN cc_start: 0.8789 (t0) cc_final: 0.8158 (t0) REVERT: A 676 SER cc_start: 0.8860 (m) cc_final: 0.8389 (p) REVERT: A 685 SER cc_start: 0.8946 (m) cc_final: 0.8439 (p) REVERT: B 578 ASP cc_start: 0.8385 (m-30) cc_final: 0.8005 (m-30) REVERT: B 626 SER cc_start: 0.9125 (m) cc_final: 0.8686 (p) REVERT: B 641 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8618 (ttpp) REVERT: B 652 GLU cc_start: 0.9029 (tt0) cc_final: 0.8516 (tt0) REVERT: B 655 GLU cc_start: 0.8984 (tp30) cc_final: 0.8687 (tp30) REVERT: B 668 ASN cc_start: 0.8843 (t0) cc_final: 0.8467 (t0) REVERT: B 676 SER cc_start: 0.9067 (m) cc_final: 0.8529 (p) REVERT: B 685 SER cc_start: 0.8985 (m) cc_final: 0.8727 (p) REVERT: C 575 ASN cc_start: 0.8365 (m-40) cc_final: 0.8132 (m110) REVERT: C 578 ASP cc_start: 0.8320 (m-30) cc_final: 0.8095 (m-30) REVERT: C 596 SER cc_start: 0.9394 (p) cc_final: 0.9029 (t) REVERT: C 626 SER cc_start: 0.9215 (m) cc_final: 0.8654 (p) REVERT: C 634 ASP cc_start: 0.8903 (t0) cc_final: 0.8699 (t0) REVERT: C 668 ASN cc_start: 0.8602 (t0) cc_final: 0.8173 (t0) REVERT: C 676 SER cc_start: 0.8839 (m) cc_final: 0.8585 (t) REVERT: D 560 LYS cc_start: 0.8476 (tttt) cc_final: 0.8122 (pttt) REVERT: D 572 ASN cc_start: 0.9285 (t0) cc_final: 0.8997 (t0) REVERT: D 591 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8282 (ptm-80) REVERT: D 612 SER cc_start: 0.9511 (p) cc_final: 0.9239 (m) REVERT: D 626 SER cc_start: 0.9104 (m) cc_final: 0.8683 (p) REVERT: D 652 GLU cc_start: 0.8841 (tt0) cc_final: 0.8227 (tt0) REVERT: D 668 ASN cc_start: 0.8819 (t0) cc_final: 0.8485 (t0) REVERT: D 676 SER cc_start: 0.9137 (m) cc_final: 0.8691 (p) REVERT: D 693 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: E 560 LYS cc_start: 0.8555 (tttt) cc_final: 0.8293 (pttt) REVERT: E 575 ASN cc_start: 0.8413 (m-40) cc_final: 0.7527 (m-40) REVERT: E 578 ASP cc_start: 0.8291 (m-30) cc_final: 0.7738 (m-30) REVERT: E 590 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8411 (mt-10) REVERT: E 612 SER cc_start: 0.9611 (p) cc_final: 0.9308 (m) REVERT: E 626 SER cc_start: 0.9117 (m) cc_final: 0.8415 (p) REVERT: E 648 ASP cc_start: 0.8979 (m-30) cc_final: 0.8606 (m-30) REVERT: E 652 GLU cc_start: 0.8824 (tt0) cc_final: 0.8455 (tt0) REVERT: E 655 GLU cc_start: 0.8984 (tp30) cc_final: 0.8748 (tp30) REVERT: E 658 GLU cc_start: 0.9229 (tp30) cc_final: 0.8990 (tp30) REVERT: E 660 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8306 (tpt170) REVERT: E 668 ASN cc_start: 0.8833 (t0) cc_final: 0.8183 (t0) REVERT: E 676 SER cc_start: 0.8966 (m) cc_final: 0.8515 (p) REVERT: E 685 SER cc_start: 0.9062 (m) cc_final: 0.8729 (p) REVERT: E 703 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8407 (mm110) REVERT: E 720 TYR cc_start: 0.7585 (m-10) cc_final: 0.7176 (m-10) REVERT: F 572 ASN cc_start: 0.9192 (t0) cc_final: 0.8937 (t0) REVERT: F 578 ASP cc_start: 0.8448 (m-30) cc_final: 0.8103 (m-30) REVERT: F 626 SER cc_start: 0.9175 (m) cc_final: 0.8724 (p) REVERT: F 668 ASN cc_start: 0.8759 (t0) cc_final: 0.8447 (t0) REVERT: F 676 SER cc_start: 0.9043 (m) cc_final: 0.8490 (p) REVERT: G 575 ASN cc_start: 0.8395 (m-40) cc_final: 0.8019 (m-40) REVERT: G 578 ASP cc_start: 0.8338 (m-30) cc_final: 0.7976 (m-30) REVERT: G 590 GLU cc_start: 0.8767 (tt0) cc_final: 0.8466 (mt-10) REVERT: G 612 SER cc_start: 0.9528 (p) cc_final: 0.9057 (m) REVERT: G 626 SER cc_start: 0.9242 (m) cc_final: 0.8606 (p) REVERT: G 652 GLU cc_start: 0.8886 (tt0) cc_final: 0.8579 (tt0) REVERT: G 658 GLU cc_start: 0.9236 (tp30) cc_final: 0.8935 (tp30) REVERT: G 660 ARG cc_start: 0.8858 (tpt90) cc_final: 0.8553 (tpt170) REVERT: G 668 ASN cc_start: 0.8956 (t0) cc_final: 0.8401 (t0) REVERT: G 676 SER cc_start: 0.9051 (m) cc_final: 0.8611 (p) REVERT: G 685 SER cc_start: 0.9005 (m) cc_final: 0.8607 (p) REVERT: G 693 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: G 714 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8317 (mtm-85) outliers start: 33 outliers final: 28 residues processed: 430 average time/residue: 1.0513 time to fit residues: 491.5072 Evaluate side-chains 437 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 407 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 688 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain 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 559 VAL Chi-restraints excluded: chain E residue 570 PHE Chi-restraints excluded: chain E residue 597 VAL Chi-restraints excluded: chain E residue 614 ILE Chi-restraints excluded: chain E residue 688 THR Chi-restraints excluded: chain E residue 693 GLN Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 688 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 107 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 ASN ** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 ASN E 572 ASN ** F 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.087435 restraints weight = 17630.837| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.82 r_work: 0.2743 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11669 Z= 0.277 Angle : 0.727 12.130 15883 Z= 0.370 Chirality : 0.044 0.208 1967 Planarity : 0.004 0.064 2030 Dihedral : 3.835 17.014 1631 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.89 % Allowed : 30.44 % Favored : 66.67 % 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: 2.41 (0.23), residues: 1435 helix: 2.87 (0.19), residues: 637 sheet: 0.80 (0.32), residues: 259 loop : 0.51 (0.30), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 611 HIS 0.003 0.001 HIS D 607 PHE 0.014 0.001 PHE D 567 TYR 0.013 0.001 TYR G 631 ARG 0.013 0.001 ARG F 660 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6825.81 seconds wall clock time: 127 minutes 14.31 seconds (7634.31 seconds total)