Starting phenix.real_space_refine on Sat Nov 16 18:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/11_2024/8k3q_36856.cif" } resolution = 2.6 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= -0.001 sd= 0.095 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 68 5.16 5 C 7444 2.51 5 N 1833 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11365 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5630 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 21, 'TRANS': 702} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B Time building chain proxies: 11.30, per 1000 atoms: 0.99 Number of scatterers: 11365 At special positions: 0 Unit cell: (134.62, 83.74, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 2 15.00 O 2018 8.00 N 1833 7.00 C 7444 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 62.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.099A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.968A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.619A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 3.836A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.550A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.712A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.927A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.104A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.622A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.555A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.662A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 861 through 892 removed outlier: 3.906A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 941 through 955 removed outlier: 3.557A pdb=" N TYR A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.715A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 removed outlier: 3.534A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1091 through 1125 removed outlier: 4.100A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.099A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.968A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.620A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.837A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.550A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.711A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.927A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.103A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.622A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.554A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.663A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 Processing helix chain 'B' and resid 861 through 892 removed outlier: 3.906A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 Processing helix chain 'B' and resid 936 through 941 Processing helix chain 'B' and resid 941 through 955 removed outlier: 3.557A pdb=" N TYR B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.714A pdb=" N VAL B1011 " --> pdb=" O LYS B1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B1012 " --> pdb=" O TYR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 removed outlier: 3.533A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 Processing helix chain 'B' and resid 1091 through 1125 removed outlier: 4.100A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.798A pdb=" N ARG A 376 " --> pdb=" O MET B 992 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 992 " --> pdb=" O ARG A 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.373A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 624 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS A 735 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 626 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS A 737 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS A 628 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 739 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU A 630 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 741 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 632 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 743 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.748A pdb=" N GLU A 527 " --> pdb=" O ILE B 982 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA6, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.637A pdb=" N MET A 992 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 376 " --> pdb=" O MET A 992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.373A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 624 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS B 735 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 626 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS B 737 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 628 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER B 739 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 630 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR B 741 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 632 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 743 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1947 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: 3.95 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1742 1.31 - 1.43: 3355 1.43 - 1.56: 6401 1.56 - 1.68: 28 1.68 - 1.80: 104 Bond restraints: 11630 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C31 POV B1301 " pdb=" O31 POV B1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 POV A1301 " pdb=" O21 POV A1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb="C312 POV B1301 " pdb="C313 POV B1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 11625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 15366 2.39 - 4.78: 355 4.78 - 7.17: 36 7.17 - 9.56: 6 9.56 - 11.95: 6 Bond angle restraints: 15769 Sorted by residual: angle pdb=" N ARG B 508 " pdb=" CA ARG B 508 " pdb=" C ARG B 508 " ideal model delta sigma weight residual 112.89 107.62 5.27 1.24e+00 6.50e-01 1.81e+01 angle pdb=" N ARG A 508 " pdb=" CA ARG A 508 " pdb=" C ARG A 508 " ideal model delta sigma weight residual 112.89 107.63 5.26 1.24e+00 6.50e-01 1.80e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.28 4.39 1.05e+00 9.07e-01 1.75e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.29 4.38 1.05e+00 9.07e-01 1.74e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.16 11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 15764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 6481 25.63 - 51.25: 248 51.25 - 76.88: 58 76.88 - 102.51: 6 102.51 - 128.13: 2 Dihedral angle restraints: 6795 sinusoidal: 2529 harmonic: 4266 Sorted by residual: dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual -180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA B 715 " pdb=" C ALA B 715 " pdb=" N GLU B 716 " pdb=" CA GLU B 716 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TYR B 827 " pdb=" C TYR B 827 " pdb=" N HIS B 828 " pdb=" CA HIS B 828 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1155 0.044 - 0.089: 493 0.089 - 0.133: 114 0.133 - 0.177: 24 0.177 - 0.222: 6 Chirality restraints: 1792 Sorted by residual: chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL B 435 " pdb=" N VAL B 435 " pdb=" C VAL B 435 " pdb=" CB VAL B 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C2 POV B1301 " pdb=" C1 POV B1301 " pdb=" C3 POV B1301 " pdb=" O21 POV B1301 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1789 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS B 504 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS B 504 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE B 505 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 504 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS A 504 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 504 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 505 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1015 " -0.025 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B1015 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1015 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B1015 " -0.009 2.00e-02 2.50e+03 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 2 2.18 - 2.86: 4003 2.86 - 3.54: 15476 3.54 - 4.22: 26036 4.22 - 4.90: 46789 Nonbonded interactions: 92306 Sorted by model distance: nonbonded pdb=" CB HIS B 706 " pdb=" CG HIS B 706 " model vdw 1.495 3.660 nonbonded pdb=" CB LYS B1007 " pdb=" CG LYS B1007 " model vdw 1.521 3.840 nonbonded pdb=" NH1 ARG B 817 " pdb=" O13 POV B1301 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG A 817 " pdb=" O13 POV A1301 " model vdw 2.259 3.120 nonbonded pdb=" OG1 THR A 394 " pdb=" NE2 GLN B1002 " model vdw 2.273 3.120 ... (remaining 92301 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' and (resid 245 through 705 or (resid 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 1006 or (resid 1007 and (name \ N or name CA or name C or name O or name CB )) or resid 1008 through 1125 or res \ id 1301)) } 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: 1.360 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.430 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.008 0.110 11630 Z= 0.514 Angle : 0.869 11.949 15769 Z= 0.483 Chirality : 0.051 0.222 1792 Planarity : 0.005 0.057 1945 Dihedral : 14.726 128.132 4039 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.89 % Allowed : 0.51 % Favored : 97.60 % 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: 0.38 (0.22), residues: 1420 helix: 1.35 (0.19), residues: 752 sheet: -0.21 (0.39), residues: 166 loop : -1.27 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B1103 HIS 0.005 0.002 HIS B 459 PHE 0.047 0.003 PHE B1015 TYR 0.036 0.003 TYR B 249 ARG 0.007 0.001 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.186 Fit side-chains REVERT: A 656 MET cc_start: 0.8932 (mmt) cc_final: 0.8521 (mmt) REVERT: A 689 GLN cc_start: 0.8016 (tp40) cc_final: 0.7347 (mt0) REVERT: A 859 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7682 (mppt) REVERT: A 1108 SER cc_start: 0.8412 (t) cc_final: 0.8189 (m) REVERT: B 388 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (t0) REVERT: B 594 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7653 (mmp-170) REVERT: B 656 MET cc_start: 0.8861 (mmt) cc_final: 0.8394 (mmt) REVERT: B 689 GLN cc_start: 0.7923 (tp40) cc_final: 0.7338 (mt0) REVERT: B 859 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7522 (mppt) REVERT: B 875 MET cc_start: 0.8570 (ttm) cc_final: 0.8322 (mtp) outliers start: 22 outliers final: 2 residues processed: 177 average time/residue: 1.5046 time to fit residues: 286.6952 Evaluate side-chains 131 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 817 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 426 ASN A 545 ASN A 560 GLN A 650 GLN A 856 ASN A1013 ASN B 419 GLN B 426 ASN B 545 ASN B 548 ASN B 560 GLN B 650 GLN B1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11630 Z= 0.267 Angle : 0.558 5.735 15769 Z= 0.304 Chirality : 0.043 0.174 1792 Planarity : 0.005 0.054 1945 Dihedral : 10.014 115.555 1643 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.46 % Allowed : 8.40 % Favored : 90.14 % 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: 1.14 (0.22), residues: 1420 helix: 2.04 (0.18), residues: 766 sheet: -0.14 (0.38), residues: 156 loop : -1.02 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1103 HIS 0.005 0.002 HIS A 828 PHE 0.015 0.002 PHE A 708 TYR 0.017 0.002 TYR A1008 ARG 0.005 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.278 Fit side-chains REVERT: A 471 ASP cc_start: 0.6567 (m-30) cc_final: 0.6326 (m-30) REVERT: A 689 GLN cc_start: 0.7991 (tp40) cc_final: 0.7327 (mt0) REVERT: A 749 ARG cc_start: 0.7749 (mtp180) cc_final: 0.7484 (mmm-85) REVERT: A 859 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7681 (mppt) REVERT: A 1108 SER cc_start: 0.8342 (t) cc_final: 0.8112 (m) REVERT: B 471 ASP cc_start: 0.6533 (m-30) cc_final: 0.6240 (m-30) REVERT: B 594 ARG cc_start: 0.7967 (mmt180) cc_final: 0.7767 (mmp-170) REVERT: B 689 GLN cc_start: 0.7917 (tp40) cc_final: 0.7296 (mt0) REVERT: B 859 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7671 (mppt) outliers start: 17 outliers final: 7 residues processed: 142 average time/residue: 1.2025 time to fit residues: 186.5706 Evaluate side-chains 134 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 560 GLN A 937 HIS A1013 ASN B 548 ASN B 560 GLN B 650 GLN B 937 HIS B1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11630 Z= 0.226 Angle : 0.507 5.282 15769 Z= 0.276 Chirality : 0.042 0.174 1792 Planarity : 0.004 0.046 1945 Dihedral : 8.781 98.691 1637 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.97 % Allowed : 10.46 % Favored : 87.56 % 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: 1.48 (0.22), residues: 1420 helix: 2.34 (0.18), residues: 776 sheet: 0.09 (0.38), residues: 156 loop : -0.99 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.004 0.001 HIS B 828 PHE 0.018 0.002 PHE A 911 TYR 0.013 0.002 TYR B 827 ARG 0.003 0.000 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.424 Fit side-chains REVERT: A 471 ASP cc_start: 0.6581 (m-30) cc_final: 0.6277 (m-30) REVERT: A 594 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7672 (mmp-170) REVERT: A 749 ARG cc_start: 0.7726 (mtp180) cc_final: 0.7439 (mmm-85) REVERT: A 859 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7845 (mppt) REVERT: A 875 MET cc_start: 0.8358 (mtp) cc_final: 0.8140 (ttm) REVERT: B 471 ASP cc_start: 0.6567 (m-30) cc_final: 0.6259 (m-30) REVERT: B 594 ARG cc_start: 0.7914 (mmt180) cc_final: 0.7689 (mmp-170) REVERT: B 706 HIS cc_start: 0.6507 (m-70) cc_final: 0.6151 (t-170) REVERT: B 859 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7806 (mppt) REVERT: B 875 MET cc_start: 0.8400 (mtp) cc_final: 0.8155 (ttm) outliers start: 23 outliers final: 9 residues processed: 146 average time/residue: 1.2534 time to fit residues: 200.7888 Evaluate side-chains 136 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11630 Z= 0.264 Angle : 0.525 5.476 15769 Z= 0.284 Chirality : 0.043 0.174 1792 Planarity : 0.004 0.045 1945 Dihedral : 8.317 96.846 1636 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.57 % Allowed : 10.46 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1420 helix: 2.28 (0.18), residues: 780 sheet: 0.02 (0.38), residues: 156 loop : -0.94 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.020 0.002 PHE B 911 TYR 0.014 0.002 TYR A 254 ARG 0.003 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 1.270 Fit side-chains REVERT: A 594 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7637 (mmp-170) REVERT: A 749 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7436 (mmm-85) REVERT: B 594 ARG cc_start: 0.7927 (mmt180) cc_final: 0.7677 (mmp-170) outliers start: 30 outliers final: 12 residues processed: 147 average time/residue: 1.2938 time to fit residues: 207.9121 Evaluate side-chains 141 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 650 GLN A1013 ASN B 560 GLN B 650 GLN B 706 HIS B 937 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11630 Z= 0.164 Angle : 0.459 4.986 15769 Z= 0.251 Chirality : 0.040 0.170 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.521 78.877 1636 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.80 % Allowed : 12.01 % Favored : 86.19 % 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: 1.79 (0.22), residues: 1420 helix: 2.62 (0.18), residues: 772 sheet: 0.16 (0.38), residues: 156 loop : -0.88 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.004 0.001 HIS A 828 PHE 0.017 0.001 PHE A 911 TYR 0.011 0.001 TYR B 827 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.518 Fit side-chains REVERT: A 471 ASP cc_start: 0.6500 (m-30) cc_final: 0.6252 (m-30) REVERT: A 594 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7601 (mmp-170) REVERT: A 749 ARG cc_start: 0.7677 (mtp180) cc_final: 0.7450 (mmm-85) REVERT: B 471 ASP cc_start: 0.6473 (m-30) cc_final: 0.6226 (m-30) REVERT: B 594 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7660 (mmp-170) outliers start: 21 outliers final: 11 residues processed: 148 average time/residue: 1.2353 time to fit residues: 199.6499 Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A1013 ASN B 560 GLN B 706 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11630 Z= 0.417 Angle : 0.615 7.315 15769 Z= 0.327 Chirality : 0.047 0.179 1792 Planarity : 0.005 0.046 1945 Dihedral : 8.550 100.408 1636 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.49 % Allowed : 11.92 % Favored : 85.59 % 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: 1.22 (0.22), residues: 1420 helix: 2.07 (0.17), residues: 780 sheet: -0.00 (0.39), residues: 156 loop : -1.03 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 806 HIS 0.009 0.002 HIS A 828 PHE 0.021 0.002 PHE A 911 TYR 0.015 0.002 TYR A 254 ARG 0.004 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.256 Fit side-chains REVERT: A 445 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7019 (pp20) REVERT: A 594 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7644 (mmp-170) REVERT: A 749 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7491 (mmm-85) REVERT: A 1108 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7903 (m) REVERT: B 445 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: B 1108 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7896 (m) outliers start: 29 outliers final: 12 residues processed: 154 average time/residue: 1.1878 time to fit residues: 199.5408 Evaluate side-chains 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 706 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11630 Z= 0.191 Angle : 0.478 5.179 15769 Z= 0.261 Chirality : 0.041 0.168 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.789 83.116 1636 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.57 % Allowed : 12.52 % Favored : 84.91 % 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: 1.62 (0.22), residues: 1420 helix: 2.46 (0.18), residues: 780 sheet: 0.11 (0.39), residues: 156 loop : -0.96 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 779 HIS 0.006 0.001 HIS B 828 PHE 0.019 0.001 PHE B 911 TYR 0.011 0.001 TYR B 952 ARG 0.003 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.207 Fit side-chains REVERT: A 594 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7582 (mmp-170) REVERT: A 749 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7410 (mmm-85) outliers start: 30 outliers final: 14 residues processed: 150 average time/residue: 1.1934 time to fit residues: 195.1596 Evaluate side-chains 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 11630 Z= 0.493 Angle : 0.656 7.178 15769 Z= 0.349 Chirality : 0.049 0.176 1792 Planarity : 0.005 0.049 1945 Dihedral : 8.690 102.057 1636 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.57 % Allowed : 12.86 % Favored : 84.56 % 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: 1.06 (0.22), residues: 1420 helix: 1.93 (0.17), residues: 782 sheet: -0.01 (0.39), residues: 156 loop : -1.12 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 806 HIS 0.010 0.002 HIS A 828 PHE 0.023 0.003 PHE B 911 TYR 0.016 0.002 TYR B 254 ARG 0.005 0.001 ARG A 817 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 594 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7578 (mmp80) REVERT: A 749 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7492 (mmm-85) REVERT: A 1108 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7895 (m) REVERT: B 1108 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.7896 (m) outliers start: 30 outliers final: 16 residues processed: 151 average time/residue: 1.1127 time to fit residues: 184.8868 Evaluate side-chains 150 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 937 HIS B 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11630 Z= 0.174 Angle : 0.478 5.123 15769 Z= 0.261 Chirality : 0.041 0.174 1792 Planarity : 0.004 0.045 1945 Dihedral : 7.880 81.833 1636 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.80 % Allowed : 13.81 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.22), residues: 1420 helix: 2.47 (0.18), residues: 780 sheet: 0.11 (0.40), residues: 156 loop : -0.95 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 779 HIS 0.006 0.001 HIS A 828 PHE 0.017 0.001 PHE B 911 TYR 0.011 0.001 TYR A 475 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.290 Fit side-chains REVERT: A 464 ARG cc_start: 0.7556 (mtm180) cc_final: 0.7300 (mtp-110) REVERT: A 594 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7572 (mmp-170) REVERT: A 749 ARG cc_start: 0.7724 (mtp180) cc_final: 0.7429 (mmm-85) outliers start: 21 outliers final: 10 residues processed: 141 average time/residue: 1.2557 time to fit residues: 192.8937 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 1007 LYS Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11630 Z= 0.323 Angle : 0.554 6.026 15769 Z= 0.298 Chirality : 0.044 0.175 1792 Planarity : 0.004 0.045 1945 Dihedral : 8.282 93.713 1636 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.89 % Allowed : 13.98 % Favored : 84.13 % 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: 1.48 (0.22), residues: 1420 helix: 2.31 (0.18), residues: 780 sheet: 0.05 (0.40), residues: 156 loop : -0.96 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 779 HIS 0.008 0.002 HIS A 828 PHE 0.019 0.002 PHE B 911 TYR 0.012 0.002 TYR A 254 ARG 0.003 0.001 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 464 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7374 (mtp-110) REVERT: A 594 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7641 (mmp-170) REVERT: A 749 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7475 (mmm-85) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 1.2001 time to fit residues: 189.9790 Evaluate side-chains 145 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 100 optimal weight: 0.0670 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN B 560 GLN B 937 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112346 restraints weight = 12728.121| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.75 r_work: 0.3153 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11630 Z= 0.122 Angle : 0.447 6.172 15769 Z= 0.243 Chirality : 0.039 0.171 1792 Planarity : 0.004 0.045 1945 Dihedral : 7.301 70.855 1636 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.86 % Allowed : 14.92 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1420 helix: 2.70 (0.18), residues: 776 sheet: 0.32 (0.40), residues: 156 loop : -0.86 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 779 HIS 0.005 0.001 HIS A 828 PHE 0.014 0.001 PHE B 911 TYR 0.010 0.001 TYR A 827 ARG 0.003 0.000 ARG A 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4058.47 seconds wall clock time: 77 minutes 15.16 seconds (4635.16 seconds total)