Starting phenix.real_space_refine on Sun Sep 13 04:44:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pqq_20451/09_2026/6pqq_20451.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 28 5.49 5 S 136 5.16 5 C 13200 2.51 5 N 3148 2.21 5 O 3504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20016 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4740 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 20, 'TRANS': 583} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 264 Unusual residues: {'6OU': 5, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 83 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: B, D, C Time building chain proxies: 5.64, per 1000 atoms: 0.28 Number of scatterers: 20016 At special positions: 0 Unit cell: (113.4, 113.4, 147.96, 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 136 16.00 P 28 15.00 O 3504 8.00 N 3148 7.00 C 13200 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: 1.59 Conformation dependent library (CDL) restraints added in 770.9 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 73.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.575A pdb=" N LEU A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS A 540 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 541' Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.644A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.670A pdb=" N LYS A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 796 removed outlier: 3.765A pdb=" N PHE A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.883A pdb=" N VAL A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 900 through 912 Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 969 Processing helix chain 'A' and resid 970 through 987 removed outlier: 3.552A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1012 No H-bonds generated for 'chain 'A' and resid 1012 through 1012' Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1040 through 1072 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 458 through 466 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 535 Processing helix chain 'B' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS B 540 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 541 " --> pdb=" O LEU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 537 through 541' Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.645A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 611 removed outlier: 3.669A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 740 removed outlier: 3.759A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 726 " --> pdb=" O ASN B 722 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 796 removed outlier: 3.765A pdb=" N PHE B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 820 removed outlier: 3.882A pdb=" N VAL B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 853 No H-bonds generated for 'chain 'B' and resid 851 through 853' Processing helix chain 'B' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 928 Processing helix chain 'B' and resid 933 through 948 Processing helix chain 'B' and resid 950 through 969 Processing helix chain 'B' and resid 970 through 987 removed outlier: 3.551A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1012 No H-bonds generated for 'chain 'B' and resid 1012 through 1012' Processing helix chain 'B' and resid 1016 through 1025 Processing helix chain 'B' and resid 1040 through 1072 Processing helix chain 'D' and resid 447 through 456 Processing helix chain 'D' and resid 458 through 466 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.623A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 535 Processing helix chain 'D' and resid 537 through 541 removed outlier: 3.709A pdb=" N CYS D 540 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 537 through 541' Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS D 570 " --> pdb=" O LEU D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.645A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 611 removed outlier: 3.670A pdb=" N LYS D 610 " --> pdb=" O ASP D 606 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.648A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 796 removed outlier: 3.765A pdb=" N PHE D 793 " --> pdb=" O ALA D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 820 removed outlier: 3.883A pdb=" N VAL D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 853 No H-bonds generated for 'chain 'D' and resid 851 through 853' Processing helix chain 'D' and resid 856 through 892 removed outlier: 3.730A pdb=" N ILE D 860 " --> pdb=" O CYS D 856 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 900 through 912 Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 928 Processing helix chain 'D' and resid 933 through 948 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'D' and resid 970 through 987 removed outlier: 3.552A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP D 999 " --> pdb=" O LEU D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1012 No H-bonds generated for 'chain 'D' and resid 1012 through 1012' Processing helix chain 'D' and resid 1016 through 1025 Processing helix chain 'D' and resid 1040 through 1072 Processing helix chain 'C' and resid 447 through 456 Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.622A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 516 through 525 Processing helix chain 'C' and resid 526 through 535 Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.708A pdb=" N CYS C 540 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 541 " --> pdb=" O LEU C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 541' Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.536A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.524A pdb=" N HIS C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.644A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.669A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 629 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.647A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 740 removed outlier: 3.760A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 796 removed outlier: 3.765A pdb=" N PHE C 793 " --> pdb=" O ALA C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 820 removed outlier: 3.882A pdb=" N VAL C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 850 removed outlier: 3.718A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 856 through 892 removed outlier: 3.729A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 900 through 912 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 928 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 969 Processing helix chain 'C' and resid 970 through 987 removed outlier: 3.553A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 removed outlier: 3.544A pdb=" N ASP C 999 " --> pdb=" O LEU C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1012 No H-bonds generated for 'chain 'C' and resid 1012 through 1012' Processing helix chain 'C' and resid 1016 through 1025 Processing helix chain 'C' and resid 1040 through 1072 Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'A' and resid 745 through 746 removed outlier: 4.022A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'B' and resid 745 through 746 removed outlier: 4.021A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'D' and resid 745 through 746 removed outlier: 4.022A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'C' and resid 745 through 746 removed outlier: 4.021A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3456 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: 3.38 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3012 1.30 - 1.43: 5112 1.43 - 1.56: 11738 1.56 - 1.69: 274 1.69 - 1.81: 268 Bond restraints: 20404 Sorted by residual: bond pdb=" O2 LBN D1202 " pdb=" P1 LBN D1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" O2 LBN B1202 " pdb=" P1 LBN B1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN A1202 " pdb=" P1 LBN A1202 " ideal model delta sigma weight residual 1.650 1.791 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" O2 LBN C1202 " pdb=" P1 LBN C1202 " ideal model delta sigma weight residual 1.650 1.790 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" O2 LBN B1201 " pdb=" P1 LBN B1201 " ideal model delta sigma weight residual 1.650 1.783 -0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 20399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 26430 2.96 - 5.92: 862 5.92 - 8.88: 108 8.88 - 11.84: 40 11.84 - 14.80: 32 Bond angle restraints: 27472 Sorted by residual: angle pdb=" N ILE A 611 " pdb=" CA ILE A 611 " pdb=" C ILE A 611 " ideal model delta sigma weight residual 108.12 122.55 -14.43 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE C 611 " pdb=" CA ILE C 611 " pdb=" C ILE C 611 " ideal model delta sigma weight residual 108.12 122.54 -14.42 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE B 611 " pdb=" CA ILE B 611 " pdb=" C ILE B 611 " ideal model delta sigma weight residual 108.12 122.53 -14.41 1.34e+00 5.57e-01 1.16e+02 angle pdb=" N ILE D 611 " pdb=" CA ILE D 611 " pdb=" C ILE D 611 " ideal model delta sigma weight residual 108.12 122.52 -14.40 1.34e+00 5.57e-01 1.15e+02 angle pdb=" C ILE D 611 " pdb=" CA ILE D 611 " pdb=" CB ILE D 611 " ideal model delta sigma weight residual 111.35 105.60 5.75 1.09e+00 8.42e-01 2.79e+01 ... (remaining 27467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 11828 34.26 - 68.52: 328 68.52 - 102.78: 28 102.78 - 137.04: 4 137.04 - 171.31: 20 Dihedral angle restraints: 12208 sinusoidal: 5088 harmonic: 7120 Sorted by residual: dihedral pdb=" C34 6OU C1207 " pdb=" C31 6OU C1207 " pdb=" C33 6OU C1207 " pdb=" O30 6OU C1207 " ideal model delta sinusoidal sigma weight residual 180.29 8.98 171.31 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C34 6OU A1207 " pdb=" C31 6OU A1207 " pdb=" C33 6OU A1207 " pdb=" O30 6OU A1207 " ideal model delta sinusoidal sigma weight residual 180.29 8.99 171.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C34 6OU D1207 " pdb=" C31 6OU D1207 " pdb=" C33 6OU D1207 " pdb=" O30 6OU D1207 " ideal model delta sinusoidal sigma weight residual 180.29 9.01 171.28 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3042 0.134 - 0.269: 70 0.269 - 0.403: 0 0.403 - 0.538: 8 0.538 - 0.672: 12 Chirality restraints: 3132 Sorted by residual: chirality pdb=" C20 6OU D1205 " pdb=" C19 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O30 6OU D1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU C1205 " pdb=" C19 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O30 6OU C1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C20 6OU A1205 " pdb=" C19 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O30 6OU A1205 " both_signs ideal model delta sigma weight residual False 2.35 3.02 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 3129 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 820 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 821 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 821 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 820 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO B 821 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 820 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 821 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " -0.038 5.00e-02 4.00e+02 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5760 2.83 - 3.35: 17625 3.35 - 3.87: 31401 3.87 - 4.38: 35950 4.38 - 4.90: 61651 Nonbonded interactions: 152387 Sorted by model distance: nonbonded pdb=" O ILE D 810 " pdb=" OG1 THR D 814 " model vdw 2.316 3.040 nonbonded pdb=" O ILE A 810 " pdb=" OG1 THR A 814 " model vdw 2.316 3.040 nonbonded pdb=" O ILE C 810 " pdb=" OG1 THR C 814 " model vdw 2.316 3.040 nonbonded pdb=" O ILE B 810 " pdb=" OG1 THR B 814 " model vdw 2.316 3.040 nonbonded pdb=" O MET B 744 " pdb=" NE1 TRP B 832 " model vdw 2.392 3.120 ... (remaining 152382 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } 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: 1.220 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.540 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.011 0.141 20404 Z= 0.517 Angle : 1.262 14.804 27472 Z= 0.561 Chirality : 0.070 0.672 3132 Planarity : 0.007 0.068 3304 Dihedral : 16.703 171.306 7576 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.14), residues: 2376 helix: -2.18 (0.09), residues: 1720 sheet: -0.88 (0.68), residues: 68 loop : -1.79 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 919 TYR 0.033 0.003 TYR C 842 PHE 0.019 0.002 PHE D 888 TRP 0.013 0.002 TRP D 832 HIS 0.010 0.002 HIS A 589 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.52 (20404) covalent geometry : angle 1.26156 / 0.56 (27472) hydrogen bonds : bond 0.13953 / 9.28 ( 1164) hydrogen bonds : angle 5.59426 / 3.91 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 487 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LEU cc_start: 0.9313 (mt) cc_final: 0.9078 (mp) REVERT: A 544 LEU cc_start: 0.9158 (mt) cc_final: 0.8816 (mm) REVERT: A 873 SER cc_start: 0.8434 (t) cc_final: 0.8176 (p) REVERT: A 986 LEU cc_start: 0.9074 (tt) cc_final: 0.8817 (tp) REVERT: A 992 LEU cc_start: 0.9160 (tt) cc_final: 0.8845 (tm) REVERT: B 580 GLN cc_start: 0.8506 (mp10) cc_final: 0.8119 (mp10) REVERT: B 717 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7893 (ttt90) REVERT: B 912 MET cc_start: 0.8371 (ttm) cc_final: 0.8169 (ttp) REVERT: B 1075 ILE cc_start: 0.8707 (mt) cc_final: 0.7406 (mm) REVERT: D 693 ASN cc_start: 0.8755 (m-40) cc_final: 0.8269 (t0) REVERT: D 783 PHE cc_start: 0.7805 (m-10) cc_final: 0.7510 (m-10) REVERT: D 981 GLU cc_start: 0.8049 (tp30) cc_final: 0.7848 (tp30) REVERT: D 992 LEU cc_start: 0.9092 (tt) cc_final: 0.8576 (tm) REVERT: D 1059 GLU cc_start: 0.8219 (tp30) cc_final: 0.7857 (tp30) REVERT: D 1075 ILE cc_start: 0.8795 (mt) cc_final: 0.8326 (mp) REVERT: C 475 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 634 MET cc_start: 0.8512 (tpt) cc_final: 0.7956 (tpt) REVERT: C 635 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7986 (tptp) REVERT: C 720 MET cc_start: 0.7594 (mmm) cc_final: 0.7229 (mmt) REVERT: C 854 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7761 (mp0) REVERT: C 873 SER cc_start: 0.7711 (t) cc_final: 0.7457 (p) REVERT: C 1042 MET cc_start: 0.7921 (ppp) cc_final: 0.7720 (pp-130) REVERT: C 1059 GLU cc_start: 0.8325 (tp30) cc_final: 0.7999 (tp30) outliers start: 4 outliers final: 1 residues processed: 491 average time/residue: 0.6721 time to fit residues: 369.9707 Evaluate side-chains 242 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain C residue 475 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 235 optimal weight: 30.0000 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A 460 ASN A 476 ASN A 512 HIS A 519 HIS A 644 HIS A 700 HIS A 805 ASN A 907 GLN A 983 HIS B 451 HIS B 476 ASN B 512 HIS B 519 HIS B 549 ASN B 644 HIS B 700 HIS B 805 ASN B 907 GLN B 983 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN D 512 HIS D 519 HIS D 644 HIS D 700 HIS D 805 ASN D 907 GLN D 983 HIS ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 460 ASN C 476 ASN C 512 HIS C 519 HIS C 644 HIS C 700 HIS C 747 ASN C 983 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090267 restraints weight = 32093.248| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.54 r_work: 0.3021 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20404 Z= 0.132 Angle : 0.587 8.109 27472 Z= 0.286 Chirality : 0.040 0.152 3132 Planarity : 0.005 0.063 3304 Dihedral : 18.967 179.384 3208 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.78 % Allowed : 14.53 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2376 helix: -0.15 (0.11), residues: 1740 sheet: -0.19 (0.74), residues: 68 loop : -1.20 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 975 TYR 0.011 0.001 TYR C 842 PHE 0.011 0.001 PHE B 823 TRP 0.013 0.001 TRP C 832 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20404) covalent geometry : angle 0.58728 / 0.29 (27472) hydrogen bonds : bond 0.04893 / 3.36 ( 1164) hydrogen bonds : angle 3.83683 / 2.69 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9191 (mt) cc_final: 0.8937 (mm) REVERT: A 634 MET cc_start: 0.8837 (tpt) cc_final: 0.8544 (tpp) REVERT: A 826 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8434 (pt) REVERT: A 877 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8024 (t80) REVERT: A 986 LEU cc_start: 0.9080 (tt) cc_final: 0.8825 (tp) REVERT: B 580 GLN cc_start: 0.8440 (mp10) cc_final: 0.8028 (mp10) REVERT: B 681 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: B 693 ASN cc_start: 0.9005 (m-40) cc_final: 0.8622 (t0) REVERT: B 717 ARG cc_start: 0.8634 (ttt180) cc_final: 0.8387 (ttt90) REVERT: B 826 ILE cc_start: 0.8646 (tp) cc_final: 0.8158 (pp) REVERT: B 877 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8098 (t80) REVERT: B 981 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 1075 ILE cc_start: 0.8795 (mt) cc_final: 0.8567 (mp) REVERT: D 634 MET cc_start: 0.8878 (tpt) cc_final: 0.8614 (tpp) REVERT: D 693 ASN cc_start: 0.8881 (m-40) cc_final: 0.8531 (t0) REVERT: D 783 PHE cc_start: 0.7784 (m-10) cc_final: 0.7519 (m-10) REVERT: D 852 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7651 (mpt-90) REVERT: D 877 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7750 (t80) REVERT: D 981 GLU cc_start: 0.8496 (tp30) cc_final: 0.8265 (tp30) REVERT: D 1047 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: D 1059 GLU cc_start: 0.8783 (tp30) cc_final: 0.8443 (tp30) REVERT: C 483 MET cc_start: 0.8753 (mtm) cc_final: 0.8201 (mtp) REVERT: C 635 LYS cc_start: 0.8374 (ttpt) cc_final: 0.8062 (tptp) REVERT: C 689 MET cc_start: 0.8849 (mtp) cc_final: 0.8528 (mtt) REVERT: C 808 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7545 (mp0) REVERT: C 854 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7900 (mp0) REVERT: C 872 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8124 (mtm-85) REVERT: C 873 SER cc_start: 0.8026 (t) cc_final: 0.7783 (p) REVERT: C 981 GLU cc_start: 0.8555 (tp30) cc_final: 0.8350 (tp30) REVERT: C 1042 MET cc_start: 0.8072 (ppp) cc_final: 0.7808 (pp-130) REVERT: C 1059 GLU cc_start: 0.8881 (tp30) cc_final: 0.8525 (tp30) outliers start: 56 outliers final: 17 residues processed: 290 average time/residue: 0.6199 time to fit residues: 203.7227 Evaluate side-chains 216 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 693 ASN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 873 SER Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1047 GLN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 855 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 109 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 ASN B 460 ASN B 570 HIS B 590 ASN B 747 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 460 ASN D 549 ASN D 570 HIS D 747 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 570 HIS C 590 ASN C 805 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086539 restraints weight = 32003.612| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.53 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20404 Z= 0.130 Angle : 0.561 8.380 27472 Z= 0.270 Chirality : 0.040 0.149 3132 Planarity : 0.004 0.061 3304 Dihedral : 17.116 178.708 3204 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.92 % Allowed : 13.84 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2376 helix: 0.84 (0.12), residues: 1748 sheet: 0.45 (0.77), residues: 68 loop : -0.95 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 975 TYR 0.013 0.001 TYR D 714 PHE 0.012 0.001 PHE D 888 TRP 0.012 0.001 TRP C 605 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (20404) covalent geometry : angle 0.56099 / 0.27 (27472) hydrogen bonds : bond 0.04706 / 3.23 ( 1164) hydrogen bonds : angle 3.56974 / 2.49 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 214 time to evaluate : 0.750 Fit side-chains REVERT: A 483 MET cc_start: 0.8853 (mtm) cc_final: 0.8519 (mtp) REVERT: A 544 LEU cc_start: 0.9196 (mt) cc_final: 0.8906 (mm) REVERT: A 634 MET cc_start: 0.8910 (tpt) cc_final: 0.8697 (tpt) REVERT: A 877 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (t80) REVERT: A 974 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8000 (tmtt) REVERT: A 986 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8773 (tp) REVERT: B 681 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: B 717 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8310 (ttt90) REVERT: B 826 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8057 (pp) REVERT: B 877 PHE cc_start: 0.8493 (m-80) cc_final: 0.8177 (t80) REVERT: B 881 LEU cc_start: 0.8948 (tt) cc_final: 0.8424 (tp) REVERT: D 483 MET cc_start: 0.9047 (mtp) cc_final: 0.8593 (mtp) REVERT: D 500 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8307 (tp) REVERT: D 516 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8280 (p) REVERT: D 634 MET cc_start: 0.8950 (tpt) cc_final: 0.8726 (tpp) REVERT: D 693 ASN cc_start: 0.9015 (m-40) cc_final: 0.8588 (t0) REVERT: D 783 PHE cc_start: 0.7702 (m-10) cc_final: 0.7474 (m-10) REVERT: D 852 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7553 (mtp180) REVERT: D 877 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7911 (t80) REVERT: D 912 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8942 (ttm) REVERT: D 941 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8597 (tp) REVERT: D 1059 GLU cc_start: 0.8809 (tp30) cc_final: 0.8449 (tp30) REVERT: C 483 MET cc_start: 0.8855 (mtm) cc_final: 0.8355 (mtp) REVERT: C 626 MET cc_start: 0.8462 (mtp) cc_final: 0.8124 (ttm) REVERT: C 634 MET cc_start: 0.8876 (tpt) cc_final: 0.8325 (tpt) REVERT: C 689 MET cc_start: 0.8779 (mtp) cc_final: 0.8423 (mtt) REVERT: C 873 SER cc_start: 0.8010 (t) cc_final: 0.7740 (p) REVERT: C 981 GLU cc_start: 0.8544 (tp30) cc_final: 0.8247 (tp30) REVERT: C 1042 MET cc_start: 0.7990 (ppp) cc_final: 0.7783 (ppp) REVERT: C 1059 GLU cc_start: 0.8832 (tp30) cc_final: 0.8433 (tp30) outliers start: 79 outliers final: 24 residues processed: 270 average time/residue: 0.5262 time to fit residues: 164.5220 Evaluate side-chains 223 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 877 PHE Chi-restraints excluded: chain D residue 912 MET Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085300 restraints weight = 31967.639| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.51 r_work: 0.2923 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20404 Z= 0.129 Angle : 0.555 8.084 27472 Z= 0.266 Chirality : 0.040 0.191 3132 Planarity : 0.004 0.059 3304 Dihedral : 16.127 176.546 3204 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.37 % Allowed : 15.23 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2376 helix: 1.26 (0.12), residues: 1752 sheet: 0.78 (0.78), residues: 68 loop : -0.81 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 996 TYR 0.010 0.001 TYR A 842 PHE 0.010 0.001 PHE C 823 TRP 0.010 0.001 TRP B 515 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (20404) covalent geometry : angle 0.55472 / 0.27 (27472) hydrogen bonds : bond 0.04603 / 3.16 ( 1164) hydrogen bonds : angle 3.52128 / 2.45 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 202 time to evaluate : 0.644 Fit side-chains REVERT: A 483 MET cc_start: 0.8915 (mtm) cc_final: 0.8590 (mtp) REVERT: A 544 LEU cc_start: 0.9197 (mt) cc_final: 0.8942 (mm) REVERT: A 873 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8509 (p) REVERT: A 877 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8263 (t80) REVERT: A 986 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (tp) REVERT: A 1059 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8099 (tm-30) REVERT: B 681 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: B 717 ARG cc_start: 0.8548 (ttt180) cc_final: 0.8332 (ttt90) REVERT: B 808 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 822 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (pt) REVERT: B 877 PHE cc_start: 0.8519 (m-80) cc_final: 0.8304 (t80) REVERT: B 881 LEU cc_start: 0.8947 (tt) cc_final: 0.8457 (tp) REVERT: D 483 MET cc_start: 0.9029 (mtp) cc_final: 0.8596 (mtp) REVERT: D 720 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7395 (mpt) REVERT: D 744 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: D 852 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7715 (mtp180) REVERT: D 941 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8689 (tp) REVERT: D 1059 GLU cc_start: 0.8833 (tp30) cc_final: 0.8434 (tp30) REVERT: C 483 MET cc_start: 0.8892 (mtm) cc_final: 0.8361 (mtp) REVERT: C 634 MET cc_start: 0.8910 (tpt) cc_final: 0.8448 (tpt) REVERT: C 720 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7924 (mmp) REVERT: C 744 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7549 (mmp) REVERT: C 873 SER cc_start: 0.8223 (t) cc_final: 0.7960 (p) REVERT: C 981 GLU cc_start: 0.8506 (tp30) cc_final: 0.8229 (tp30) REVERT: C 1059 GLU cc_start: 0.8830 (tp30) cc_final: 0.8427 (tp30) outliers start: 68 outliers final: 26 residues processed: 243 average time/residue: 0.5319 time to fit residues: 148.6412 Evaluate side-chains 216 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 606 ASP Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 2 optimal weight: 0.0970 chunk 6 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085018 restraints weight = 31736.609| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.50 r_work: 0.2919 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20404 Z= 0.128 Angle : 0.550 8.504 27472 Z= 0.262 Chirality : 0.040 0.198 3132 Planarity : 0.004 0.056 3304 Dihedral : 15.561 179.331 3204 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2376 helix: 1.47 (0.12), residues: 1752 sheet: 0.94 (0.78), residues: 68 loop : -0.75 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 996 TYR 0.010 0.001 TYR A 456 PHE 0.009 0.001 PHE D 818 TRP 0.008 0.001 TRP B 832 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20404) covalent geometry : angle 0.54996 / 0.26 (27472) hydrogen bonds : bond 0.04525 / 3.11 ( 1164) hydrogen bonds : angle 3.51147 / 2.44 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 193 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9198 (mt) cc_final: 0.8928 (mm) REVERT: A 826 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8379 (pt) REVERT: A 842 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: A 877 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 986 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8858 (tp) REVERT: A 1059 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8083 (tm-30) REVERT: B 464 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8027 (mtp180) REVERT: B 483 MET cc_start: 0.8785 (mtp) cc_final: 0.8153 (mmt) REVERT: B 681 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7447 (pp20) REVERT: B 717 ARG cc_start: 0.8538 (ttt180) cc_final: 0.8313 (ttt90) REVERT: B 720 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8409 (mmp) REVERT: B 822 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8272 (pt) REVERT: B 826 ILE cc_start: 0.8588 (tp) cc_final: 0.8134 (pp) REVERT: B 852 ARG cc_start: 0.8610 (mpt-90) cc_final: 0.7905 (mtp180) REVERT: B 877 PHE cc_start: 0.8517 (m-80) cc_final: 0.8304 (t80) REVERT: B 881 LEU cc_start: 0.8947 (tt) cc_final: 0.8478 (tp) REVERT: D 483 MET cc_start: 0.9039 (mtp) cc_final: 0.8636 (mtp) REVERT: D 500 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8225 (tm) REVERT: D 720 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7958 (mmm) REVERT: D 721 MET cc_start: 0.8228 (mmt) cc_final: 0.7933 (mtm) REVERT: D 744 MET cc_start: 0.8155 (mmp) cc_final: 0.7854 (mmm) REVERT: D 941 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8673 (tp) REVERT: D 1059 GLU cc_start: 0.8834 (tp30) cc_final: 0.8437 (tp30) REVERT: C 483 MET cc_start: 0.8867 (mtm) cc_final: 0.8400 (mtp) REVERT: C 720 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7942 (mmp) REVERT: C 873 SER cc_start: 0.8204 (t) cc_final: 0.7918 (p) REVERT: C 981 GLU cc_start: 0.8508 (tp30) cc_final: 0.8198 (tp30) REVERT: C 1059 GLU cc_start: 0.8793 (tp30) cc_final: 0.8368 (tp30) outliers start: 68 outliers final: 32 residues processed: 236 average time/residue: 0.5607 time to fit residues: 151.1242 Evaluate side-chains 223 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 216 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN A 619 ASN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086830 restraints weight = 32134.601| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.53 r_work: 0.2985 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20404 Z= 0.101 Angle : 0.523 8.741 27472 Z= 0.249 Chirality : 0.039 0.169 3132 Planarity : 0.004 0.054 3304 Dihedral : 15.001 173.036 3204 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.27 % Allowed : 15.92 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.18), residues: 2376 helix: 1.69 (0.12), residues: 1752 sheet: 1.12 (0.78), residues: 68 loop : -0.64 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 996 TYR 0.011 0.001 TYR D 842 PHE 0.008 0.001 PHE C 823 TRP 0.009 0.001 TRP A 809 HIS 0.004 0.000 HIS B 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20404) covalent geometry : angle 0.52321 / 0.25 (27472) hydrogen bonds : bond 0.03872 / 2.66 ( 1164) hydrogen bonds : angle 3.40626 / 2.37 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 530 MET cc_start: 0.8529 (mtp) cc_final: 0.8289 (mtp) REVERT: A 544 LEU cc_start: 0.9173 (mt) cc_final: 0.8912 (mm) REVERT: A 720 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8269 (mmp) REVERT: A 744 MET cc_start: 0.8005 (mmp) cc_final: 0.7568 (mtm) REVERT: A 826 ILE cc_start: 0.8754 (tp) cc_final: 0.8442 (pt) REVERT: A 873 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8480 (p) REVERT: A 877 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8176 (t80) REVERT: A 974 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7937 (tmtt) REVERT: A 986 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 1059 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8069 (tm-30) REVERT: B 464 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7936 (mtp180) REVERT: B 483 MET cc_start: 0.8708 (mtp) cc_final: 0.8143 (mmt) REVERT: B 681 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: B 717 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8357 (ttt90) REVERT: B 720 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8313 (mmp) REVERT: B 826 ILE cc_start: 0.8467 (tp) cc_final: 0.7968 (pp) REVERT: B 844 MET cc_start: 0.9347 (tpt) cc_final: 0.9133 (tpp) REVERT: B 852 ARG cc_start: 0.8613 (mpt-90) cc_final: 0.7897 (mtp180) REVERT: B 881 LEU cc_start: 0.8833 (tt) cc_final: 0.8361 (tp) REVERT: B 1073 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: D 483 MET cc_start: 0.9022 (mtp) cc_final: 0.8639 (mtp) REVERT: D 500 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8183 (tm) REVERT: D 720 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: D 721 MET cc_start: 0.8197 (mmt) cc_final: 0.7922 (mtm) REVERT: D 744 MET cc_start: 0.8040 (mmp) cc_final: 0.7780 (mmm) REVERT: D 941 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8643 (tp) REVERT: D 981 GLU cc_start: 0.8666 (tp30) cc_final: 0.8397 (tp30) REVERT: D 1059 GLU cc_start: 0.8841 (tp30) cc_final: 0.8438 (tp30) REVERT: C 483 MET cc_start: 0.8895 (mtm) cc_final: 0.8431 (mtp) REVERT: C 720 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7866 (mmp) REVERT: C 744 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7832 (mmm) REVERT: C 854 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7538 (mp0) REVERT: C 873 SER cc_start: 0.8104 (t) cc_final: 0.7796 (p) REVERT: C 981 GLU cc_start: 0.8488 (tp30) cc_final: 0.8183 (tp30) REVERT: C 1047 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6695 (mt0) REVERT: C 1059 GLU cc_start: 0.8844 (tp30) cc_final: 0.8411 (tp30) outliers start: 66 outliers final: 25 residues processed: 253 average time/residue: 0.5341 time to fit residues: 155.5755 Evaluate side-chains 229 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1073 GLU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 42 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 199 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.119623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085149 restraints weight = 32082.372| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.50 r_work: 0.2941 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20404 Z= 0.124 Angle : 0.549 9.595 27472 Z= 0.263 Chirality : 0.040 0.208 3132 Planarity : 0.004 0.054 3304 Dihedral : 14.642 171.914 3204 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.08 % Allowed : 16.52 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.18), residues: 2376 helix: 1.75 (0.13), residues: 1752 sheet: 1.20 (0.78), residues: 68 loop : -0.63 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 996 TYR 0.010 0.001 TYR C 456 PHE 0.017 0.001 PHE B 877 TRP 0.019 0.001 TRP B 809 HIS 0.005 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (20404) covalent geometry : angle 0.54893 / 0.26 (27472) hydrogen bonds : bond 0.04341 / 2.99 ( 1164) hydrogen bonds : angle 3.44358 / 2.39 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9192 (mt) cc_final: 0.8928 (mm) REVERT: A 720 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8281 (mmp) REVERT: A 744 MET cc_start: 0.7992 (mmp) cc_final: 0.7565 (mtm) REVERT: A 873 SER cc_start: 0.8832 (t) cc_final: 0.8564 (p) REVERT: A 877 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8148 (t80) REVERT: A 974 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7946 (tmtt) REVERT: A 986 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8806 (tp) REVERT: A 1059 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8058 (tm-30) REVERT: B 464 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7904 (mtp180) REVERT: B 483 MET cc_start: 0.8591 (mtp) cc_final: 0.7870 (mmt) REVERT: B 681 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: B 717 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8357 (ttt90) REVERT: B 720 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8342 (mmp) REVERT: B 826 ILE cc_start: 0.8478 (tp) cc_final: 0.7978 (pp) REVERT: B 844 MET cc_start: 0.9409 (tpt) cc_final: 0.9178 (tpp) REVERT: B 852 ARG cc_start: 0.8622 (mpt-90) cc_final: 0.7908 (mtp180) REVERT: B 881 LEU cc_start: 0.8850 (tt) cc_final: 0.8402 (tp) REVERT: B 987 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: D 483 MET cc_start: 0.9014 (mtp) cc_final: 0.8703 (mtp) REVERT: D 500 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8280 (tm) REVERT: D 720 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7895 (mmm) REVERT: D 721 MET cc_start: 0.8205 (mmt) cc_final: 0.7923 (mtm) REVERT: D 744 MET cc_start: 0.8026 (mmp) cc_final: 0.7782 (mmm) REVERT: D 941 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (tp) REVERT: D 981 GLU cc_start: 0.8688 (tp30) cc_final: 0.8414 (tp30) REVERT: D 1059 GLU cc_start: 0.8811 (tp30) cc_final: 0.8387 (tp30) REVERT: C 475 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7994 (tp) REVERT: C 483 MET cc_start: 0.8928 (mtm) cc_final: 0.8571 (mtp) REVERT: C 720 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7887 (mmp) REVERT: C 744 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: C 854 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7517 (mp0) REVERT: C 873 SER cc_start: 0.8224 (t) cc_final: 0.7927 (p) REVERT: C 981 GLU cc_start: 0.8484 (tp30) cc_final: 0.8153 (tp30) REVERT: C 1047 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: C 1059 GLU cc_start: 0.8806 (tp30) cc_final: 0.8364 (tp30) outliers start: 62 outliers final: 29 residues processed: 227 average time/residue: 0.5554 time to fit residues: 144.1564 Evaluate side-chains 226 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 61 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 149 optimal weight: 0.0570 chunk 208 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.085204 restraints weight = 32288.190| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.48 r_work: 0.2935 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20404 Z= 0.125 Angle : 0.549 9.605 27472 Z= 0.262 Chirality : 0.040 0.190 3132 Planarity : 0.004 0.052 3304 Dihedral : 14.275 171.724 3204 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.22 % Allowed : 16.42 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.18), residues: 2376 helix: 1.80 (0.12), residues: 1752 sheet: 1.21 (0.77), residues: 68 loop : -0.57 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 872 TYR 0.017 0.001 TYR B 842 PHE 0.011 0.001 PHE B 877 TRP 0.010 0.001 TRP C 515 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (20404) covalent geometry : angle 0.54911 / 0.26 (27472) hydrogen bonds : bond 0.04368 / 3.00 ( 1164) hydrogen bonds : angle 3.45840 / 2.40 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.751 Fit side-chains REVERT: A 544 LEU cc_start: 0.9199 (mt) cc_final: 0.8939 (mm) REVERT: A 720 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (mmp) REVERT: A 744 MET cc_start: 0.7998 (mmp) cc_final: 0.7640 (mtm) REVERT: A 826 ILE cc_start: 0.8710 (tp) cc_final: 0.8382 (pt) REVERT: A 873 SER cc_start: 0.8834 (t) cc_final: 0.8573 (p) REVERT: A 877 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 974 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7962 (tmtt) REVERT: A 986 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8833 (tp) REVERT: A 1059 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8051 (tm-30) REVERT: B 464 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7850 (mtp180) REVERT: B 483 MET cc_start: 0.8517 (mtp) cc_final: 0.7838 (mmt) REVERT: B 681 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: B 717 ARG cc_start: 0.8603 (ttt180) cc_final: 0.8389 (ttm-80) REVERT: B 720 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8345 (mmp) REVERT: B 826 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 844 MET cc_start: 0.9409 (tpt) cc_final: 0.9171 (tpp) REVERT: B 852 ARG cc_start: 0.8625 (mpt-90) cc_final: 0.7921 (mtp180) REVERT: B 881 LEU cc_start: 0.8880 (tt) cc_final: 0.8447 (tp) REVERT: B 987 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: D 483 MET cc_start: 0.9066 (mtp) cc_final: 0.8553 (mtp) REVERT: D 500 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8256 (tm) REVERT: D 744 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7748 (mmm) REVERT: D 852 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7809 (mtp85) REVERT: D 941 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8643 (tp) REVERT: D 981 GLU cc_start: 0.8677 (tp30) cc_final: 0.8419 (tp30) REVERT: D 1059 GLU cc_start: 0.8824 (tp30) cc_final: 0.8387 (tp30) REVERT: C 475 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7999 (tp) REVERT: C 483 MET cc_start: 0.8956 (mtm) cc_final: 0.8474 (mtp) REVERT: C 720 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7958 (mmp) REVERT: C 744 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: C 854 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7498 (mp0) REVERT: C 873 SER cc_start: 0.8241 (t) cc_final: 0.7948 (p) REVERT: C 981 GLU cc_start: 0.8504 (tp30) cc_final: 0.8172 (tp30) REVERT: C 1047 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: C 1059 GLU cc_start: 0.8852 (tp30) cc_final: 0.8397 (tp30) outliers start: 65 outliers final: 29 residues processed: 223 average time/residue: 0.5605 time to fit residues: 142.8413 Evaluate side-chains 229 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 96 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 209 optimal weight: 0.1980 chunk 204 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085841 restraints weight = 31962.958| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.53 r_work: 0.2945 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20404 Z= 0.108 Angle : 0.536 10.019 27472 Z= 0.256 Chirality : 0.039 0.188 3132 Planarity : 0.004 0.052 3304 Dihedral : 13.892 172.544 3204 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.08 % Allowed : 16.91 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.18), residues: 2376 helix: 1.88 (0.13), residues: 1752 sheet: 1.32 (0.78), residues: 68 loop : -0.54 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 996 TYR 0.016 0.001 TYR B 842 PHE 0.012 0.001 PHE B 877 TRP 0.011 0.001 TRP B 809 HIS 0.003 0.001 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (20404) covalent geometry : angle 0.53557 / 0.26 (27472) hydrogen bonds : bond 0.03990 / 2.74 ( 1164) hydrogen bonds : angle 3.39964 / 2.36 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 0.729 Fit side-chains REVERT: A 544 LEU cc_start: 0.9189 (mt) cc_final: 0.8930 (mm) REVERT: A 720 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8295 (mmp) REVERT: A 744 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7631 (mtm) REVERT: A 826 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (pt) REVERT: A 873 SER cc_start: 0.8792 (t) cc_final: 0.8527 (p) REVERT: A 877 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 974 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7977 (tmtt) REVERT: A 986 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8805 (tp) REVERT: A 1059 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8061 (tm-30) REVERT: B 464 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: B 483 MET cc_start: 0.8435 (mtp) cc_final: 0.7782 (mmt) REVERT: B 681 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: B 717 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8396 (ttm-80) REVERT: B 720 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8368 (mmp) REVERT: B 826 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.7951 (pp) REVERT: B 844 MET cc_start: 0.9384 (tpt) cc_final: 0.9159 (tpp) REVERT: B 852 ARG cc_start: 0.8628 (mpt-90) cc_final: 0.7938 (mtp180) REVERT: B 877 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 881 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8410 (tp) REVERT: B 987 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: D 483 MET cc_start: 0.9045 (mtp) cc_final: 0.8501 (mtp) REVERT: D 500 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8277 (tm) REVERT: D 530 MET cc_start: 0.8421 (mtp) cc_final: 0.8117 (mtt) REVERT: D 720 MET cc_start: 0.8016 (mmm) cc_final: 0.7765 (mmp) REVERT: D 744 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7733 (mmm) REVERT: D 852 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7830 (mtp85) REVERT: D 941 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8640 (tp) REVERT: D 981 GLU cc_start: 0.8665 (tp30) cc_final: 0.8448 (tp30) REVERT: D 1059 GLU cc_start: 0.8829 (tp30) cc_final: 0.8405 (tp30) REVERT: C 475 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8082 (tp) REVERT: C 483 MET cc_start: 0.8941 (mtm) cc_final: 0.8464 (mtp) REVERT: C 720 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7933 (mmp) REVERT: C 744 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7822 (mmm) REVERT: C 785 TYR cc_start: 0.7586 (m-10) cc_final: 0.7379 (m-10) REVERT: C 854 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7481 (mp0) REVERT: C 873 SER cc_start: 0.8173 (t) cc_final: 0.7874 (p) REVERT: C 981 GLU cc_start: 0.8470 (tp30) cc_final: 0.8139 (tp30) REVERT: C 1047 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: C 1059 GLU cc_start: 0.8868 (tp30) cc_final: 0.8414 (tp30) outliers start: 62 outliers final: 30 residues processed: 232 average time/residue: 0.5644 time to fit residues: 150.0410 Evaluate side-chains 235 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain C residue 642 MET Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 217 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086369 restraints weight = 32175.351| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.58 r_work: 0.2955 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20404 Z= 0.114 Angle : 0.553 10.938 27472 Z= 0.265 Chirality : 0.039 0.177 3132 Planarity : 0.004 0.052 3304 Dihedral : 13.535 172.574 3204 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.73 % Allowed : 17.41 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.18), residues: 2376 helix: 1.92 (0.13), residues: 1752 sheet: 1.38 (0.79), residues: 68 loop : -0.52 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 872 TYR 0.015 0.001 TYR B 842 PHE 0.011 0.001 PHE B 877 TRP 0.010 0.001 TRP B 809 HIS 0.003 0.001 HIS D 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (20404) covalent geometry : angle 0.55339 / 0.26 (27472) hydrogen bonds : bond 0.04065 / 2.79 ( 1164) hydrogen bonds : angle 3.38983 / 2.35 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 0.812 Fit side-chains REVERT: A 544 LEU cc_start: 0.9185 (mt) cc_final: 0.8929 (mm) REVERT: A 720 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8298 (mmp) REVERT: A 744 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7621 (mtm) REVERT: A 826 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8378 (pt) REVERT: A 873 SER cc_start: 0.8803 (t) cc_final: 0.8539 (p) REVERT: A 877 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8173 (t80) REVERT: A 974 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7958 (tmtt) REVERT: A 986 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8823 (tp) REVERT: A 1059 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8045 (tm-30) REVERT: B 464 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (mtp180) REVERT: B 483 MET cc_start: 0.8402 (mtp) cc_final: 0.7762 (mmt) REVERT: B 681 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7343 (pp20) REVERT: B 717 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8404 (ttm-80) REVERT: B 720 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8372 (mmp) REVERT: B 826 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 844 MET cc_start: 0.9397 (tpt) cc_final: 0.9169 (tpp) REVERT: B 852 ARG cc_start: 0.8637 (mpt-90) cc_final: 0.7940 (mtp180) REVERT: B 877 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7952 (t80) REVERT: B 881 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8378 (tp) REVERT: B 987 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8556 (mt-10) REVERT: D 483 MET cc_start: 0.9069 (mtp) cc_final: 0.8527 (mtp) REVERT: D 500 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8279 (tm) REVERT: D 530 MET cc_start: 0.8460 (mtp) cc_final: 0.8127 (mtt) REVERT: D 720 MET cc_start: 0.8032 (mmm) cc_final: 0.7766 (mmp) REVERT: D 852 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7839 (mtp85) REVERT: D 941 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8638 (tp) REVERT: D 981 GLU cc_start: 0.8651 (tp30) cc_final: 0.8423 (tp30) REVERT: D 1059 GLU cc_start: 0.8834 (tp30) cc_final: 0.8412 (tp30) REVERT: C 475 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8099 (tp) REVERT: C 483 MET cc_start: 0.8947 (mtm) cc_final: 0.8472 (mtp) REVERT: C 720 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7916 (mmp) REVERT: C 744 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7837 (mmm) REVERT: C 854 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7477 (mp0) REVERT: C 873 SER cc_start: 0.8189 (t) cc_final: 0.7883 (p) REVERT: C 981 GLU cc_start: 0.8454 (tp30) cc_final: 0.8137 (tp30) REVERT: C 1047 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: C 1059 GLU cc_start: 0.8868 (tp30) cc_final: 0.8408 (tp30) outliers start: 55 outliers final: 27 residues processed: 215 average time/residue: 0.5846 time to fit residues: 143.7002 Evaluate side-chains 229 residues out of total 2188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 748 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 912 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 681 GLU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 877 PHE Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 709 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 720 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1047 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 29 optimal weight: 0.0070 chunk 16 optimal weight: 0.4980 chunk 173 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 223 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.087103 restraints weight = 32168.084| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.55 r_work: 0.2971 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20404 Z= 0.101 Angle : 0.538 11.482 27472 Z= 0.257 Chirality : 0.039 0.175 3132 Planarity : 0.004 0.052 3304 Dihedral : 13.127 172.991 3204 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.58 % Allowed : 17.81 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.18), residues: 2376 helix: 1.98 (0.13), residues: 1752 sheet: 1.47 (0.78), residues: 68 loop : -0.50 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 872 TYR 0.016 0.001 TYR B 842 PHE 0.010 0.001 PHE D 877 TRP 0.011 0.001 TRP B 809 HIS 0.003 0.000 HIS B 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (20404) covalent geometry : angle 0.53839 / 0.26 (27472) hydrogen bonds : bond 0.03667 / 2.52 ( 1164) hydrogen bonds : angle 3.32849 / 2.31 ( 3456) =============================================================================== Job complete usr+sys time: 5975.03 seconds wall clock time: 103 minutes 7.13 seconds (6187.13 seconds total)