Starting phenix.real_space_refine on Sun Sep 29 00:51:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_20451.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_20451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_20451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_20451.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqq_20451/09_2024/6pqq_20451.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 4} 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: 89 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: C, B, D Time building chain proxies: 11.45, per 1000 atoms: 0.57 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: 4.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.02 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: 5.54 Time building geometry restraints manager: 5.51 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 - 35.71: 11992 35.71 - 71.42: 360 71.42 - 107.12: 64 107.12 - 142.83: 28 142.83 - 178.54: 32 Dihedral angle restraints: 12476 sinusoidal: 5356 harmonic: 7120 Sorted by residual: dihedral pdb=" C19 6OU D1205 " pdb=" C20 6OU D1205 " pdb=" C21 6OU D1205 " pdb=" O22 6OU D1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU C1205 " pdb=" C20 6OU C1205 " pdb=" C21 6OU C1205 " pdb=" O22 6OU C1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.54 -178.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A1205 " pdb=" C20 6OU A1205 " pdb=" C21 6OU A1205 " pdb=" O22 6OU A1205 " ideal model delta sinusoidal sigma weight residual -59.00 119.53 -178.53 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12473 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.950 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: 0.000 Extract box with map and model: 0.580 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 41.450 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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= 0.687 Angle : 1.262 14.804 27472 Z= 0.561 Chirality : 0.070 0.672 3132 Planarity : 0.007 0.068 3304 Dihedral : 21.090 178.540 7844 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP D 832 HIS 0.010 0.002 HIS A 589 PHE 0.019 0.002 PHE D 888 TYR 0.033 0.003 TYR C 842 ARG 0.005 0.001 ARG D 919 *********************** 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 fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 2.246 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: 1.2652 time to fit residues: 696.0623 Evaluate side-chains 242 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 202 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.0060 chunk 122 optimal weight: 0.2980 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 HIS A 460 ASN A 476 ASN A 494 HIS 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 700 HIS D 805 ASN D 907 GLN D 983 HIS C 451 HIS C 460 ASN C 476 ASN C 494 HIS C 512 HIS C 519 HIS C 644 HIS C 700 HIS C 747 ASN C 907 GLN C 983 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20404 Z= 0.156 Angle : 0.582 8.167 27472 Z= 0.281 Chirality : 0.040 0.148 3132 Planarity : 0.005 0.063 3304 Dihedral : 23.822 178.638 3476 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.83 % Allowed : 14.29 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2376 helix: -0.18 (0.11), residues: 1736 sheet: -0.21 (0.73), residues: 68 loop : -1.25 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 832 HIS 0.004 0.001 HIS A 451 PHE 0.010 0.001 PHE B 823 TYR 0.012 0.001 TYR B 714 ARG 0.012 0.001 ARG D 975 *********************** 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 329 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 LEU cc_start: 0.9095 (mt) cc_final: 0.8783 (mm) REVERT: A 634 MET cc_start: 0.8550 (tpt) cc_final: 0.8264 (tpp) REVERT: A 661 LYS cc_start: 0.8822 (pttt) cc_final: 0.8604 (ptpt) REVERT: A 826 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8395 (pt) REVERT: A 877 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 986 LEU cc_start: 0.9065 (tt) cc_final: 0.8820 (tp) REVERT: B 530 MET cc_start: 0.8454 (ttp) cc_final: 0.8236 (mtp) REVERT: B 580 GLN cc_start: 0.8340 (mp10) cc_final: 0.7922 (mp10) REVERT: B 693 ASN cc_start: 0.8828 (m-40) cc_final: 0.8483 (t0) REVERT: B 826 ILE cc_start: 0.8547 (tp) cc_final: 0.8194 (pt) REVERT: B 877 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 912 MET cc_start: 0.8479 (ttm) cc_final: 0.8214 (ttp) REVERT: B 1075 ILE cc_start: 0.8722 (mt) cc_final: 0.8488 (mp) REVERT: D 634 MET cc_start: 0.8562 (tpt) cc_final: 0.8317 (tpp) REVERT: D 693 ASN cc_start: 0.8697 (m-40) cc_final: 0.8310 (t0) REVERT: D 783 PHE cc_start: 0.7767 (m-10) cc_final: 0.7524 (m-10) REVERT: D 852 ARG cc_start: 0.7728 (mmt90) cc_final: 0.7244 (mpt-90) REVERT: D 877 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7289 (t80) REVERT: D 1047 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6585 (tt0) REVERT: D 1059 GLU cc_start: 0.8204 (tp30) cc_final: 0.7840 (tp30) REVERT: C 634 MET cc_start: 0.8456 (tpt) cc_final: 0.7982 (tpp) REVERT: C 635 LYS cc_start: 0.8168 (ttpt) cc_final: 0.7921 (tptp) REVERT: C 689 MET cc_start: 0.8429 (mtp) cc_final: 0.8063 (mtt) REVERT: C 720 MET cc_start: 0.7628 (mmm) cc_final: 0.7271 (mmp) REVERT: C 808 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7037 (mp0) REVERT: C 873 SER cc_start: 0.7652 (t) cc_final: 0.7377 (p) REVERT: C 978 MET cc_start: 0.8196 (mtm) cc_final: 0.7902 (mtm) REVERT: C 981 GLU cc_start: 0.8071 (tp30) cc_final: 0.7832 (tp30) REVERT: C 1059 GLU cc_start: 0.8320 (tp30) cc_final: 0.8002 (tp30) outliers start: 57 outliers final: 16 residues processed: 311 average time/residue: 1.1861 time to fit residues: 420.2911 Evaluate side-chains 230 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 635 LYS Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 LEU 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 121 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 0.4980 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 693 ASN A 722 ASN B 460 ASN B 570 HIS B 722 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 460 ASN D 570 HIS D 644 HIS D 855 ASN C 570 HIS C 590 ASN C 691 GLN C 805 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20404 Z= 0.396 Angle : 0.695 9.170 27472 Z= 0.334 Chirality : 0.046 0.171 3132 Planarity : 0.005 0.063 3304 Dihedral : 22.317 166.567 3472 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.76 % Allowed : 14.48 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2376 helix: 0.58 (0.12), residues: 1752 sheet: 0.28 (0.79), residues: 68 loop : -0.97 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 605 HIS 0.007 0.002 HIS D 494 PHE 0.022 0.002 PHE B 888 TYR 0.017 0.002 TYR C 706 ARG 0.005 0.001 ARG A 919 *********************** 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 318 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 222 time to evaluate : 2.470 Fit side-chains REVERT: A 483 MET cc_start: 0.8810 (mtm) cc_final: 0.8476 (mtp) REVERT: A 488 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 544 LEU cc_start: 0.9142 (mt) cc_final: 0.8813 (mm) REVERT: A 871 LEU cc_start: 0.8530 (tm) cc_final: 0.8117 (mt) REVERT: A 1072 MET cc_start: 0.8964 (ttp) cc_final: 0.8751 (ttp) REVERT: B 681 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7513 (pp20) REVERT: B 852 ARG cc_start: 0.8256 (mpt-90) cc_final: 0.7449 (mtp180) REVERT: B 941 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8199 (tp) REVERT: D 483 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8617 (mtp) REVERT: D 744 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7513 (mmp) REVERT: D 852 ARG cc_start: 0.7807 (mmt90) cc_final: 0.7252 (mtp180) REVERT: D 873 SER cc_start: 0.7950 (t) cc_final: 0.7677 (p) REVERT: C 483 MET cc_start: 0.8800 (mtm) cc_final: 0.8214 (mtp) REVERT: C 873 SER cc_start: 0.7973 (t) cc_final: 0.7758 (p) REVERT: C 981 GLU cc_start: 0.8123 (tp30) cc_final: 0.7800 (tp30) REVERT: C 1059 GLU cc_start: 0.8261 (tp30) cc_final: 0.7837 (tp30) outliers start: 96 outliers final: 30 residues processed: 287 average time/residue: 1.0779 time to fit residues: 356.9562 Evaluate side-chains 208 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 709 MET Chi-restraints excluded: chain A residue 748 SER 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 779 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 873 SER Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 606 ASP 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 782 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 998 VAL Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 855 ASN Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1003 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN A 747 ASN A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 722 ASN B 747 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN C 979 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20404 Z= 0.159 Angle : 0.554 8.791 27472 Z= 0.266 Chirality : 0.040 0.187 3132 Planarity : 0.004 0.064 3304 Dihedral : 21.580 174.228 3472 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.27 % Allowed : 15.97 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2376 helix: 1.17 (0.12), residues: 1752 sheet: 0.57 (0.77), residues: 68 loop : -0.89 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 832 HIS 0.003 0.001 HIS D 494 PHE 0.009 0.001 PHE C 823 TYR 0.011 0.001 TYR D 842 ARG 0.004 0.000 ARG A 996 *********************** 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 269 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 203 time to evaluate : 2.258 Fit side-chains REVERT: A 544 LEU cc_start: 0.9123 (mt) cc_final: 0.8814 (mm) REVERT: A 974 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7703 (tmtt) REVERT: A 1059 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7510 (tm-30) REVERT: B 488 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 681 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7453 (pp20) REVERT: B 826 ILE cc_start: 0.8554 (tp) cc_final: 0.8352 (pt) REVERT: B 852 ARG cc_start: 0.8267 (mpt-90) cc_final: 0.7501 (mtp180) REVERT: B 877 PHE cc_start: 0.8285 (m-80) cc_final: 0.8068 (t80) REVERT: B 881 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8086 (tp) REVERT: B 1047 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6649 (tt0) REVERT: B 1073 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: D 483 MET cc_start: 0.8989 (mtp) cc_final: 0.8525 (mtp) REVERT: D 500 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8090 (tm) REVERT: D 634 MET cc_start: 0.8609 (tpt) cc_final: 0.8338 (tpp) REVERT: D 720 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7367 (mmm) REVERT: D 852 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7358 (mtp180) REVERT: D 873 SER cc_start: 0.7900 (t) cc_final: 0.7621 (p) REVERT: D 1059 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7576 (tp30) REVERT: C 483 MET cc_start: 0.8756 (mtm) cc_final: 0.8209 (mtp) REVERT: C 626 MET cc_start: 0.7881 (mtp) cc_final: 0.7553 (ttm) REVERT: C 720 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7346 (mmp) REVERT: C 733 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: C 744 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7561 (mmm) REVERT: C 873 SER cc_start: 0.7867 (t) cc_final: 0.7509 (p) REVERT: C 981 GLU cc_start: 0.8035 (tp30) cc_final: 0.7702 (tp30) REVERT: C 1059 GLU cc_start: 0.8234 (tp30) cc_final: 0.7805 (tp30) outliers start: 66 outliers final: 18 residues processed: 248 average time/residue: 1.1466 time to fit residues: 326.0636 Evaluate side-chains 207 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 974 LYS 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 881 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN 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 720 MET Chi-restraints excluded: chain D residue 748 SER Chi-restraints excluded: chain D residue 779 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 720 MET Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 855 ASN 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 193 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20404 Z= 0.243 Angle : 0.582 8.777 27472 Z= 0.278 Chirality : 0.041 0.157 3132 Planarity : 0.004 0.058 3304 Dihedral : 20.927 170.590 3472 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.57 % Allowed : 16.52 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2376 helix: 1.38 (0.12), residues: 1752 sheet: 0.78 (0.76), residues: 68 loop : -0.76 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.005 0.001 HIS D 494 PHE 0.011 0.001 PHE C 846 TYR 0.011 0.001 TYR C 456 ARG 0.009 0.001 ARG A 996 *********************** 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 fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 2.370 Fit side-chains REVERT: A 544 LEU cc_start: 0.9135 (mt) cc_final: 0.8803 (mm) REVERT: A 842 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: A 871 LEU cc_start: 0.8574 (tm) cc_final: 0.7955 (mt) REVERT: A 873 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 911 MET cc_start: 0.8636 (mtp) cc_final: 0.8428 (mtm) REVERT: A 1059 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7515 (tm-30) REVERT: A 1072 MET cc_start: 0.8873 (ttp) cc_final: 0.8652 (ttp) REVERT: B 483 MET cc_start: 0.8496 (mtp) cc_final: 0.7786 (mmt) REVERT: B 488 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7846 (mm) REVERT: B 681 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: B 822 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (pt) REVERT: B 852 ARG cc_start: 0.8301 (mpt-90) cc_final: 0.7527 (mtp180) REVERT: B 877 PHE cc_start: 0.8274 (m-80) cc_final: 0.8027 (t80) REVERT: B 881 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8175 (tp) REVERT: B 1047 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6397 (mt0) REVERT: D 483 MET cc_start: 0.8994 (mtp) cc_final: 0.8532 (mtp) REVERT: D 500 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (tm) REVERT: D 634 MET cc_start: 0.8626 (tpt) cc_final: 0.8362 (tpp) REVERT: D 720 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7369 (mmm) REVERT: D 852 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7429 (mtp180) REVERT: D 873 SER cc_start: 0.7917 (t) cc_final: 0.7655 (p) REVERT: D 981 GLU cc_start: 0.8030 (tp30) cc_final: 0.7821 (tp30) REVERT: D 1059 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 544 LEU cc_start: 0.8939 (mt) cc_final: 0.8707 (mm) REVERT: C 626 MET cc_start: 0.7937 (mtp) cc_final: 0.7392 (ttm) REVERT: C 720 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7392 (mmp) REVERT: C 733 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: C 744 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7493 (mmm) REVERT: C 842 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.6593 (t80) REVERT: C 873 SER cc_start: 0.7963 (t) cc_final: 0.7620 (p) REVERT: C 981 GLU cc_start: 0.8038 (tp30) cc_final: 0.7691 (tp30) REVERT: C 1059 GLU cc_start: 0.8313 (tp30) cc_final: 0.7818 (tp30) outliers start: 72 outliers final: 26 residues processed: 239 average time/residue: 1.1646 time to fit residues: 318.0106 Evaluate side-chains 218 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 779 LEU Chi-restraints excluded: chain A residue 842 TYR Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 998 VAL 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 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1067 LEU 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 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 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 733 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 842 TYR 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 78 optimal weight: 1.9990 chunk 208 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 0.0010 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN A1047 GLN ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 ASN D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20404 Z= 0.167 Angle : 0.543 8.248 27472 Z= 0.260 Chirality : 0.040 0.189 3132 Planarity : 0.004 0.056 3304 Dihedral : 20.483 164.979 3472 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 17.21 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.18), residues: 2376 helix: 1.59 (0.12), residues: 1752 sheet: 0.98 (0.77), residues: 68 loop : -0.70 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 832 HIS 0.003 0.001 HIS D 494 PHE 0.009 0.001 PHE C 823 TYR 0.010 0.001 TYR D 842 ARG 0.012 0.000 ARG A 996 *********************** 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 254 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 2.135 Fit side-chains REVERT: A 488 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 544 LEU cc_start: 0.9128 (mt) cc_final: 0.8804 (mm) REVERT: A 744 MET cc_start: 0.7797 (mmp) cc_final: 0.7460 (mtm) REVERT: A 842 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8670 (m-80) REVERT: A 871 LEU cc_start: 0.8580 (tm) cc_final: 0.7979 (mt) REVERT: A 881 LEU cc_start: 0.8665 (tp) cc_final: 0.8429 (tp) REVERT: A 1059 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7490 (tm-30) REVERT: A 1072 MET cc_start: 0.8789 (ttp) cc_final: 0.8589 (ttp) REVERT: B 464 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7922 (mtp180) REVERT: B 483 MET cc_start: 0.8436 (mtp) cc_final: 0.7708 (mmt) REVERT: B 488 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 681 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7439 (pp20) REVERT: B 720 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7907 (mmp) REVERT: B 852 ARG cc_start: 0.8279 (mpt-90) cc_final: 0.7543 (mtp180) REVERT: B 877 PHE cc_start: 0.8227 (m-80) cc_final: 0.8011 (t80) REVERT: B 881 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 912 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8307 (ttp) REVERT: B 1047 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6594 (mt0) REVERT: D 483 MET cc_start: 0.8957 (mtp) cc_final: 0.8528 (mtp) REVERT: D 488 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7409 (mm) REVERT: D 500 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8080 (tm) REVERT: D 634 MET cc_start: 0.8605 (tpt) cc_final: 0.8395 (tpp) REVERT: D 720 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7293 (mmm) REVERT: D 744 MET cc_start: 0.7855 (mmp) cc_final: 0.7578 (mmm) REVERT: D 852 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: D 871 LEU cc_start: 0.8636 (tp) cc_final: 0.8335 (mt) REVERT: D 873 SER cc_start: 0.7951 (t) cc_final: 0.7656 (p) REVERT: D 981 GLU cc_start: 0.8053 (tp30) cc_final: 0.7848 (tp30) REVERT: D 1059 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7494 (tp30) REVERT: C 544 LEU cc_start: 0.8950 (mt) cc_final: 0.8726 (mm) REVERT: C 626 MET cc_start: 0.7987 (mtp) cc_final: 0.7628 (ttm) REVERT: C 720 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7390 (mmp) REVERT: C 733 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7704 (ttp) REVERT: C 744 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7461 (mmm) REVERT: C 873 SER cc_start: 0.7917 (t) cc_final: 0.7573 (p) REVERT: C 981 GLU cc_start: 0.8022 (tp30) cc_final: 0.7667 (tp30) REVERT: C 1047 GLN cc_start: 0.6957 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: C 1059 GLU cc_start: 0.8308 (tp30) cc_final: 0.7811 (tp30) outliers start: 67 outliers final: 25 residues processed: 229 average time/residue: 1.1443 time to fit residues: 301.0561 Evaluate side-chains 223 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 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 842 TYR Chi-restraints excluded: chain A residue 941 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 881 LEU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 488 LEU 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 998 VAL 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 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 733 MET Chi-restraints excluded: chain C residue 744 MET Chi-restraints excluded: chain C residue 941 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 223 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 0.0040 chunk 169 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20404 Z= 0.173 Angle : 0.542 9.195 27472 Z= 0.260 Chirality : 0.040 0.194 3132 Planarity : 0.004 0.055 3304 Dihedral : 19.970 165.823 3472 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.32 % Allowed : 17.56 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2376 helix: 1.73 (0.13), residues: 1752 sheet: 1.14 (0.78), residues: 68 loop : -0.64 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.005 0.001 HIS B 481 PHE 0.009 0.001 PHE C 823 TYR 0.009 0.001 TYR D 842 ARG 0.009 0.000 ARG A 996 *********************** 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 267 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 200 time to evaluate : 2.439 Fit side-chains REVERT: A 488 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 544 LEU cc_start: 0.9146 (mt) cc_final: 0.8826 (mm) REVERT: A 720 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8045 (mmp) REVERT: A 744 MET cc_start: 0.7753 (mmp) cc_final: 0.7454 (mtm) REVERT: A 842 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: A 871 LEU cc_start: 0.8536 (tm) cc_final: 0.7967 (mt) REVERT: A 1059 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7500 (tm-30) REVERT: B 464 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: B 483 MET cc_start: 0.8392 (mtp) cc_final: 0.7600 (mmt) REVERT: B 488 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7917 (mm) REVERT: B 681 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7440 (pp20) REVERT: B 720 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7912 (mmp) REVERT: B 852 ARG cc_start: 0.8277 (mpt-90) cc_final: 0.7552 (mtp180) REVERT: B 881 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 912 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: B 987 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: B 1047 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6607 (mt0) REVERT: D 483 MET cc_start: 0.8905 (mtp) cc_final: 0.8553 (mtp) REVERT: D 488 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7419 (mm) REVERT: D 530 MET cc_start: 0.8249 (mtp) cc_final: 0.7920 (mtt) REVERT: D 720 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7229 (mmp) REVERT: D 744 MET cc_start: 0.7800 (mmp) cc_final: 0.7550 (mmm) REVERT: D 852 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7510 (mtp85) REVERT: D 871 LEU cc_start: 0.8766 (tp) cc_final: 0.8353 (mt) REVERT: D 873 SER cc_start: 0.7940 (t) cc_final: 0.7645 (p) REVERT: D 981 GLU cc_start: 0.8016 (tp30) cc_final: 0.7811 (tp30) REVERT: D 1059 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7551 (tp30) REVERT: C 475 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8054 (tp) REVERT: C 544 LEU cc_start: 0.8996 (mt) cc_final: 0.8786 (mm) REVERT: C 720 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7433 (mmp) REVERT: C 733 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7764 (ttp) REVERT: C 744 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7506 (mmm) REVERT: C 873 SER cc_start: 0.7940 (t) cc_final: 0.7656 (p) REVERT: C 877 PHE cc_start: 0.8202 (m-80) cc_final: 0.7895 (t80) REVERT: C 981 GLU cc_start: 0.8056 (tp30) cc_final: 0.7703 (tp30) REVERT: C 1047 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6547 (mt0) REVERT: C 1059 GLU cc_start: 0.8310 (tp30) cc_final: 0.7806 (tp30) outliers start: 67 outliers final: 27 residues processed: 242 average time/residue: 1.1059 time to fit residues: 308.1991 Evaluate side-chains 229 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 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 842 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU 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 723 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 881 LEU Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain D residue 488 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 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 609 LEU 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 733 MET Chi-restraints excluded: chain C residue 744 MET 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 143 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20404 Z= 0.211 Angle : 0.572 9.136 27472 Z= 0.277 Chirality : 0.041 0.212 3132 Planarity : 0.004 0.058 3304 Dihedral : 19.574 171.743 3472 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.03 % Allowed : 17.56 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.18), residues: 2376 helix: 1.75 (0.13), residues: 1752 sheet: 1.23 (0.78), residues: 68 loop : -0.64 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 515 HIS 0.004 0.001 HIS D 494 PHE 0.010 0.001 PHE A 818 TYR 0.011 0.001 TYR C 456 ARG 0.008 0.000 ARG A 996 *********************** 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 250 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 189 time to evaluate : 2.287 Fit side-chains REVERT: A 488 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7842 (mm) REVERT: A 544 LEU cc_start: 0.9148 (mt) cc_final: 0.8830 (mm) REVERT: A 720 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8040 (mmp) REVERT: A 744 MET cc_start: 0.7721 (mmp) cc_final: 0.7457 (mtm) REVERT: A 842 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: A 871 LEU cc_start: 0.8568 (tm) cc_final: 0.7985 (mt) REVERT: A 974 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7712 (tmtt) REVERT: A 1059 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7492 (tm-30) REVERT: B 464 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7882 (mtp180) REVERT: B 681 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7418 (pp20) REVERT: B 720 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7919 (mmp) REVERT: B 852 ARG cc_start: 0.8338 (mpt-90) cc_final: 0.7613 (mtp180) REVERT: B 881 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8214 (tp) REVERT: B 987 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: B 1047 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6608 (mt0) REVERT: D 483 MET cc_start: 0.9001 (mtp) cc_final: 0.8535 (mtp) REVERT: D 488 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7519 (mm) REVERT: D 523 MET cc_start: 0.8524 (tpp) cc_final: 0.8134 (ttp) REVERT: D 530 MET cc_start: 0.8227 (mtp) cc_final: 0.7932 (mtt) REVERT: D 720 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7242 (mmp) REVERT: D 744 MET cc_start: 0.7794 (mmp) cc_final: 0.7556 (mmm) REVERT: D 852 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: D 871 LEU cc_start: 0.8805 (tp) cc_final: 0.8399 (mt) REVERT: D 873 SER cc_start: 0.7958 (t) cc_final: 0.7674 (p) REVERT: D 953 MET cc_start: 0.8239 (mmt) cc_final: 0.8009 (mmp) REVERT: D 981 GLU cc_start: 0.7987 (tp30) cc_final: 0.7778 (tp30) REVERT: D 1059 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7542 (tp30) REVERT: C 475 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8079 (tp) REVERT: C 544 LEU cc_start: 0.9040 (mt) cc_final: 0.8830 (mm) REVERT: C 720 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7439 (mmp) REVERT: C 744 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: C 873 SER cc_start: 0.7989 (t) cc_final: 0.7720 (p) REVERT: C 877 PHE cc_start: 0.8270 (m-80) cc_final: 0.7954 (t80) REVERT: C 981 GLU cc_start: 0.8050 (tp30) cc_final: 0.7690 (tp30) REVERT: C 1047 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: C 1059 GLU cc_start: 0.8294 (tp30) cc_final: 0.7832 (tp30) outliers start: 61 outliers final: 28 residues processed: 226 average time/residue: 1.1709 time to fit residues: 303.7265 Evaluate side-chains 230 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 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 842 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain B residue 464 ARG 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 720 MET Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 819 VAL 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 B residue 1047 GLN Chi-restraints excluded: chain D residue 488 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 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 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 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 210 optimal weight: 7.9990 chunk 221 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 0.0770 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 0.1980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1061 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4218 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= 0.180 Angle : 0.561 10.093 27472 Z= 0.268 Chirality : 0.040 0.210 3132 Planarity : 0.004 0.058 3304 Dihedral : 19.148 174.122 3472 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.98 % Allowed : 17.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2376 helix: 1.84 (0.13), residues: 1752 sheet: 1.30 (0.79), residues: 68 loop : -0.60 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 809 HIS 0.004 0.001 HIS D 494 PHE 0.012 0.001 PHE B 877 TYR 0.010 0.001 TYR D 842 ARG 0.008 0.000 ARG A 996 *********************** 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 250 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 190 time to evaluate : 2.311 Fit side-chains REVERT: A 483 MET cc_start: 0.8871 (mtm) cc_final: 0.8563 (mtp) REVERT: A 488 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7804 (mm) REVERT: A 544 LEU cc_start: 0.9138 (mt) cc_final: 0.8825 (mm) REVERT: A 720 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8046 (mmp) REVERT: A 744 MET cc_start: 0.7687 (mmp) cc_final: 0.7468 (mtm) REVERT: A 842 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: A 871 LEU cc_start: 0.8550 (tm) cc_final: 0.7976 (mt) REVERT: A 974 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7706 (tmtt) REVERT: A 1059 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7462 (tm-30) REVERT: B 464 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7889 (mtp180) REVERT: B 483 MET cc_start: 0.8064 (mtp) cc_final: 0.7624 (mmt) REVERT: B 681 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: B 720 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7960 (mmp) REVERT: B 852 ARG cc_start: 0.8339 (mpt-90) cc_final: 0.7634 (mtp180) REVERT: B 881 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 987 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: B 1047 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: D 483 MET cc_start: 0.9007 (mtp) cc_final: 0.8524 (mtp) REVERT: D 530 MET cc_start: 0.8223 (mtp) cc_final: 0.7936 (mtt) REVERT: D 720 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7244 (mmp) REVERT: D 744 MET cc_start: 0.7762 (mmp) cc_final: 0.7530 (mmm) REVERT: D 852 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7529 (mtp85) REVERT: D 871 LEU cc_start: 0.8779 (tp) cc_final: 0.8367 (mt) REVERT: D 873 SER cc_start: 0.7940 (t) cc_final: 0.7644 (p) REVERT: D 912 MET cc_start: 0.8539 (ttm) cc_final: 0.8321 (ttt) REVERT: D 981 GLU cc_start: 0.8015 (tp30) cc_final: 0.7804 (tp30) REVERT: D 1059 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7531 (tp30) REVERT: C 475 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8090 (tp) REVERT: C 720 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7456 (mmp) REVERT: C 744 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7492 (mmm) REVERT: C 873 SER cc_start: 0.7954 (t) cc_final: 0.7690 (p) REVERT: C 877 PHE cc_start: 0.8198 (m-80) cc_final: 0.7882 (t80) REVERT: C 981 GLU cc_start: 0.8053 (tp30) cc_final: 0.7687 (tp30) REVERT: C 1047 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6548 (mt0) REVERT: C 1059 GLU cc_start: 0.8292 (tp30) cc_final: 0.7826 (tp30) outliers start: 60 outliers final: 29 residues processed: 230 average time/residue: 1.1497 time to fit residues: 304.0451 Evaluate side-chains 228 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 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 842 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU 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 881 LEU Chi-restraints excluded: chain B residue 987 GLU Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain B residue 1047 GLN 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 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 627 ILE 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 751 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4273 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= 0.169 Angle : 0.561 11.362 27472 Z= 0.268 Chirality : 0.040 0.212 3132 Planarity : 0.004 0.058 3304 Dihedral : 18.858 177.411 3472 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.63 % Allowed : 18.15 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.18), residues: 2376 helix: 1.87 (0.13), residues: 1752 sheet: 1.39 (0.78), residues: 68 loop : -0.61 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 809 HIS 0.003 0.001 HIS B 494 PHE 0.010 0.001 PHE A 823 TYR 0.010 0.001 TYR D1049 ARG 0.007 0.000 ARG A 996 ********************** 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 fitting. rotamer outliers: 53 poor density : 189 time to evaluate : 2.259 Fit side-chains REVERT: A 464 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7831 (ttm-80) REVERT: A 488 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (mm) REVERT: A 544 LEU cc_start: 0.9133 (mt) cc_final: 0.8826 (mm) REVERT: A 720 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8050 (mmp) REVERT: A 842 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: A 871 LEU cc_start: 0.8546 (tm) cc_final: 0.7968 (mt) REVERT: A 974 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7722 (tmtt) REVERT: A 1059 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7448 (tm-30) REVERT: B 464 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7842 (mtp180) REVERT: B 483 MET cc_start: 0.8119 (mtp) cc_final: 0.7549 (mmt) REVERT: B 681 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7376 (pp20) REVERT: B 720 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7996 (mmp) REVERT: B 852 ARG cc_start: 0.8344 (mpt-90) cc_final: 0.7658 (mtp180) REVERT: B 877 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 881 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 987 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: B 1047 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6577 (mt0) REVERT: D 483 MET cc_start: 0.9009 (mtp) cc_final: 0.8530 (mtp) REVERT: D 530 MET cc_start: 0.8141 (mtp) cc_final: 0.7874 (mtt) REVERT: D 720 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7197 (mmp) REVERT: D 852 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: D 871 LEU cc_start: 0.8784 (tp) cc_final: 0.8374 (mt) REVERT: D 873 SER cc_start: 0.7933 (t) cc_final: 0.7639 (p) REVERT: D 981 GLU cc_start: 0.8014 (tp30) cc_final: 0.7804 (tp30) REVERT: D 1059 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7533 (tp30) REVERT: C 720 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7459 (mmp) REVERT: C 744 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7478 (mmm) REVERT: C 842 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.6740 (t80) REVERT: C 873 SER cc_start: 0.7938 (t) cc_final: 0.7670 (p) REVERT: C 877 PHE cc_start: 0.8183 (m-80) cc_final: 0.7877 (t80) REVERT: C 981 GLU cc_start: 0.8038 (tp30) cc_final: 0.7685 (tp30) REVERT: C 1047 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6566 (mt0) REVERT: C 1059 GLU cc_start: 0.8295 (tp30) cc_final: 0.7829 (tp30) outliers start: 53 outliers final: 30 residues processed: 223 average time/residue: 1.1662 time to fit residues: 297.9110 Evaluate side-chains 232 residues out of total 2188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 488 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 842 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 998 VAL Chi-restraints excluded: chain A residue 1045 LEU 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 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 B residue 1047 GLN 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 998 VAL 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 627 ILE 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 751 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 842 TYR Chi-restraints excluded: chain C residue 941 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 151 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 40.0000 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085268 restraints weight = 32108.813| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.50 r_work: 0.2944 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4340 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= 0.160 Angle : 0.556 11.003 27472 Z= 0.265 Chirality : 0.039 0.205 3132 Planarity : 0.004 0.058 3304 Dihedral : 18.472 179.155 3472 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.68 % Allowed : 18.15 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2376 helix: 1.93 (0.13), residues: 1752 sheet: 1.43 (0.78), residues: 68 loop : -0.54 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 809 HIS 0.003 0.000 HIS B 494 PHE 0.008 0.001 PHE B 877 TYR 0.011 0.001 TYR D1049 ARG 0.007 0.000 ARG A 996 =============================================================================== Job complete usr+sys time: 6361.71 seconds wall clock time: 112 minutes 47.22 seconds (6767.22 seconds total)