Starting phenix.real_space_refine on Thu Apr 11 01:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/04_2024/7wta_32773_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 13396 2.51 5 N 3616 2.21 5 O 3920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "D GLU 865": "OE1" <-> "OE2" Residue "D GLU 961": "OE1" <-> "OE2" Residue "D GLU 1097": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.67, per 1000 atoms: 0.55 Number of scatterers: 21080 At special positions: 0 Unit cell: (161.7, 147.4, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 3920 8.00 N 3616 7.00 C 13396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.02 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.03 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.82 Conformation dependent library (CDL) restraints added in 4.4 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 19 sheets defined 39.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 541 through 559 Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.511A pdb=" N ALA A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.528A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.728A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.605A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 829 through 845 removed outlier: 4.233A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 871 through 881 Processing helix chain 'A' and resid 887 through 900 removed outlier: 4.002A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 894 " --> pdb=" O VAL A 890 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 584 through 589 removed outlier: 4.572A pdb=" N LYS B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 609 through 616 removed outlier: 4.167A pdb=" N PHE B 612 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASP B 613 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 614 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 633 removed outlier: 3.661A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 720 through 733 Processing helix chain 'B' and resid 749 through 762 removed outlier: 3.849A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 828 through 845 removed outlier: 3.736A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 853 No H-bonds generated for 'chain 'B' and resid 850 through 853' Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 871 through 880 Processing helix chain 'B' and resid 887 through 901 removed outlier: 3.566A pdb=" N LYS B 891 " --> pdb=" O PHE B 887 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 894 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 924 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 978 through 981 No H-bonds generated for 'chain 'B' and resid 978 through 981' Processing helix chain 'B' and resid 988 through 998 Processing helix chain 'B' and resid 1004 through 1012 Processing helix chain 'B' and resid 1014 through 1027 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'C' and resid 497 through 509 Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 609 through 615 removed outlier: 4.072A pdb=" N PHE C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP C 613 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 614 " --> pdb=" O THR C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 631 Processing helix chain 'C' and resid 656 through 668 Processing helix chain 'C' and resid 683 through 696 Processing helix chain 'C' and resid 720 through 733 Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.541A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 790 removed outlier: 4.176A pdb=" N GLY C 790 " --> pdb=" O CYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 828 through 845 removed outlier: 3.958A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 868 through 881 removed outlier: 4.884A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 901 removed outlier: 4.177A pdb=" N VAL C 895 " --> pdb=" O LYS C 891 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU C 896 " --> pdb=" O LYS C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 924 Processing helix chain 'C' and resid 928 through 933 Processing helix chain 'C' and resid 942 through 949 Processing helix chain 'C' and resid 961 through 968 Processing helix chain 'C' and resid 978 through 981 No H-bonds generated for 'chain 'C' and resid 978 through 981' Processing helix chain 'C' and resid 988 through 998 removed outlier: 3.663A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1012 Processing helix chain 'C' and resid 1014 through 1027 Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'D' and resid 497 through 510 Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 572 through 577 Processing helix chain 'D' and resid 585 through 597 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 611 through 616 Processing helix chain 'D' and resid 623 through 633 Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 683 through 696 Processing helix chain 'D' and resid 720 through 732 Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 810 through 816 Processing helix chain 'D' and resid 828 through 844 removed outlier: 3.511A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 852 No H-bonds generated for 'chain 'D' and resid 850 through 852' Processing helix chain 'D' and resid 868 through 881 removed outlier: 3.970A pdb=" N TYR D 871 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR D 872 " --> pdb=" O GLY D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 900 removed outlier: 4.706A pdb=" N LYS D 888 " --> pdb=" O SER D 885 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 891 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 895 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 942 through 949 Processing helix chain 'D' and resid 961 through 968 Processing helix chain 'D' and resid 978 through 981 No H-bonds generated for 'chain 'D' and resid 978 through 981' Processing helix chain 'D' and resid 989 through 997 Processing helix chain 'D' and resid 1004 through 1012 Processing helix chain 'D' and resid 1014 through 1027 Processing helix chain 'D' and resid 1035 through 1039 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= B, first strand: chain 'A' and resid 603 through 605 removed outlier: 6.905A pdb=" N VAL A 673 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEU A 643 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG A 675 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 699 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL A 676 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU A 701 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 737 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N ILE A 704 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS A 739 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE A 740 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS A 769 " --> pdb=" O ILE A 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 6.726A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1146 through 1149 removed outlier: 3.587A pdb=" N THR A1147 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1122 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER A1141 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A1120 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 4.010A pdb=" N LEU A1175 " --> pdb=" O ILE A1112 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 564 through 567 Processing sheet with id= G, first strand: chain 'B' and resid 768 through 770 removed outlier: 6.030A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 737 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 674 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.851A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1139 through 1141 Processing sheet with id= J, first strand: chain 'C' and resid 564 through 567 Processing sheet with id= K, first strand: chain 'C' and resid 640 through 642 removed outlier: 6.871A pdb=" N VAL C 673 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 699 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL C 676 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU C 701 " --> pdb=" O VAL C 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 740 through 742 Processing sheet with id= M, first strand: chain 'C' and resid 1046 through 1051 removed outlier: 3.934A pdb=" N GLU C1046 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1062 " --> pdb=" O GLU C1046 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1073 through 1079 Processing sheet with id= O, first strand: chain 'C' and resid 1119 through 1123 removed outlier: 3.653A pdb=" N LYS C1119 " --> pdb=" O SER C1141 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C1141 " --> pdb=" O LYS C1119 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C1135 " --> pdb=" O SER C1151 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 564 through 567 Processing sheet with id= Q, first strand: chain 'D' and resid 768 through 772 removed outlier: 6.846A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 737 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA D 702 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 741 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.836A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.510A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.204A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D1137 " --> pdb=" O VAL D1149 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL D1149 " --> pdb=" O LEU D1137 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2019 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: 6.52 Time building geometry restraints manager: 9.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3570 1.31 - 1.43: 5335 1.43 - 1.56: 12365 1.56 - 1.69: 26 1.69 - 1.82: 260 Bond restraints: 21556 Sorted by residual: bond pdb=" C6 BTI A1900 " pdb=" S1 BTI A1900 " ideal model delta sigma weight residual 1.811 1.440 0.371 2.00e-02 2.50e+03 3.44e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.442 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI B1900 " pdb=" S1 BTI B1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" C3 BTI B1900 " pdb=" N3 BTI B1900 " ideal model delta sigma weight residual 1.356 1.577 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 21551 not shown) Histogram of bond angle deviations from ideal: 91.49 - 100.03: 22 100.03 - 108.56: 1357 108.56 - 117.09: 14239 117.09 - 125.62: 13288 125.62 - 134.16: 314 Bond angle restraints: 29220 Sorted by residual: angle pdb=" C10 BTI C1900 " pdb=" C11 BTI C1900 " pdb=" O11 BTI C1900 " ideal model delta sigma weight residual 125.49 91.49 34.00 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C10 BTI B1900 " pdb=" C11 BTI B1900 " pdb=" O11 BTI B1900 " ideal model delta sigma weight residual 125.49 92.99 32.50 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 BTI A1900 " pdb=" C11 BTI A1900 " pdb=" O11 BTI A1900 " ideal model delta sigma weight residual 125.49 99.42 26.07 3.00e+00 1.11e-01 7.55e+01 angle pdb=" C10 BTI D1900 " pdb=" C11 BTI D1900 " pdb=" O11 BTI D1900 " ideal model delta sigma weight residual 125.49 101.36 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" C2 BTI B1900 " pdb=" S1 BTI B1900 " pdb=" C6 BTI B1900 " ideal model delta sigma weight residual 89.29 106.58 -17.29 3.00e+00 1.11e-01 3.32e+01 ... (remaining 29215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11916 17.47 - 34.93: 1006 34.93 - 52.40: 179 52.40 - 69.86: 20 69.86 - 87.33: 15 Dihedral angle restraints: 13136 sinusoidal: 5300 harmonic: 7836 Sorted by residual: dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 176.35 -83.35 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 142.68 -49.68 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA CYS B 786 " pdb=" C CYS B 786 " pdb=" N ALA B 787 " pdb=" CA ALA B 787 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 13133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2410 0.041 - 0.083: 614 0.083 - 0.124: 220 0.124 - 0.166: 15 0.166 - 0.207: 5 Chirality restraints: 3264 Sorted by residual: chirality pdb=" C5 BTI C1900 " pdb=" C4 BTI C1900 " pdb=" C6 BTI C1900 " pdb=" N3 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.73 2.94 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C5 BTI A1900 " pdb=" C4 BTI A1900 " pdb=" C6 BTI A1900 " pdb=" N3 BTI A1900 " both_signs ideal model delta sigma weight residual False 2.73 2.92 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" C4 BTI C1900 " pdb=" C2 BTI C1900 " pdb=" C5 BTI C1900 " pdb=" N2 BTI C1900 " both_signs ideal model delta sigma weight residual False 2.75 2.57 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3261 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 535 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO D 536 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 536 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 536 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 807 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 808 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 808 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 808 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 807 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.64e+00 pdb=" N PRO D 808 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 808 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 808 " -0.022 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1134 2.72 - 3.26: 23614 3.26 - 3.81: 37584 3.81 - 4.35: 43475 4.35 - 4.90: 70173 Nonbonded interactions: 175980 Sorted by model distance: nonbonded pdb=" O TYR B 593 " pdb=" ND2 ASN B 597 " model vdw 2.171 2.520 nonbonded pdb=" OD2 ASP A 613 " pdb=" OH TYR A 651 " model vdw 2.183 2.440 nonbonded pdb=" NE2 GLN A1075 " pdb=" OG SER A1086 " model vdw 2.185 2.520 nonbonded pdb=" OG SER D1066 " pdb=" O GLN D1075 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLU B 961 " pdb=" NH2 ARG B 964 " model vdw 2.188 2.520 ... (remaining 175975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.020 Extract box with map and model: 6.200 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.510 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.110 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.371 21556 Z= 0.456 Angle : 0.820 33.998 29220 Z= 0.393 Chirality : 0.042 0.207 3264 Planarity : 0.005 0.083 3828 Dihedral : 13.247 87.331 8092 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.21 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.51 (0.16), residues: 2728 helix: 0.82 (0.16), residues: 1116 sheet: -0.33 (0.28), residues: 344 loop : -1.39 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 838 HIS 0.005 0.001 HIS C 574 PHE 0.024 0.002 PHE C1078 TYR 0.018 0.002 TYR B 951 ARG 0.009 0.001 ARG C1070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9522 (mmp) cc_final: 0.9148 (mmm) REVERT: A 566 MET cc_start: 0.5803 (ppp) cc_final: 0.5588 (ppp) REVERT: A 1166 MET cc_start: 0.8807 (ptp) cc_final: 0.8289 (pmm) REVERT: B 641 MET cc_start: 0.8239 (tmm) cc_final: 0.7886 (ppp) REVERT: B 686 MET cc_start: 0.9269 (mpp) cc_final: 0.9000 (mpp) REVERT: B 724 MET cc_start: 0.8967 (mmt) cc_final: 0.8397 (mmm) REVERT: B 1116 MET cc_start: 0.8360 (mmm) cc_final: 0.7914 (ppp) REVERT: B 1145 MET cc_start: 0.6365 (ptt) cc_final: 0.5686 (ptt) REVERT: C 754 MET cc_start: 0.9467 (ppp) cc_final: 0.9160 (ppp) REVERT: C 755 LEU cc_start: 0.9704 (mt) cc_final: 0.9261 (mt) REVERT: C 783 MET cc_start: 0.9073 (tpp) cc_final: 0.8863 (tpp) REVERT: C 804 MET cc_start: 0.8607 (tpp) cc_final: 0.8143 (tpp) REVERT: C 1145 MET cc_start: 0.5515 (pmm) cc_final: 0.4796 (pmm) REVERT: D 574 HIS cc_start: 0.8922 (m-70) cc_final: 0.8687 (m170) REVERT: D 604 MET cc_start: 0.8388 (tpt) cc_final: 0.8119 (tpp) REVERT: D 810 MET cc_start: 0.9017 (mmp) cc_final: 0.8441 (mmm) REVERT: D 881 MET cc_start: 0.9230 (mmp) cc_final: 0.9028 (mmm) REVERT: D 947 PHE cc_start: 0.9254 (t80) cc_final: 0.9046 (t80) REVERT: D 1098 MET cc_start: 0.6401 (mmt) cc_final: 0.6199 (mmt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3317 time to fit residues: 87.7287 Evaluate side-chains 144 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 114 optimal weight: 0.0870 chunk 70 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 158 optimal weight: 0.0050 chunk 247 optimal weight: 4.9990 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN D 864 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21556 Z= 0.159 Angle : 0.603 9.155 29220 Z= 0.294 Chirality : 0.041 0.277 3264 Planarity : 0.004 0.058 3828 Dihedral : 5.242 56.368 3016 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 0.31 % Allowed : 7.54 % Favored : 92.15 % 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: -0.51 (0.16), residues: 2728 helix: 0.64 (0.16), residues: 1168 sheet: 0.05 (0.29), residues: 342 loop : -1.42 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 838 HIS 0.004 0.001 HIS C 574 PHE 0.013 0.001 PHE D 602 TYR 0.015 0.001 TYR B 834 ARG 0.004 0.000 ARG D 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 3.049 Fit side-chains REVERT: A 508 MET cc_start: 0.9537 (mmp) cc_final: 0.9088 (mmm) REVERT: A 641 MET cc_start: 0.7980 (tmm) cc_final: 0.7697 (tmm) REVERT: A 671 MET cc_start: 0.4589 (tpt) cc_final: 0.4336 (tpt) REVERT: A 854 MET cc_start: 0.6098 (tmm) cc_final: 0.5566 (tmm) REVERT: A 900 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8059 (mmt) REVERT: A 1153 MET cc_start: 0.8284 (ppp) cc_final: 0.7934 (ppp) REVERT: A 1166 MET cc_start: 0.8682 (ptp) cc_final: 0.8100 (pmm) REVERT: B 616 MET cc_start: 0.7940 (mmp) cc_final: 0.7726 (mmp) REVERT: B 686 MET cc_start: 0.9299 (mpp) cc_final: 0.8978 (mpp) REVERT: B 724 MET cc_start: 0.8950 (mmt) cc_final: 0.8466 (mmm) REVERT: B 1145 MET cc_start: 0.6459 (ptt) cc_final: 0.5494 (ptt) REVERT: C 508 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8079 (mmp) REVERT: C 754 MET cc_start: 0.9446 (ppp) cc_final: 0.9125 (ppp) REVERT: C 755 LEU cc_start: 0.9671 (mt) cc_final: 0.9140 (mt) REVERT: C 783 MET cc_start: 0.9024 (tpp) cc_final: 0.8777 (tpp) REVERT: C 804 MET cc_start: 0.8541 (tpp) cc_final: 0.8151 (tpp) REVERT: C 881 MET cc_start: 0.9221 (tpp) cc_final: 0.8928 (tpp) REVERT: D 508 MET cc_start: 0.9167 (mmp) cc_final: 0.8939 (mmp) REVERT: D 574 HIS cc_start: 0.8843 (m-70) cc_final: 0.8585 (m90) REVERT: D 604 MET cc_start: 0.8336 (tpt) cc_final: 0.7953 (tpp) REVERT: D 729 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4972 (pm20) REVERT: D 730 LEU cc_start: 0.8163 (tp) cc_final: 0.7905 (mm) REVERT: D 810 MET cc_start: 0.8888 (mmp) cc_final: 0.8464 (mmm) REVERT: D 854 MET cc_start: 0.8387 (ttt) cc_final: 0.8038 (ttt) REVERT: D 881 MET cc_start: 0.9272 (mmp) cc_final: 0.8865 (mmm) REVERT: D 947 PHE cc_start: 0.9247 (t80) cc_final: 0.9020 (t80) REVERT: D 1098 MET cc_start: 0.6316 (mmt) cc_final: 0.6060 (mmt) outliers start: 7 outliers final: 0 residues processed: 157 average time/residue: 0.3275 time to fit residues: 83.8210 Evaluate side-chains 146 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain D residue 729 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 168 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A1059 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 559 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21556 Z= 0.196 Angle : 0.589 9.748 29220 Z= 0.289 Chirality : 0.040 0.151 3264 Planarity : 0.004 0.050 3828 Dihedral : 5.031 59.235 3016 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 0.75 % Allowed : 9.35 % Favored : 89.89 % 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: -0.43 (0.16), residues: 2728 helix: 0.67 (0.16), residues: 1174 sheet: 0.00 (0.29), residues: 358 loop : -1.34 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 PHE 0.019 0.001 PHE B 674 TYR 0.014 0.001 TYR B 834 ARG 0.004 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 2.486 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9563 (mmp) cc_final: 0.9123 (mmm) REVERT: A 641 MET cc_start: 0.8089 (tmm) cc_final: 0.7797 (tmm) REVERT: A 690 MET cc_start: 0.8270 (tpt) cc_final: 0.7941 (mmm) REVERT: A 804 MET cc_start: 0.8782 (mmm) cc_final: 0.8567 (tpp) REVERT: A 900 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: A 1153 MET cc_start: 0.8178 (ppp) cc_final: 0.7766 (ppp) REVERT: A 1166 MET cc_start: 0.8634 (ptp) cc_final: 0.8038 (pmm) REVERT: B 508 MET cc_start: 0.8819 (mmp) cc_final: 0.8350 (mmt) REVERT: B 566 MET cc_start: 0.8146 (tpp) cc_final: 0.7875 (tpp) REVERT: B 616 MET cc_start: 0.7980 (mmp) cc_final: 0.7511 (mmp) REVERT: B 671 MET cc_start: 0.6528 (tpt) cc_final: 0.6244 (tpt) REVERT: B 686 MET cc_start: 0.9307 (mpp) cc_final: 0.9018 (mpp) REVERT: B 1012 MET cc_start: 0.8391 (pmm) cc_final: 0.8063 (pmm) REVERT: B 1116 MET cc_start: 0.8471 (mmt) cc_final: 0.7279 (ptm) REVERT: C 508 MET cc_start: 0.8530 (mmt) cc_final: 0.8068 (mmp) REVERT: C 754 MET cc_start: 0.9437 (ppp) cc_final: 0.9039 (ppp) REVERT: C 755 LEU cc_start: 0.9698 (mt) cc_final: 0.9207 (mt) REVERT: C 783 MET cc_start: 0.9038 (tpp) cc_final: 0.8786 (tpp) REVERT: D 574 HIS cc_start: 0.8891 (m-70) cc_final: 0.8675 (m90) REVERT: D 604 MET cc_start: 0.8600 (tpt) cc_final: 0.8150 (tpp) REVERT: D 616 MET cc_start: 0.8131 (mmp) cc_final: 0.7840 (mmp) REVERT: D 730 LEU cc_start: 0.8255 (tp) cc_final: 0.7949 (mm) REVERT: D 810 MET cc_start: 0.8954 (mmp) cc_final: 0.8548 (mmm) REVERT: D 854 MET cc_start: 0.8540 (ttt) cc_final: 0.8291 (ttt) REVERT: D 881 MET cc_start: 0.9240 (mmp) cc_final: 0.8836 (mmm) REVERT: D 947 PHE cc_start: 0.9263 (t80) cc_final: 0.9035 (t80) REVERT: D 1098 MET cc_start: 0.6257 (mmt) cc_final: 0.6030 (mmt) outliers start: 17 outliers final: 7 residues processed: 161 average time/residue: 0.3195 time to fit residues: 83.1422 Evaluate side-chains 154 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 166 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 262 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 70 optimal weight: 0.0040 overall best weight: 2.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21556 Z= 0.169 Angle : 0.577 9.758 29220 Z= 0.280 Chirality : 0.040 0.153 3264 Planarity : 0.004 0.045 3828 Dihedral : 4.915 59.313 3016 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 1.11 % Allowed : 11.52 % Favored : 87.37 % 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: -0.40 (0.16), residues: 2728 helix: 0.68 (0.16), residues: 1174 sheet: 0.02 (0.29), residues: 356 loop : -1.29 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 PHE 0.011 0.001 PHE C1078 TYR 0.014 0.001 TYR B 834 ARG 0.005 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 2.616 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9536 (mmp) cc_final: 0.9095 (mmm) REVERT: A 566 MET cc_start: 0.5546 (ppp) cc_final: 0.4454 (ppp) REVERT: A 641 MET cc_start: 0.7978 (tmm) cc_final: 0.7730 (tmm) REVERT: A 690 MET cc_start: 0.8291 (tpt) cc_final: 0.7939 (mmm) REVERT: A 795 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5296 (p0) REVERT: A 900 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7935 (mmt) REVERT: A 921 MET cc_start: 0.7530 (ptt) cc_final: 0.6873 (ppp) REVERT: A 1106 LYS cc_start: 0.9560 (tptp) cc_final: 0.9271 (mmmt) REVERT: A 1153 MET cc_start: 0.8195 (ppp) cc_final: 0.7688 (ppp) REVERT: A 1166 MET cc_start: 0.8550 (ptp) cc_final: 0.8013 (pmm) REVERT: B 508 MET cc_start: 0.8741 (mmp) cc_final: 0.8524 (mmp) REVERT: B 616 MET cc_start: 0.7904 (mmp) cc_final: 0.7548 (mmp) REVERT: B 671 MET cc_start: 0.6559 (tpt) cc_final: 0.6151 (tpt) REVERT: B 686 MET cc_start: 0.9312 (mpp) cc_final: 0.9038 (mpp) REVERT: B 1116 MET cc_start: 0.8433 (mmt) cc_final: 0.7443 (ptm) REVERT: B 1145 MET cc_start: 0.6599 (ptt) cc_final: 0.5749 (ptt) REVERT: C 508 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8101 (mmp) REVERT: C 754 MET cc_start: 0.9438 (ppp) cc_final: 0.9022 (ppp) REVERT: C 755 LEU cc_start: 0.9707 (mt) cc_final: 0.9213 (mt) REVERT: C 783 MET cc_start: 0.8992 (tpp) cc_final: 0.8753 (tpp) REVERT: C 801 MET cc_start: 0.9382 (mmp) cc_final: 0.9146 (mmp) REVERT: C 804 MET cc_start: 0.8606 (tpp) cc_final: 0.8206 (tpp) REVERT: D 574 HIS cc_start: 0.8959 (m-70) cc_final: 0.8726 (m90) REVERT: D 604 MET cc_start: 0.8556 (tpt) cc_final: 0.8060 (tpp) REVERT: D 616 MET cc_start: 0.8093 (mmp) cc_final: 0.7812 (mmp) REVERT: D 730 LEU cc_start: 0.8328 (tp) cc_final: 0.8086 (mm) REVERT: D 810 MET cc_start: 0.8921 (mmp) cc_final: 0.8549 (mmm) REVERT: D 881 MET cc_start: 0.9243 (mmp) cc_final: 0.9012 (mmm) REVERT: D 947 PHE cc_start: 0.9250 (t80) cc_final: 0.9020 (t80) outliers start: 25 outliers final: 9 residues processed: 172 average time/residue: 0.3129 time to fit residues: 86.9713 Evaluate side-chains 159 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 224 optimal weight: 30.0000 chunk 181 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 235 optimal weight: 20.0000 chunk 66 optimal weight: 0.0670 overall best weight: 2.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21556 Z= 0.176 Angle : 0.581 9.591 29220 Z= 0.282 Chirality : 0.040 0.202 3264 Planarity : 0.004 0.044 3828 Dihedral : 4.923 59.532 3016 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.18 % Favored : 92.74 % Rotamer: Outliers : 1.29 % Allowed : 12.68 % Favored : 86.04 % 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: -0.36 (0.16), residues: 2728 helix: 0.72 (0.16), residues: 1172 sheet: 0.11 (0.29), residues: 346 loop : -1.28 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 PHE 0.014 0.001 PHE B 674 TYR 0.013 0.001 TYR B 834 ARG 0.012 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9528 (mmp) cc_final: 0.9046 (mmp) REVERT: A 566 MET cc_start: 0.5572 (ppp) cc_final: 0.4625 (ppp) REVERT: A 921 MET cc_start: 0.7738 (ptt) cc_final: 0.7443 (ppp) REVERT: A 1106 LYS cc_start: 0.9572 (tptp) cc_final: 0.9284 (mmmt) REVERT: A 1153 MET cc_start: 0.8259 (ppp) cc_final: 0.7723 (ppp) REVERT: B 508 MET cc_start: 0.8841 (mmp) cc_final: 0.8578 (mmp) REVERT: B 566 MET cc_start: 0.7920 (tpp) cc_final: 0.7654 (tpp) REVERT: B 616 MET cc_start: 0.7938 (mmp) cc_final: 0.7722 (mmp) REVERT: B 671 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6558 (tpt) REVERT: B 686 MET cc_start: 0.9318 (mpp) cc_final: 0.9056 (mpp) REVERT: B 1116 MET cc_start: 0.8362 (mmt) cc_final: 0.7346 (ptm) REVERT: B 1145 MET cc_start: 0.6480 (ptt) cc_final: 0.5519 (ptt) REVERT: C 508 MET cc_start: 0.8589 (mmt) cc_final: 0.8155 (mmp) REVERT: C 754 MET cc_start: 0.9449 (ppp) cc_final: 0.9220 (ppp) REVERT: C 783 MET cc_start: 0.9002 (tpp) cc_final: 0.8755 (tpp) REVERT: C 804 MET cc_start: 0.8704 (tpp) cc_final: 0.8305 (tpp) REVERT: D 566 MET cc_start: 0.2451 (tpp) cc_final: 0.2247 (tpt) REVERT: D 574 HIS cc_start: 0.8929 (m90) cc_final: 0.8727 (m90) REVERT: D 604 MET cc_start: 0.8554 (tpt) cc_final: 0.8028 (tpp) REVERT: D 616 MET cc_start: 0.8093 (mmp) cc_final: 0.7836 (mmp) REVERT: D 730 LEU cc_start: 0.8318 (tp) cc_final: 0.8055 (mm) REVERT: D 810 MET cc_start: 0.8933 (mmp) cc_final: 0.8571 (mmm) REVERT: D 854 MET cc_start: 0.8409 (ttt) cc_final: 0.8043 (ttt) REVERT: D 881 MET cc_start: 0.9272 (mmp) cc_final: 0.8986 (mmm) REVERT: D 947 PHE cc_start: 0.9267 (t80) cc_final: 0.9043 (t80) outliers start: 29 outliers final: 16 residues processed: 171 average time/residue: 0.3065 time to fit residues: 85.4086 Evaluate side-chains 164 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 1052 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 21 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.0060 overall best weight: 1.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21556 Z= 0.154 Angle : 0.597 10.348 29220 Z= 0.285 Chirality : 0.041 0.252 3264 Planarity : 0.004 0.043 3828 Dihedral : 4.887 57.396 3016 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 1.15 % Allowed : 13.39 % Favored : 85.46 % 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: -0.36 (0.16), residues: 2728 helix: 0.68 (0.16), residues: 1174 sheet: 0.19 (0.29), residues: 346 loop : -1.28 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 PHE 0.010 0.001 PHE C1078 TYR 0.013 0.001 TYR B 834 ARG 0.008 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9585 (mmp) cc_final: 0.9047 (mmp) REVERT: A 566 MET cc_start: 0.5620 (ppp) cc_final: 0.4961 (ppp) REVERT: A 690 MET cc_start: 0.8129 (tpt) cc_final: 0.7827 (mmm) REVERT: A 801 MET cc_start: 0.9225 (mmp) cc_final: 0.8970 (mmp) REVERT: A 804 MET cc_start: 0.8633 (mmm) cc_final: 0.7812 (tpt) REVERT: A 854 MET cc_start: 0.6332 (tmm) cc_final: 0.5946 (tmm) REVERT: A 921 MET cc_start: 0.7679 (ptt) cc_final: 0.7363 (ppp) REVERT: A 1008 LEU cc_start: 0.9673 (OUTLIER) cc_final: 0.9423 (tt) REVERT: A 1106 LYS cc_start: 0.9579 (tptp) cc_final: 0.9291 (mmmt) REVERT: A 1153 MET cc_start: 0.8268 (ppp) cc_final: 0.7708 (ppp) REVERT: A 1166 MET cc_start: 0.8764 (ptp) cc_final: 0.8212 (pmm) REVERT: B 508 MET cc_start: 0.8762 (mmp) cc_final: 0.8502 (mmp) REVERT: B 566 MET cc_start: 0.8039 (tpp) cc_final: 0.7813 (tpp) REVERT: B 671 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6530 (tpt) REVERT: B 686 MET cc_start: 0.9327 (mpp) cc_final: 0.9060 (mpp) REVERT: B 1116 MET cc_start: 0.8298 (mmt) cc_final: 0.7268 (ptm) REVERT: B 1143 MET cc_start: 0.8507 (tpt) cc_final: 0.8290 (tpt) REVERT: B 1145 MET cc_start: 0.6447 (ptt) cc_final: 0.5483 (ptt) REVERT: C 508 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8141 (mmp) REVERT: C 754 MET cc_start: 0.9456 (ppp) cc_final: 0.9216 (ppp) REVERT: C 783 MET cc_start: 0.8995 (tpp) cc_final: 0.8751 (tpp) REVERT: C 801 MET cc_start: 0.9383 (mmp) cc_final: 0.9181 (mmp) REVERT: D 566 MET cc_start: 0.2543 (tpp) cc_final: 0.2103 (tpt) REVERT: D 604 MET cc_start: 0.8645 (tpt) cc_final: 0.8086 (tpp) REVERT: D 616 MET cc_start: 0.8085 (mmp) cc_final: 0.7835 (mmp) REVERT: D 810 MET cc_start: 0.8822 (mmp) cc_final: 0.8474 (mmm) REVERT: D 854 MET cc_start: 0.8539 (ttt) cc_final: 0.8226 (ttt) REVERT: D 881 MET cc_start: 0.9283 (mmp) cc_final: 0.9002 (mmm) REVERT: D 947 PHE cc_start: 0.9244 (t80) cc_final: 0.9026 (t80) outliers start: 26 outliers final: 16 residues processed: 168 average time/residue: 0.3230 time to fit residues: 91.6672 Evaluate side-chains 166 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 629 GLU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 1052 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 899 GLN A 934 GLN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 873 ASN C 875 HIS ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21556 Z= 0.321 Angle : 0.725 14.730 29220 Z= 0.361 Chirality : 0.042 0.192 3264 Planarity : 0.005 0.048 3828 Dihedral : 5.358 57.961 3016 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 25.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.83 % Favored : 91.06 % Rotamer: Outliers : 1.68 % Allowed : 14.01 % Favored : 84.31 % 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: -0.66 (0.16), residues: 2728 helix: 0.38 (0.15), residues: 1164 sheet: 0.01 (0.29), residues: 350 loop : -1.36 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 624 HIS 0.008 0.001 HIS C 560 PHE 0.019 0.002 PHE B 618 TYR 0.018 0.002 TYR C 503 ARG 0.008 0.001 ARG A1074 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9603 (mmp) cc_final: 0.8999 (mmp) REVERT: A 566 MET cc_start: 0.5876 (ppp) cc_final: 0.3836 (ppp) REVERT: A 671 MET cc_start: 0.4959 (tpt) cc_final: 0.4681 (tpt) REVERT: A 795 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.5211 (p0) REVERT: A 804 MET cc_start: 0.8608 (mmm) cc_final: 0.7771 (tpp) REVERT: A 854 MET cc_start: 0.6675 (tmm) cc_final: 0.5949 (tmm) REVERT: A 921 MET cc_start: 0.7794 (ptt) cc_final: 0.7496 (ppp) REVERT: A 1088 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9098 (mt) REVERT: A 1106 LYS cc_start: 0.9610 (tptp) cc_final: 0.9359 (mmmt) REVERT: A 1153 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7650 (ppp) REVERT: A 1166 MET cc_start: 0.8679 (ptp) cc_final: 0.8219 (pmm) REVERT: B 508 MET cc_start: 0.8956 (mmp) cc_final: 0.8687 (mmp) REVERT: B 566 MET cc_start: 0.8203 (tpp) cc_final: 0.7849 (tpp) REVERT: B 671 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6950 (tpt) REVERT: B 724 MET cc_start: 0.8855 (mmt) cc_final: 0.8626 (mmm) REVERT: B 959 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5985 (p90) REVERT: B 1145 MET cc_start: 0.6407 (ptt) cc_final: 0.5412 (ptt) REVERT: C 754 MET cc_start: 0.9513 (ppp) cc_final: 0.9311 (ppp) REVERT: C 783 MET cc_start: 0.9034 (tpp) cc_final: 0.8815 (tpp) REVERT: C 804 MET cc_start: 0.8698 (tpp) cc_final: 0.8227 (tpp) REVERT: C 1069 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.8831 (p0) REVERT: D 566 MET cc_start: 0.4277 (tpp) cc_final: 0.4044 (tpp) REVERT: D 729 GLU cc_start: 0.6212 (OUTLIER) cc_final: 0.5703 (pm20) REVERT: D 746 LEU cc_start: 0.9306 (mt) cc_final: 0.8998 (pt) REVERT: D 810 MET cc_start: 0.9095 (mmp) cc_final: 0.8611 (mmm) REVERT: D 854 MET cc_start: 0.8675 (ttt) cc_final: 0.8446 (ttt) REVERT: D 881 MET cc_start: 0.9307 (mmp) cc_final: 0.8997 (mmm) outliers start: 38 outliers final: 19 residues processed: 176 average time/residue: 0.3017 time to fit residues: 87.7011 Evaluate side-chains 169 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 1052 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 24 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 21556 Z= 0.281 Angle : 0.688 11.412 29220 Z= 0.340 Chirality : 0.042 0.193 3264 Planarity : 0.004 0.049 3828 Dihedral : 5.436 58.864 3016 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 1.60 % Allowed : 14.80 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.16), residues: 2728 helix: 0.32 (0.15), residues: 1164 sheet: -0.08 (0.29), residues: 350 loop : -1.38 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 838 HIS 0.010 0.001 HIS D 574 PHE 0.018 0.002 PHE A 553 TYR 0.013 0.002 TYR A 706 ARG 0.006 0.001 ARG D 928 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9584 (mmp) cc_final: 0.9024 (mmp) REVERT: A 566 MET cc_start: 0.5935 (ppp) cc_final: 0.5446 (ppp) REVERT: A 671 MET cc_start: 0.5481 (tpt) cc_final: 0.5220 (tpt) REVERT: A 690 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: A 724 MET cc_start: 0.7933 (mmt) cc_final: 0.7595 (mmt) REVERT: A 804 MET cc_start: 0.8566 (mmm) cc_final: 0.8039 (tpt) REVERT: A 854 MET cc_start: 0.6777 (tmm) cc_final: 0.6499 (tmm) REVERT: A 900 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8195 (mmt) REVERT: A 921 MET cc_start: 0.7725 (ptt) cc_final: 0.7463 (ppp) REVERT: A 1012 MET cc_start: 0.6727 (mpp) cc_final: 0.6439 (pmm) REVERT: A 1013 TYR cc_start: 0.9204 (m-10) cc_final: 0.8858 (m-80) REVERT: A 1088 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9125 (mt) REVERT: A 1106 LYS cc_start: 0.9640 (tptp) cc_final: 0.9381 (mmmt) REVERT: A 1153 MET cc_start: 0.8220 (ppp) cc_final: 0.7657 (ppp) REVERT: A 1166 MET cc_start: 0.8743 (ptp) cc_final: 0.8310 (pmm) REVERT: B 508 MET cc_start: 0.8887 (mmp) cc_final: 0.8601 (mmp) REVERT: B 671 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7316 (tpt) REVERT: B 959 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.6058 (p90) REVERT: B 1058 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9437 (pp) REVERT: B 1078 PHE cc_start: 0.9047 (m-80) cc_final: 0.8450 (t80) REVERT: B 1145 MET cc_start: 0.6409 (ptt) cc_final: 0.5463 (ptt) REVERT: C 783 MET cc_start: 0.9041 (tpp) cc_final: 0.8805 (tpp) REVERT: C 1069 ASN cc_start: 0.9408 (OUTLIER) cc_final: 0.8814 (p0) REVERT: D 604 MET cc_start: 0.8806 (tpt) cc_final: 0.8169 (tpp) REVERT: D 706 TYR cc_start: 0.6925 (t80) cc_final: 0.6397 (t80) REVERT: D 746 LEU cc_start: 0.9305 (mt) cc_final: 0.8602 (pt) REVERT: D 810 MET cc_start: 0.9059 (mmp) cc_final: 0.8615 (mmm) REVERT: D 854 MET cc_start: 0.8682 (ttt) cc_final: 0.8473 (ttt) REVERT: D 881 MET cc_start: 0.9298 (mmp) cc_final: 0.9002 (mmm) outliers start: 36 outliers final: 24 residues processed: 170 average time/residue: 0.3020 time to fit residues: 85.5468 Evaluate side-chains 175 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 229 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 HIS ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 HIS D1093 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21556 Z= 0.212 Angle : 0.676 11.938 29220 Z= 0.326 Chirality : 0.042 0.219 3264 Planarity : 0.004 0.042 3828 Dihedral : 5.309 57.587 3016 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 1.55 % Allowed : 15.43 % Favored : 83.02 % 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: -0.62 (0.16), residues: 2728 helix: 0.48 (0.15), residues: 1158 sheet: -0.04 (0.29), residues: 350 loop : -1.38 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 838 HIS 0.005 0.001 HIS D1019 PHE 0.024 0.001 PHE C1078 TYR 0.012 0.001 TYR B 834 ARG 0.007 0.001 ARG D 928 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 2.733 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.9579 (mmp) cc_final: 0.9029 (mmp) REVERT: A 566 MET cc_start: 0.5930 (ppp) cc_final: 0.5411 (ppp) REVERT: A 690 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: A 724 MET cc_start: 0.7934 (mmt) cc_final: 0.7581 (mmt) REVERT: A 804 MET cc_start: 0.8512 (mmm) cc_final: 0.7967 (tpt) REVERT: A 854 MET cc_start: 0.6671 (tmm) cc_final: 0.6414 (tmm) REVERT: A 921 MET cc_start: 0.7664 (ptt) cc_final: 0.7415 (ppp) REVERT: A 1013 TYR cc_start: 0.9173 (m-10) cc_final: 0.8916 (m-80) REVERT: A 1106 LYS cc_start: 0.9645 (tptp) cc_final: 0.9382 (mmmt) REVERT: A 1143 MET cc_start: 0.6570 (mtt) cc_final: 0.5573 (pmm) REVERT: A 1153 MET cc_start: 0.8203 (ppp) cc_final: 0.7636 (ppp) REVERT: A 1166 MET cc_start: 0.8771 (ptp) cc_final: 0.8331 (pmm) REVERT: B 508 MET cc_start: 0.8799 (mmp) cc_final: 0.8505 (mmp) REVERT: B 671 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7271 (tpt) REVERT: B 959 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.6214 (p90) REVERT: B 1145 MET cc_start: 0.6397 (ptt) cc_final: 0.5608 (ptt) REVERT: C 508 MET cc_start: 0.8708 (mmt) cc_final: 0.8310 (mmp) REVERT: C 783 MET cc_start: 0.9027 (tpp) cc_final: 0.8789 (tpp) REVERT: C 1069 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.8894 (p0) REVERT: D 604 MET cc_start: 0.8705 (tpt) cc_final: 0.8065 (tpp) REVERT: D 706 TYR cc_start: 0.6934 (t80) cc_final: 0.6529 (t80) REVERT: D 746 LEU cc_start: 0.9260 (mt) cc_final: 0.9023 (pt) REVERT: D 810 MET cc_start: 0.9004 (mmp) cc_final: 0.8586 (mmm) REVERT: D 854 MET cc_start: 0.8658 (ttt) cc_final: 0.8440 (ttt) REVERT: D 881 MET cc_start: 0.9324 (mmp) cc_final: 0.8981 (mmm) outliers start: 35 outliers final: 26 residues processed: 168 average time/residue: 0.3020 time to fit residues: 84.3484 Evaluate side-chains 171 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 959 PHE Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1069 ASN Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 270 optimal weight: 0.5980 chunk 249 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21556 Z= 0.210 Angle : 0.694 12.650 29220 Z= 0.332 Chirality : 0.042 0.254 3264 Planarity : 0.004 0.050 3828 Dihedral : 5.292 59.300 3016 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.88 % Favored : 92.05 % Rotamer: Outliers : 1.37 % Allowed : 15.78 % Favored : 82.85 % 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: -0.63 (0.16), residues: 2728 helix: 0.48 (0.16), residues: 1148 sheet: -0.07 (0.29), residues: 350 loop : -1.38 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 838 HIS 0.004 0.001 HIS C 574 PHE 0.013 0.001 PHE C1077 TYR 0.011 0.001 TYR D 845 ARG 0.007 0.001 ARG D 928 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9564 (mmp) cc_final: 0.8988 (mmp) REVERT: A 566 MET cc_start: 0.5890 (ppp) cc_final: 0.5386 (ppp) REVERT: A 671 MET cc_start: 0.5317 (tpt) cc_final: 0.4937 (tpt) REVERT: A 690 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7811 (mmm) REVERT: A 724 MET cc_start: 0.7962 (mmt) cc_final: 0.7607 (mmt) REVERT: A 804 MET cc_start: 0.8364 (mmm) cc_final: 0.7787 (tpt) REVERT: A 854 MET cc_start: 0.6809 (tmm) cc_final: 0.6450 (tmm) REVERT: A 921 MET cc_start: 0.7606 (ptt) cc_final: 0.7262 (ppp) REVERT: A 1012 MET cc_start: 0.6075 (pmm) cc_final: 0.5718 (pmm) REVERT: A 1013 TYR cc_start: 0.9041 (m-10) cc_final: 0.8699 (m-80) REVERT: A 1106 LYS cc_start: 0.9657 (tptp) cc_final: 0.9396 (mmmt) REVERT: A 1143 MET cc_start: 0.6445 (mtt) cc_final: 0.5509 (pmm) REVERT: A 1153 MET cc_start: 0.8197 (ppp) cc_final: 0.7652 (ppp) REVERT: A 1166 MET cc_start: 0.8762 (ptp) cc_final: 0.8331 (pmm) REVERT: B 508 MET cc_start: 0.8764 (mmp) cc_final: 0.8497 (mmp) REVERT: B 671 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7146 (tpt) REVERT: B 1078 PHE cc_start: 0.8997 (m-80) cc_final: 0.8418 (t80) REVERT: B 1145 MET cc_start: 0.6394 (ptt) cc_final: 0.5501 (ptt) REVERT: C 508 MET cc_start: 0.8739 (mmt) cc_final: 0.8358 (mmp) REVERT: C 783 MET cc_start: 0.9022 (tpp) cc_final: 0.8792 (tpp) REVERT: C 1069 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.8847 (p0) REVERT: D 604 MET cc_start: 0.8747 (tpt) cc_final: 0.8055 (tpp) REVERT: D 706 TYR cc_start: 0.7011 (t80) cc_final: 0.6567 (t80) REVERT: D 746 LEU cc_start: 0.9241 (mt) cc_final: 0.8688 (pt) REVERT: D 810 MET cc_start: 0.9020 (mmp) cc_final: 0.8610 (mmm) REVERT: D 881 MET cc_start: 0.9341 (mmp) cc_final: 0.8982 (mmm) outliers start: 31 outliers final: 26 residues processed: 166 average time/residue: 0.3019 time to fit residues: 82.5433 Evaluate side-chains 171 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 752 CYS Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 671 MET Chi-restraints excluded: chain B residue 850 CYS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 952 ILE Chi-restraints excluded: chain B residue 970 ASP Chi-restraints excluded: chain B residue 1069 ASN Chi-restraints excluded: chain B residue 1148 VAL Chi-restraints excluded: chain C residue 908 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain D residue 521 SER Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 690 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 796 VAL Chi-restraints excluded: chain D residue 987 LEU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1166 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.0870 chunk 229 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.0570 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 0.0370 chunk 221 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.0010 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 510 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.045978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.034301 restraints weight = 238592.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.034961 restraints weight = 185157.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.035428 restraints weight = 153399.015| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21556 Z= 0.161 Angle : 0.690 12.410 29220 Z= 0.322 Chirality : 0.042 0.226 3264 Planarity : 0.004 0.042 3828 Dihedral : 5.055 58.236 3016 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 1.11 % Allowed : 16.40 % Favored : 82.49 % 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: -0.55 (0.16), residues: 2728 helix: 0.53 (0.16), residues: 1144 sheet: 0.05 (0.30), residues: 350 loop : -1.33 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 838 HIS 0.004 0.001 HIS B 574 PHE 0.026 0.001 PHE C1078 TYR 0.015 0.001 TYR B 834 ARG 0.006 0.000 ARG D 928 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.27 seconds wall clock time: 66 minutes 31.27 seconds (3991.27 seconds total)