Starting phenix.real_space_refine (version: dev) on Thu Feb 23 20:57:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/02_2023/7wta_32773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/02_2023/7wta_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_32773/02_2023/7wta_32773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/02_2023/7wta_32773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/02_2023/7wta_32773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wta_32773/02_2023/7wta_32773_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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-4877/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: 11.34, per 1000 atoms: 0.54 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: 8.63 Conformation dependent library (CDL) restraints added in 3.0 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: 2.68 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: 6.68 Time building geometry restraints manager: 9.22 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: 11875 17.47 - 34.93: 988 34.93 - 52.40: 178 52.40 - 69.86: 20 69.86 - 87.33: 15 Dihedral angle restraints: 13076 sinusoidal: 5240 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 13073 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 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. 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: 0.910 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: 6.860 Check model and map are aligned: 0.320 Process input model: 52.420 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 13.226 87.331 8032 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.21 % Favored : 91.75 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 2.455 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3359 time to fit residues: 88.6906 Evaluate side-chains 141 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6240 ------------------------------------------------------------------------------- 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: 7.9990 chunk 247 optimal weight: 4.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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** ** 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 510 ASN ** 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 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21556 Z= 0.179 Angle : 0.615 8.090 29220 Z= 0.301 Chirality : 0.041 0.291 3264 Planarity : 0.004 0.058 3828 Dihedral : 5.089 59.098 2956 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.18 % Favored : 92.74 % Rotamer Outliers : 0.31 % 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: -0.52 (0.16), residues: 2728 helix: 0.65 (0.16), residues: 1166 sheet: 0.02 (0.29), residues: 326 loop : -1.41 (0.17), residues: 1236 *********************** 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 156 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 2.597 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 152 average time/residue: 0.3202 time to fit residues: 78.9742 Evaluate side-chains 142 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2060 time to fit residues: 4.1291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 247 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 198 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 ASN 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 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 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1118 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= 0.208 Angle : 0.610 9.530 29220 Z= 0.298 Chirality : 0.040 0.160 3264 Planarity : 0.004 0.050 3828 Dihedral : 4.904 58.855 2956 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2728 helix: 0.61 (0.16), residues: 1170 sheet: -0.08 (0.28), residues: 356 loop : -1.35 (0.17), residues: 1202 *********************** 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 160 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 156 average time/residue: 0.3315 time to fit residues: 83.3319 Evaluate side-chains 151 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2151 time to fit residues: 6.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 118 optimal weight: 0.0470 chunk 166 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 235 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- 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 506 HIS B 510 ASN ** 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 864 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 21556 Z= 0.175 Angle : 0.595 9.233 29220 Z= 0.288 Chirality : 0.040 0.160 3264 Planarity : 0.004 0.045 3828 Dihedral : 4.821 58.900 2956 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.22 % Favored : 92.71 % Rotamer Outliers : 0.84 % 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: -0.46 (0.16), residues: 2728 helix: 0.65 (0.16), residues: 1172 sheet: -0.02 (0.29), residues: 350 loop : -1.33 (0.17), residues: 1206 *********************** 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 176 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 2.789 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 3 residues processed: 172 average time/residue: 0.3144 time to fit residues: 87.8260 Evaluate side-chains 147 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 2.486 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1961 time to fit residues: 4.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 3 optimal weight: 50.0000 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 chunk 181 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 66 optimal weight: 0.0470 overall best weight: 5.2086 ------------------------------------------------------------------------------- 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** A 873 ASN A 899 GLN 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 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 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 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 21556 Z= 0.297 Angle : 0.681 8.802 29220 Z= 0.341 Chirality : 0.041 0.159 3264 Planarity : 0.005 0.042 3828 Dihedral : 5.186 57.432 2956 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.83 % Favored : 91.09 % Rotamer Outliers : 1.46 % 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: -0.65 (0.16), residues: 2728 helix: 0.45 (0.15), residues: 1160 sheet: -0.07 (0.29), residues: 350 loop : -1.39 (0.17), residues: 1218 *********************** 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 180 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 2.699 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 173 average time/residue: 0.3098 time to fit residues: 88.6464 Evaluate side-chains 160 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 2.895 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2050 time to fit residues: 9.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 51 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.0980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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** B 506 HIS B 510 ASN ** 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 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 898 ASN D 899 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2022 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= 0.161 Angle : 0.639 11.560 29220 Z= 0.305 Chirality : 0.042 0.225 3264 Planarity : 0.004 0.039 3828 Dihedral : 4.947 54.849 2956 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.00 % Favored : 92.93 % Rotamer Outliers : 0.62 % 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: -0.47 (0.16), residues: 2728 helix: 0.61 (0.16), residues: 1162 sheet: 0.00 (0.29), residues: 356 loop : -1.30 (0.17), residues: 1210 *********************** 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 163 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 2.734 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 161 average time/residue: 0.3128 time to fit residues: 83.1118 Evaluate side-chains 153 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 2.795 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1961 time to fit residues: 5.7903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 681 ASN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21556 Z= 0.190 Angle : 0.648 10.538 29220 Z= 0.310 Chirality : 0.041 0.185 3264 Planarity : 0.004 0.039 3828 Dihedral : 4.907 56.803 2956 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer Outliers : 0.66 % 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: -0.41 (0.16), residues: 2728 helix: 0.71 (0.16), residues: 1162 sheet: 0.02 (0.29), residues: 360 loop : -1.33 (0.17), residues: 1206 *********************** 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 162 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 159 average time/residue: 0.3136 time to fit residues: 81.8550 Evaluate side-chains 149 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 2.592 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2194 time to fit residues: 5.8050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 24 optimal weight: 30.0000 chunk 206 optimal weight: 0.5980 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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** 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 ** 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 875 HIS ** C1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 21556 Z= 0.249 Angle : 0.688 10.003 29220 Z= 0.333 Chirality : 0.041 0.223 3264 Planarity : 0.004 0.041 3828 Dihedral : 5.113 55.802 2956 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.32 % Favored : 91.61 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.16), residues: 2728 helix: 0.65 (0.16), residues: 1154 sheet: -0.05 (0.29), residues: 360 loop : -1.33 (0.17), residues: 1214 *********************** 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 154 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 2.450 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 152 average time/residue: 0.3230 time to fit residues: 80.3765 Evaluate side-chains 146 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2038 time to fit residues: 5.0210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 244 optimal weight: 0.0070 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 overall best weight: 4.3604 ------------------------------------------------------------------------------- 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 510 ASN ** 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 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 21556 Z= 0.250 Angle : 0.711 14.091 29220 Z= 0.343 Chirality : 0.042 0.307 3264 Planarity : 0.004 0.066 3828 Dihedral : 5.248 54.243 2956 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer Outliers : 0.31 % 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: -0.61 (0.16), residues: 2728 helix: 0.53 (0.16), residues: 1154 sheet: -0.12 (0.29), residues: 360 loop : -1.38 (0.17), residues: 1214 *********************** 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 150 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 2.595 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 146 average time/residue: 0.3172 time to fit residues: 76.0904 Evaluate side-chains 146 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2016 time to fit residues: 4.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 157 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 270 optimal weight: 0.0270 chunk 249 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 510 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 21556 Z= 0.213 Angle : 0.707 13.163 29220 Z= 0.336 Chirality : 0.043 0.292 3264 Planarity : 0.004 0.055 3828 Dihedral : 5.252 55.889 2956 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.72 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2728 helix: 0.55 (0.16), residues: 1158 sheet: -0.14 (0.29), residues: 360 loop : -1.36 (0.18), residues: 1210 ********************** 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 143 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 2.627 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 142 average time/residue: 0.3149 time to fit residues: 73.8734 Evaluate side-chains 141 residues out of total 2256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1979 time to fit residues: 4.2760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 198 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 681 ASN A 934 GLN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 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 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.043603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032132 restraints weight = 249854.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.032805 restraints weight = 192804.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.033134 restraints weight = 157534.920| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 21556 Z= 0.292 Angle : 0.754 15.080 29220 Z= 0.364 Chirality : 0.043 0.303 3264 Planarity : 0.005 0.051 3828 Dihedral : 5.459 59.972 2956 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 25.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.20 % Favored : 90.73 % Rotamer Outliers : 0.31 % 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: -0.75 (0.16), residues: 2728 helix: 0.37 (0.15), residues: 1156 sheet: -0.27 (0.29), residues: 360 loop : -1.38 (0.18), residues: 1212 =============================================================================== Job complete usr+sys time: 3185.42 seconds wall clock time: 60 minutes 1.74 seconds (3601.74 seconds total)