Starting phenix.real_space_refine on Wed Jul 30 22:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvh_34293/07_2025/8gvh_34293.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.100 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 64 5.16 5 C 8250 2.51 5 N 2100 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12602 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6266 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 41, 'TRANS': 746} Chain breaks: 3 Chain: "B" Number of atoms: 6266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6266 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 41, 'TRANS': 746} Chain breaks: 3 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.58, per 1000 atoms: 0.60 Number of scatterers: 12602 At special positions: 0 Unit cell: (97.9, 122.1, 123.2, 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 64 16.00 O 2188 8.00 N 2100 7.00 C 8250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 5 sheets defined 60.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 370 through 380 Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.510A pdb=" N HIS A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.808A pdb=" N ARG A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.626A pdb=" N LEU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 582 through 590 removed outlier: 3.853A pdb=" N ALA A 588 " --> pdb=" O GLN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.588A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 4.198A pdb=" N LEU A 622 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 623 " --> pdb=" O GLU A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 623' Processing helix chain 'A' and resid 625 through 642 Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.808A pdb=" N ILE A 686 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 705 through 734 removed outlier: 3.852A pdb=" N LEU A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 717 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.857A pdb=" N LEU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 758 removed outlier: 3.573A pdb=" N LEU A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 785 removed outlier: 3.726A pdb=" N SER A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 3.937A pdb=" N GLY A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A 799 " --> pdb=" O TRP A 795 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 801 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 802 " --> pdb=" O PHE A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 819 removed outlier: 4.304A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.527A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 825 " --> pdb=" O ARG A 821 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 826 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 827 " --> pdb=" O THR A 823 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 923 removed outlier: 3.589A pdb=" N LEU A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 904 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 935 removed outlier: 3.629A pdb=" N VAL A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 954 removed outlier: 3.521A pdb=" N SER A 953 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.601A pdb=" N MET A 993 " --> pdb=" O PRO A 990 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 994 " --> pdb=" O VAL A 991 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 990 through 994' Processing helix chain 'A' and resid 997 through 1020 removed outlier: 3.587A pdb=" N ALA A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1047 removed outlier: 4.089A pdb=" N LEU A1036 " --> pdb=" O PHE A1032 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1037 " --> pdb=" O HIS A1033 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1057 through 1068 removed outlier: 3.872A pdb=" N LEU A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1103 Processing helix chain 'A' and resid 1106 through 1111 Processing helix chain 'A' and resid 1116 through 1129 Processing helix chain 'A' and resid 1135 through 1141 Processing helix chain 'A' and resid 1142 through 1144 No H-bonds generated for 'chain 'A' and resid 1142 through 1144' Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1152 through 1157 removed outlier: 3.724A pdb=" N LYS A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A1157 " --> pdb=" O THR A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1152 through 1157' Processing helix chain 'A' and resid 1159 through 1182 Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.523A pdb=" N ILE A1192 " --> pdb=" O ALA A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1202 Processing helix chain 'A' and resid 1202 through 1208 removed outlier: 3.830A pdb=" N ARG A1206 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A1207 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE A1208 " --> pdb=" O LEU A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1202 through 1208' Processing helix chain 'A' and resid 1209 through 1217 Processing helix chain 'A' and resid 1232 through 1236 Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 393 through 408 Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.701A pdb=" N GLU B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 582 through 590 removed outlier: 3.808A pdb=" N ALA B 588 " --> pdb=" O GLN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.577A pdb=" N LEU B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 642 removed outlier: 4.116A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 removed outlier: 3.615A pdb=" N ILE B 686 " --> pdb=" O PHE B 682 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 690 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG B 691 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.894A pdb=" N PHE B 700 " --> pdb=" O TYR B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 734 removed outlier: 4.142A pdb=" N ALA B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 721 " --> pdb=" O PHE B 717 " (cutoff:3.500A) Proline residue: B 722 - end of helix removed outlier: 3.749A pdb=" N LEU B 729 " --> pdb=" O THR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.530A pdb=" N LEU B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 783 Processing helix chain 'B' and resid 788 through 810 removed outlier: 3.857A pdb=" N TRP B 799 " --> pdb=" O TRP B 795 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 801 " --> pdb=" O GLY B 797 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 802 " --> pdb=" O PHE B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 825 through 850 removed outlier: 3.534A pdb=" N ILE B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 850 " --> pdb=" O ILE B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 923 removed outlier: 3.847A pdb=" N LEU B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 912 " --> pdb=" O MET B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 935 removed outlier: 3.688A pdb=" N VAL B 934 " --> pdb=" O ARG B 930 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 930 through 935' Processing helix chain 'B' and resid 939 through 954 removed outlier: 3.668A pdb=" N LEU B 945 " --> pdb=" O PRO B 941 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 951 " --> pdb=" O MET B 947 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 953 " --> pdb=" O LEU B 949 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 997 Processing helix chain 'B' and resid 997 through 1020 removed outlier: 3.629A pdb=" N ALA B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1047 removed outlier: 3.629A pdb=" N LEU B1037 " --> pdb=" O HIS B1033 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B1038 " --> pdb=" O LEU B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1057 through 1068 removed outlier: 3.877A pdb=" N LEU B1068 " --> pdb=" O HIS B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1103 Processing helix chain 'B' and resid 1106 through 1111 removed outlier: 3.625A pdb=" N ARG B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1129 removed outlier: 4.233A pdb=" N LEU B1118 " --> pdb=" O PRO B1114 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B1119 " --> pdb=" O LEU B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1141 removed outlier: 4.113A pdb=" N GLU B1137 " --> pdb=" O ILE B1133 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG B1138 " --> pdb=" O GLN B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1144 No H-bonds generated for 'chain 'B' and resid 1142 through 1144' Processing helix chain 'B' and resid 1145 through 1149 Processing helix chain 'B' and resid 1152 through 1157 removed outlier: 3.709A pdb=" N LYS B1156 " --> pdb=" O VAL B1152 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B1157 " --> pdb=" O THR B1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1152 through 1157' Processing helix chain 'B' and resid 1159 through 1182 Processing helix chain 'B' and resid 1188 through 1208 Proline residue: B1198 - end of helix removed outlier: 3.828A pdb=" N MET B1201 " --> pdb=" O VAL B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1213 removed outlier: 4.218A pdb=" N GLU B1212 " --> pdb=" O PHE B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1237 removed outlier: 3.915A pdb=" N GLU B1236 " --> pdb=" O ASP B1232 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B1237 " --> pdb=" O GLU B1233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1232 through 1237' Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 352 removed outlier: 6.598A pdb=" N LEU A 327 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG A 345 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A 325 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU A 322 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 517 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE A 324 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 519 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU A 326 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL A 521 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN A 328 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N CYS A 523 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A 330 " --> pdb=" O CYS A 523 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 553 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA A 516 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 555 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 518 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 522 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 561 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG A 554 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 384 " --> pdb=" O MET A 532 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG A 538 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 369 Processing sheet with id=AA3, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.682A pdb=" N GLU A1085 " --> pdb=" O VAL A1070 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 352 removed outlier: 6.551A pdb=" N LEU B 327 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG B 345 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 325 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 521 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N CYS B 523 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 553 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ALA B 516 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE B 555 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 518 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 561 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG B 554 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 556 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 535 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL B 385 " --> pdb=" O PHE B 534 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG B 536 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU B 387 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ARG B 538 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 389 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA B 540 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1069 through 1071 removed outlier: 3.602A pdb=" N GLU B1085 " --> pdb=" O VAL B1070 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2005 1.32 - 1.44: 3302 1.44 - 1.56: 7474 1.56 - 1.69: 3 1.69 - 1.81: 110 Bond restraints: 12894 Sorted by residual: bond pdb=" C VAL B1197 " pdb=" N PRO B1198 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.72e+00 bond pdb=" CAR Y01 A1301 " pdb=" CBC Y01 A1301 " ideal model delta sigma weight residual 1.515 1.467 0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" CAR Y01 B1301 " pdb=" CBC Y01 B1301 " ideal model delta sigma weight residual 1.515 1.467 0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" CAK Y01 A1301 " pdb=" CBD Y01 A1301 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" CAK Y01 B1301 " pdb=" CBD Y01 B1301 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.79e+00 ... (remaining 12889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 17223 2.33 - 4.65: 226 4.65 - 6.98: 35 6.98 - 9.31: 5 9.31 - 11.63: 5 Bond angle restraints: 17494 Sorted by residual: angle pdb=" N VAL A 995 " pdb=" CA VAL A 995 " pdb=" C VAL A 995 " ideal model delta sigma weight residual 113.71 107.83 5.88 9.50e-01 1.11e+00 3.84e+01 angle pdb=" CAR Y01 B1301 " pdb=" CBC Y01 B1301 " pdb=" OAW Y01 B1301 " ideal model delta sigma weight residual 107.47 95.84 11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CAV Y01 B1301 " pdb=" CBC Y01 B1301 " pdb=" OAW Y01 B1301 " ideal model delta sigma weight residual 110.72 100.23 10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" CAR Y01 B1301 " pdb=" CBC Y01 B1301 " pdb=" CAV Y01 B1301 " ideal model delta sigma weight residual 110.42 100.38 10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CAR Y01 A1301 " pdb=" CBC Y01 A1301 " pdb=" CAV Y01 A1301 " ideal model delta sigma weight residual 110.42 100.41 10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 17489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6927 17.94 - 35.87: 742 35.87 - 53.81: 145 53.81 - 71.74: 15 71.74 - 89.68: 15 Dihedral angle restraints: 7844 sinusoidal: 3272 harmonic: 4572 Sorted by residual: dihedral pdb=" CA SER A 625 " pdb=" C SER A 625 " pdb=" N VAL A 626 " pdb=" CA VAL A 626 " ideal model delta harmonic sigma weight residual -180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA SER B 625 " pdb=" C SER B 625 " pdb=" N VAL B 626 " pdb=" CA VAL B 626 " ideal model delta harmonic sigma weight residual -180.00 -154.20 -25.80 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ILE B 411 " pdb=" C ILE B 411 " pdb=" N LYS B 412 " pdb=" CA LYS B 412 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.052: 2041 1.052 - 2.104: 0 2.104 - 3.155: 0 3.155 - 4.207: 0 4.207 - 5.259: 1 Chirality restraints: 2042 Sorted by residual: chirality pdb=" CBB Y01 B1301 " pdb=" CAC Y01 B1301 " pdb=" CAO Y01 B1301 " pdb=" CBE Y01 B1301 " both_signs ideal model delta sigma weight residual False 2.58 -2.68 5.26 2.00e-01 2.50e+01 6.91e+02 chirality pdb=" CBC Y01 B1301 " pdb=" CAR Y01 B1301 " pdb=" CAV Y01 B1301 " pdb=" OAW Y01 B1301 " both_signs ideal model delta sigma weight residual False -2.54 -3.09 0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CBB Y01 A1301 " pdb=" CAC Y01 A1301 " pdb=" CAO Y01 A1301 " pdb=" CBE Y01 A1301 " both_signs ideal model delta sigma weight residual False 2.58 2.14 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 2039 not shown) Planarity restraints: 2190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 693 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 694 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 693 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 694 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 694 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 694 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B1197 " 0.038 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B1198 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B1198 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1198 " 0.033 5.00e-02 4.00e+02 ... (remaining 2187 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2058 2.77 - 3.30: 11741 3.30 - 3.83: 19119 3.83 - 4.37: 21453 4.37 - 4.90: 39189 Nonbonded interactions: 93560 Sorted by model distance: nonbonded pdb=" OE1 GLU A 775 " pdb=" OH TYR A 789 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLU B 775 " pdb=" OH TYR B 789 " model vdw 2.247 3.040 nonbonded pdb=" O PHE B1208 " pdb=" OG1 THR B1209 " model vdw 2.254 3.040 nonbonded pdb=" NE2 HIS A 429 " pdb=" O LEU A 547 " model vdw 2.299 3.120 nonbonded pdb=" O LEU B 730 " pdb=" OG1 THR B 734 " model vdw 2.314 3.040 ... (remaining 93555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.720 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.003 0.048 12894 Z= 0.139 Angle : 0.656 11.633 17494 Z= 0.332 Chirality : 0.125 5.259 2042 Planarity : 0.005 0.061 2190 Dihedral : 15.156 89.677 4868 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1560 helix: 0.79 (0.19), residues: 814 sheet: -0.57 (0.53), residues: 76 loop : -1.56 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 992 HIS 0.005 0.001 HIS B 399 PHE 0.015 0.001 PHE B 827 TYR 0.009 0.001 TYR B1136 ARG 0.008 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.21220 ( 600) hydrogen bonds : angle 5.93770 ( 1737) covalent geometry : bond 0.00282 (12894) covalent geometry : angle 0.65602 (17494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.330 Fit side-chains REVERT: A 698 SER cc_start: 0.8470 (t) cc_final: 0.8204 (t) REVERT: A 1042 MET cc_start: 0.7033 (mmm) cc_final: 0.6740 (tpt) REVERT: B 333 ASP cc_start: 0.7234 (t70) cc_final: 0.6737 (t70) REVERT: B 421 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7857 (mtp180) REVERT: B 702 ASP cc_start: 0.8017 (t0) cc_final: 0.7422 (t0) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2557 time to fit residues: 84.5904 Evaluate side-chains 181 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117786 restraints weight = 14526.708| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.81 r_work: 0.3039 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12894 Z= 0.146 Angle : 0.594 9.244 17494 Z= 0.298 Chirality : 0.041 0.157 2042 Planarity : 0.005 0.062 2190 Dihedral : 5.920 57.902 1832 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 1.02 % Allowed : 8.89 % Favored : 90.09 % 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: 0.09 (0.22), residues: 1560 helix: 1.32 (0.19), residues: 806 sheet: -0.41 (0.54), residues: 76 loop : -1.48 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.004 0.001 HIS A 586 PHE 0.017 0.001 PHE A 827 TYR 0.015 0.001 TYR B 789 ARG 0.005 0.000 ARG B1200 Details of bonding type rmsd hydrogen bonds : bond 0.05737 ( 600) hydrogen bonds : angle 4.44349 ( 1737) covalent geometry : bond 0.00339 (12894) covalent geometry : angle 0.59421 (17494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.275 Fit side-chains REVERT: A 632 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 688 ASP cc_start: 0.7455 (m-30) cc_final: 0.7067 (m-30) REVERT: A 745 MET cc_start: 0.8409 (ttm) cc_final: 0.8183 (mtm) REVERT: A 1042 MET cc_start: 0.7294 (mmm) cc_final: 0.6672 (tpt) REVERT: B 421 ARG cc_start: 0.8187 (ttp-170) cc_final: 0.7868 (ttp-110) REVERT: B 587 GLU cc_start: 0.8071 (tp30) cc_final: 0.7587 (mm-30) REVERT: B 620 GLU cc_start: 0.6970 (tp30) cc_final: 0.6749 (tp30) REVERT: B 702 ASP cc_start: 0.7928 (t0) cc_final: 0.7245 (t0) REVERT: B 1142 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7888 (mp) outliers start: 14 outliers final: 11 residues processed: 204 average time/residue: 0.2346 time to fit residues: 70.3998 Evaluate side-chains 199 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116747 restraints weight = 14696.044| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.83 r_work: 0.3032 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12894 Z= 0.135 Angle : 0.555 8.586 17494 Z= 0.278 Chirality : 0.040 0.156 2042 Planarity : 0.004 0.060 2190 Dihedral : 5.286 55.837 1832 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 1.60 % Allowed : 11.73 % Favored : 86.66 % 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: 0.24 (0.22), residues: 1560 helix: 1.49 (0.19), residues: 808 sheet: -0.18 (0.55), residues: 76 loop : -1.50 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 340 HIS 0.005 0.001 HIS B 586 PHE 0.018 0.001 PHE A 827 TYR 0.016 0.001 TYR B 789 ARG 0.003 0.000 ARG B1200 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 600) hydrogen bonds : angle 4.18452 ( 1737) covalent geometry : bond 0.00324 (12894) covalent geometry : angle 0.55531 (17494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.508 Fit side-chains revert: symmetry clash REVERT: A 539 GLU cc_start: 0.7995 (pm20) cc_final: 0.7748 (pm20) REVERT: A 632 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 1042 MET cc_start: 0.7387 (mmm) cc_final: 0.6722 (tpt) REVERT: B 421 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7811 (ttp-110) REVERT: B 587 GLU cc_start: 0.7994 (tp30) cc_final: 0.7489 (mm-30) REVERT: B 620 GLU cc_start: 0.6955 (tp30) cc_final: 0.6745 (tp30) REVERT: B 702 ASP cc_start: 0.7884 (t0) cc_final: 0.7175 (t0) REVERT: B 849 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: B 1137 GLU cc_start: 0.7555 (mp0) cc_final: 0.7250 (mp0) REVERT: B 1142 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7998 (mp) outliers start: 22 outliers final: 15 residues processed: 208 average time/residue: 0.2453 time to fit residues: 74.0007 Evaluate side-chains 206 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111775 restraints weight = 14573.983| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.84 r_work: 0.2962 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12894 Z= 0.207 Angle : 0.608 7.295 17494 Z= 0.308 Chirality : 0.043 0.170 2042 Planarity : 0.005 0.060 2190 Dihedral : 5.308 57.028 1832 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.72 % Rotamer: Outliers : 2.19 % Allowed : 13.27 % Favored : 84.55 % 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: 0.03 (0.22), residues: 1560 helix: 1.27 (0.19), residues: 818 sheet: -0.21 (0.56), residues: 76 loop : -1.59 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.009 0.001 HIS B1064 PHE 0.029 0.002 PHE A 827 TYR 0.018 0.001 TYR B 789 ARG 0.004 0.000 ARG B1211 Details of bonding type rmsd hydrogen bonds : bond 0.06296 ( 600) hydrogen bonds : angle 4.31620 ( 1737) covalent geometry : bond 0.00523 (12894) covalent geometry : angle 0.60781 (17494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 539 GLU cc_start: 0.8075 (pm20) cc_final: 0.7864 (pm20) REVERT: A 632 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 1042 MET cc_start: 0.7778 (mmm) cc_final: 0.7087 (tpt) REVERT: B 399 HIS cc_start: 0.8875 (t70) cc_final: 0.8549 (t70) REVERT: B 421 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7878 (ttp-110) REVERT: B 587 GLU cc_start: 0.8257 (tp30) cc_final: 0.7855 (tp30) REVERT: B 620 GLU cc_start: 0.7369 (tp30) cc_final: 0.7127 (tp30) REVERT: B 633 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7492 (ttp) REVERT: B 702 ASP cc_start: 0.8048 (t0) cc_final: 0.7335 (t0) REVERT: B 849 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: B 1137 GLU cc_start: 0.7794 (mp0) cc_final: 0.7389 (mp0) REVERT: B 1142 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8360 (mp) outliers start: 30 outliers final: 16 residues processed: 203 average time/residue: 0.2400 time to fit residues: 71.3576 Evaluate side-chains 201 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.113845 restraints weight = 14616.104| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.80 r_work: 0.3003 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12894 Z= 0.153 Angle : 0.556 7.824 17494 Z= 0.282 Chirality : 0.041 0.164 2042 Planarity : 0.004 0.059 2190 Dihedral : 5.287 57.465 1832 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 2.19 % Allowed : 14.87 % Favored : 82.94 % 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: 0.09 (0.22), residues: 1560 helix: 1.26 (0.19), residues: 832 sheet: -0.13 (0.56), residues: 76 loop : -1.54 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 340 HIS 0.007 0.001 HIS B 586 PHE 0.022 0.001 PHE A 827 TYR 0.016 0.001 TYR B 789 ARG 0.005 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 600) hydrogen bonds : angle 4.16843 ( 1737) covalent geometry : bond 0.00379 (12894) covalent geometry : angle 0.55554 (17494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 539 GLU cc_start: 0.8047 (pm20) cc_final: 0.7801 (pm20) REVERT: A 632 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 1042 MET cc_start: 0.7538 (mmm) cc_final: 0.6794 (tpt) REVERT: A 1137 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6565 (tp30) REVERT: B 399 HIS cc_start: 0.8907 (t70) cc_final: 0.8607 (t70) REVERT: B 421 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7815 (ttp-110) REVERT: B 587 GLU cc_start: 0.8085 (tp30) cc_final: 0.7640 (tp30) REVERT: B 620 GLU cc_start: 0.7281 (tp30) cc_final: 0.6985 (tp30) REVERT: B 633 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7237 (ttp) REVERT: B 702 ASP cc_start: 0.7918 (t0) cc_final: 0.7277 (t0) REVERT: B 849 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: B 994 MET cc_start: 0.8061 (mmp) cc_final: 0.7663 (mmt) REVERT: B 1137 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7221 (mp0) REVERT: B 1142 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8192 (mp) outliers start: 30 outliers final: 20 residues processed: 200 average time/residue: 0.2485 time to fit residues: 72.8542 Evaluate side-chains 204 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.112270 restraints weight = 14805.335| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.94 r_work: 0.2980 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12894 Z= 0.182 Angle : 0.582 7.499 17494 Z= 0.295 Chirality : 0.042 0.167 2042 Planarity : 0.005 0.059 2190 Dihedral : 5.344 58.753 1832 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 2.70 % Allowed : 15.52 % Favored : 81.78 % 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: 0.05 (0.22), residues: 1560 helix: 1.22 (0.19), residues: 832 sheet: -0.07 (0.56), residues: 76 loop : -1.56 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.008 0.001 HIS B1064 PHE 0.024 0.002 PHE A 827 TYR 0.016 0.001 TYR B 789 ARG 0.004 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.05872 ( 600) hydrogen bonds : angle 4.20322 ( 1737) covalent geometry : bond 0.00457 (12894) covalent geometry : angle 0.58242 (17494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 539 GLU cc_start: 0.7998 (pm20) cc_final: 0.7695 (pm20) REVERT: A 632 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 1042 MET cc_start: 0.7420 (mmm) cc_final: 0.6634 (tpt) REVERT: A 1137 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6483 (tp30) REVERT: B 399 HIS cc_start: 0.8920 (t70) cc_final: 0.8636 (t70) REVERT: B 421 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7787 (ttp-110) REVERT: B 587 GLU cc_start: 0.7918 (tp30) cc_final: 0.7450 (tp30) REVERT: B 620 GLU cc_start: 0.7230 (tp30) cc_final: 0.6870 (tp30) REVERT: B 633 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7171 (ttp) REVERT: B 702 ASP cc_start: 0.7823 (t0) cc_final: 0.7187 (t0) REVERT: B 849 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: B 1137 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7259 (mp0) REVERT: B 1142 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8052 (mp) REVERT: B 1147 LYS cc_start: 0.8281 (mptt) cc_final: 0.7901 (pttt) outliers start: 37 outliers final: 25 residues processed: 211 average time/residue: 0.2452 time to fit residues: 75.8396 Evaluate side-chains 211 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111559 restraints weight = 14529.793| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.73 r_work: 0.3016 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12894 Z= 0.114 Angle : 0.539 8.856 17494 Z= 0.268 Chirality : 0.040 0.174 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.251 57.113 1832 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.83 % Favored : 94.04 % Rotamer: Outliers : 2.41 % Allowed : 16.47 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1560 helix: 1.44 (0.19), residues: 836 sheet: 0.08 (0.56), residues: 76 loop : -1.48 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 340 HIS 0.007 0.001 HIS B 586 PHE 0.015 0.001 PHE B1122 TYR 0.014 0.001 TYR B 789 ARG 0.006 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 600) hydrogen bonds : angle 3.98894 ( 1737) covalent geometry : bond 0.00267 (12894) covalent geometry : angle 0.53907 (17494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.7832 (ttm) cc_final: 0.7478 (ttm) REVERT: A 539 GLU cc_start: 0.7962 (pm20) cc_final: 0.7701 (pm20) REVERT: A 632 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 1042 MET cc_start: 0.7307 (mmm) cc_final: 0.6578 (tpt) REVERT: A 1137 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6352 (tp30) REVERT: B 399 HIS cc_start: 0.8857 (t70) cc_final: 0.8587 (t70) REVERT: B 587 GLU cc_start: 0.7776 (tp30) cc_final: 0.7149 (mm-30) REVERT: B 620 GLU cc_start: 0.7122 (tp30) cc_final: 0.6779 (tp30) REVERT: B 702 ASP cc_start: 0.7814 (t0) cc_final: 0.7218 (t0) REVERT: B 849 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5635 (mp0) REVERT: B 925 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7676 (ttp-110) REVERT: B 994 MET cc_start: 0.7892 (mmp) cc_final: 0.7544 (mmt) REVERT: B 1137 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7163 (mp0) REVERT: B 1142 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 1147 LYS cc_start: 0.8259 (mptt) cc_final: 0.7874 (pttt) outliers start: 33 outliers final: 21 residues processed: 215 average time/residue: 0.2787 time to fit residues: 87.1787 Evaluate side-chains 214 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1194 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS B 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105503 restraints weight = 15042.418| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.69 r_work: 0.2941 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12894 Z= 0.179 Angle : 0.602 10.229 17494 Z= 0.300 Chirality : 0.042 0.166 2042 Planarity : 0.005 0.058 2190 Dihedral : 5.317 59.547 1832 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 17.27 % Favored : 80.25 % 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: 0.19 (0.22), residues: 1560 helix: 1.33 (0.19), residues: 832 sheet: 0.10 (0.58), residues: 76 loop : -1.50 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.007 0.001 HIS B 586 PHE 0.025 0.002 PHE A1122 TYR 0.016 0.001 TYR B 789 ARG 0.007 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.05766 ( 600) hydrogen bonds : angle 4.14192 ( 1737) covalent geometry : bond 0.00449 (12894) covalent geometry : angle 0.60225 (17494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.7960 (ttm) cc_final: 0.7551 (ttm) REVERT: A 539 GLU cc_start: 0.7942 (pm20) cc_final: 0.7645 (pm20) REVERT: A 632 GLN cc_start: 0.7634 (tm-30) cc_final: 0.7380 (tm-30) REVERT: A 1042 MET cc_start: 0.7295 (mmm) cc_final: 0.6541 (tpt) REVERT: A 1137 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6382 (tp30) REVERT: B 399 HIS cc_start: 0.8871 (t70) cc_final: 0.8600 (t70) REVERT: B 421 ARG cc_start: 0.7942 (ptm-80) cc_final: 0.7360 (ptp90) REVERT: B 587 GLU cc_start: 0.7834 (tp30) cc_final: 0.7470 (tp30) REVERT: B 620 GLU cc_start: 0.7106 (tp30) cc_final: 0.6761 (tp30) REVERT: B 702 ASP cc_start: 0.7824 (t0) cc_final: 0.7255 (t0) REVERT: B 849 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: B 925 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7585 (ttp-110) REVERT: B 1137 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7135 (mp0) REVERT: B 1142 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7963 (mp) REVERT: B 1147 LYS cc_start: 0.8195 (mptt) cc_final: 0.7796 (pttt) outliers start: 34 outliers final: 26 residues processed: 208 average time/residue: 0.2375 time to fit residues: 72.4646 Evaluate side-chains 215 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1201 MET Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1143 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 125 optimal weight: 0.0670 chunk 42 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117409 restraints weight = 14453.776| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.79 r_work: 0.3026 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12894 Z= 0.109 Angle : 0.547 10.130 17494 Z= 0.267 Chirality : 0.039 0.178 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.206 59.054 1832 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.45 % Favored : 94.42 % Rotamer: Outliers : 2.11 % Allowed : 17.93 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1560 helix: 1.53 (0.19), residues: 834 sheet: 0.14 (0.57), residues: 76 loop : -1.45 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.006 0.001 HIS B 586 PHE 0.014 0.001 PHE B 324 TYR 0.014 0.001 TYR B 789 ARG 0.008 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 600) hydrogen bonds : angle 3.91030 ( 1737) covalent geometry : bond 0.00251 (12894) covalent geometry : angle 0.54723 (17494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.7867 (ttm) cc_final: 0.7536 (ttm) REVERT: A 539 GLU cc_start: 0.7980 (pm20) cc_final: 0.7716 (pm20) REVERT: A 632 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 1042 MET cc_start: 0.7342 (mmm) cc_final: 0.6945 (tpt) REVERT: A 1137 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: B 399 HIS cc_start: 0.8822 (t70) cc_final: 0.8557 (t70) REVERT: B 421 ARG cc_start: 0.8050 (ptm-80) cc_final: 0.7501 (ptp90) REVERT: B 587 GLU cc_start: 0.7700 (tp30) cc_final: 0.7076 (mm-30) REVERT: B 620 GLU cc_start: 0.7123 (tp30) cc_final: 0.6898 (tp30) REVERT: B 702 ASP cc_start: 0.7912 (t0) cc_final: 0.7391 (t0) REVERT: B 849 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5585 (mp0) REVERT: B 925 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7621 (ttp-110) REVERT: B 1142 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 1147 LYS cc_start: 0.8199 (mptt) cc_final: 0.7801 (pttt) outliers start: 29 outliers final: 21 residues processed: 216 average time/residue: 0.2416 time to fit residues: 76.8780 Evaluate side-chains 212 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 993 MET Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 798 PHE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117492 restraints weight = 14383.163| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.78 r_work: 0.3030 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12894 Z= 0.109 Angle : 0.561 10.158 17494 Z= 0.271 Chirality : 0.040 0.176 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.108 59.666 1832 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 1.82 % Allowed : 18.80 % Favored : 79.37 % 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: 0.53 (0.22), residues: 1560 helix: 1.63 (0.19), residues: 836 sheet: 0.26 (0.58), residues: 76 loop : -1.41 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.006 0.001 HIS B 586 PHE 0.018 0.001 PHE B1122 TYR 0.013 0.001 TYR B 789 ARG 0.008 0.000 ARG A 680 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 600) hydrogen bonds : angle 3.84923 ( 1737) covalent geometry : bond 0.00256 (12894) covalent geometry : angle 0.56114 (17494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.7903 (ttm) cc_final: 0.7496 (ttm) REVERT: A 539 GLU cc_start: 0.7972 (pm20) cc_final: 0.7726 (pm20) REVERT: A 632 GLN cc_start: 0.7687 (tm-30) cc_final: 0.7449 (tm-30) REVERT: A 1042 MET cc_start: 0.7558 (mmm) cc_final: 0.6966 (tpt) REVERT: A 1137 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6404 (tp30) REVERT: B 375 GLU cc_start: 0.7907 (tp30) cc_final: 0.7664 (mt-10) REVERT: B 399 HIS cc_start: 0.8802 (t70) cc_final: 0.8546 (t70) REVERT: B 421 ARG cc_start: 0.8099 (ptm-80) cc_final: 0.7550 (ptp90) REVERT: B 587 GLU cc_start: 0.7686 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 620 GLU cc_start: 0.7148 (tp30) cc_final: 0.6821 (tp30) REVERT: B 702 ASP cc_start: 0.7906 (t0) cc_final: 0.7399 (t0) REVERT: B 849 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5573 (mp0) REVERT: B 1142 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 1147 LYS cc_start: 0.8209 (mptt) cc_final: 0.7814 (pttt) outliers start: 25 outliers final: 19 residues processed: 210 average time/residue: 0.2353 time to fit residues: 72.6387 Evaluate side-chains 214 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1137 GLU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 321 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 590 TYR Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1046 CYS Chi-restraints excluded: chain B residue 1142 LEU Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1210 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116916 restraints weight = 14440.724| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.79 r_work: 0.3020 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12894 Z= 0.119 Angle : 0.567 10.031 17494 Z= 0.274 Chirality : 0.040 0.179 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.090 58.257 1832 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 1.82 % Allowed : 18.95 % Favored : 79.23 % 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: 0.57 (0.22), residues: 1560 helix: 1.65 (0.19), residues: 836 sheet: 0.31 (0.58), residues: 76 loop : -1.38 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 340 HIS 0.007 0.001 HIS B 586 PHE 0.019 0.001 PHE B1122 TYR 0.013 0.001 TYR B 789 ARG 0.008 0.000 ARG B 925 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 600) hydrogen bonds : angle 3.83920 ( 1737) covalent geometry : bond 0.00285 (12894) covalent geometry : angle 0.56660 (17494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5766.59 seconds wall clock time: 100 minutes 40.07 seconds (6040.07 seconds total)