Starting phenix.real_space_refine on Mon Dec 30 09:43:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gvh_34293/12_2024/8gvh_34293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gvh_34293/12_2024/8gvh_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_34293/12_2024/8gvh_34293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gvh_34293/12_2024/8gvh_34293.map" model { file = "/net/cci-nas-00/data/ceres_data/8gvh_34293/12_2024/8gvh_34293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gvh_34293/12_2024/8gvh_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-5532/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: 8.21, per 1000 atoms: 0.65 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 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: 1.40 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: 3.85 Time building geometry restraints manager: 3.75 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: 0.00 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: 1.390 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.530 Find NCS groups from input model: 0.380 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- 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= 0.181 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 *********************** 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 : 1.591 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: 0.2583 time to fit residues: 84.9601 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 : 1.327 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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= 0.222 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 *********************** 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 : 1.481 Fit side-chains REVERT: A 632 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 688 ASP cc_start: 0.7587 (m-30) cc_final: 0.7182 (m-30) REVERT: A 1042 MET cc_start: 0.7236 (mmm) cc_final: 0.6886 (tpt) REVERT: B 421 ARG cc_start: 0.8081 (ttp-170) cc_final: 0.7754 (ttp-110) REVERT: B 702 ASP cc_start: 0.8126 (t0) cc_final: 0.7475 (t0) REVERT: B 749 LEU cc_start: 0.8396 (tp) cc_final: 0.8140 (tp) REVERT: B 1142 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8283 (mp) outliers start: 14 outliers final: 11 residues processed: 204 average time/residue: 0.2630 time to fit residues: 78.2764 Evaluate side-chains 198 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 78 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1387 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= 0.185 Angle : 0.544 9.011 17494 Z= 0.271 Chirality : 0.040 0.153 2042 Planarity : 0.004 0.060 2190 Dihedral : 5.255 56.456 1832 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer: Outliers : 1.68 % Allowed : 11.52 % Favored : 86.81 % 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: 0.30 (0.22), residues: 1560 helix: 1.54 (0.19), residues: 808 sheet: -0.16 (0.55), residues: 76 loop : -1.48 (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 0.017 0.001 PHE A 827 TYR 0.015 0.001 TYR B 789 ARG 0.004 0.000 ARG B1200 *********************** 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 233 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 587 GLU cc_start: 0.7868 (tp30) cc_final: 0.7322 (mm-30) REVERT: A 632 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 1042 MET cc_start: 0.7247 (mmm) cc_final: 0.6860 (tpt) REVERT: B 421 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7714 (ttp-110) REVERT: B 702 ASP cc_start: 0.8067 (t0) cc_final: 0.7389 (t0) REVERT: B 749 LEU cc_start: 0.8270 (tp) cc_final: 0.7963 (tp) REVERT: B 849 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5967 (mp0) REVERT: B 1137 GLU cc_start: 0.7140 (mp0) cc_final: 0.6863 (mp0) REVERT: B 1142 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8347 (mp) outliers start: 23 outliers final: 15 residues processed: 215 average time/residue: 0.2569 time to fit residues: 79.6524 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 : 1.442 ------------------------------------------------------------------------------- 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 140 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12894 Z= 0.313 Angle : 0.602 9.949 17494 Z= 0.303 Chirality : 0.043 0.168 2042 Planarity : 0.005 0.060 2190 Dihedral : 5.256 56.392 1832 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.15 % Favored : 93.72 % Rotamer: Outliers : 2.11 % Allowed : 13.70 % Favored : 84.18 % 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: 0.11 (0.22), residues: 1560 helix: 1.32 (0.19), residues: 820 sheet: -0.10 (0.56), residues: 76 loop : -1.56 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.008 0.001 HIS B1064 PHE 0.028 0.002 PHE A 827 TYR 0.018 0.001 TYR B 789 ARG 0.005 0.000 ARG B1211 *********************** 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 222 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 1042 MET cc_start: 0.7382 (mmm) cc_final: 0.6920 (tpt) REVERT: B 399 HIS cc_start: 0.8515 (t70) cc_final: 0.8245 (t70) REVERT: B 421 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7723 (ttp-110) REVERT: B 633 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7622 (ttp) REVERT: B 702 ASP cc_start: 0.8091 (t0) cc_final: 0.7395 (t0) REVERT: B 749 LEU cc_start: 0.8305 (tp) cc_final: 0.7951 (tp) REVERT: B 849 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6264 (mp0) REVERT: B 1137 GLU cc_start: 0.7190 (mp0) cc_final: 0.6830 (mp0) REVERT: B 1142 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8397 (mp) outliers start: 29 outliers final: 16 residues processed: 205 average time/residue: 0.2582 time to fit residues: 76.4569 Evaluate side-chains 200 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 532 MET 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 1210 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12894 Z= 0.347 Angle : 0.605 8.686 17494 Z= 0.307 Chirality : 0.043 0.172 2042 Planarity : 0.005 0.059 2190 Dihedral : 5.390 58.486 1832 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.53 % Rotamer: Outliers : 2.41 % Allowed : 15.16 % Favored : 82.43 % 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: 1.14 (0.19), residues: 830 sheet: -0.13 (0.56), residues: 76 loop : -1.61 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 340 HIS 0.009 0.001 HIS B1064 PHE 0.029 0.002 PHE A 827 TYR 0.017 0.001 TYR B 789 ARG 0.005 0.000 ARG B1211 *********************** 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 221 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 688 ASP cc_start: 0.7511 (m-30) cc_final: 0.7095 (m-30) REVERT: A 1042 MET cc_start: 0.7399 (mmm) cc_final: 0.6911 (tpt) REVERT: A 1137 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: B 399 HIS cc_start: 0.8458 (t70) cc_final: 0.8210 (t70) REVERT: B 421 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7704 (ttp-110) REVERT: B 633 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: B 702 ASP cc_start: 0.8093 (t0) cc_final: 0.7485 (t0) REVERT: B 749 LEU cc_start: 0.8287 (tp) cc_final: 0.7949 (tp) REVERT: B 806 LEU cc_start: 0.8461 (tp) cc_final: 0.8190 (tt) REVERT: B 849 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: B 994 MET cc_start: 0.7890 (mmp) cc_final: 0.7446 (mmt) REVERT: B 1137 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6727 (mp0) REVERT: B 1142 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8410 (mp) outliers start: 33 outliers final: 21 residues processed: 204 average time/residue: 0.2513 time to fit residues: 74.6409 Evaluate side-chains 206 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0060 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 37 optimal weight: 0.0060 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 0.6014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12894 Z= 0.163 Angle : 0.530 9.207 17494 Z= 0.266 Chirality : 0.039 0.169 2042 Planarity : 0.004 0.059 2190 Dihedral : 5.198 56.598 1832 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.77 % Favored : 94.10 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % Favored : 81.63 % 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: 0.28 (0.22), residues: 1560 helix: 1.42 (0.19), residues: 836 sheet: 0.12 (0.56), residues: 76 loop : -1.50 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 340 HIS 0.006 0.001 HIS B 586 PHE 0.014 0.001 PHE A 827 TYR 0.014 0.001 TYR B 789 ARG 0.005 0.000 ARG B1211 *********************** 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 224 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 1042 MET cc_start: 0.7267 (mmm) cc_final: 0.6815 (tpt) REVERT: A 1137 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: B 399 HIS cc_start: 0.8426 (t70) cc_final: 0.8206 (t70) REVERT: B 702 ASP cc_start: 0.8065 (t0) cc_final: 0.7537 (t0) REVERT: B 749 LEU cc_start: 0.8202 (tp) cc_final: 0.7868 (tp) REVERT: B 806 LEU cc_start: 0.8428 (tp) cc_final: 0.8185 (tt) REVERT: B 849 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5885 (mp0) REVERT: B 994 MET cc_start: 0.7707 (mmp) cc_final: 0.7395 (mmp) REVERT: B 1137 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6721 (mp0) REVERT: B 1142 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8355 (mp) REVERT: B 1147 LYS cc_start: 0.8467 (mptt) cc_final: 0.8203 (pttt) outliers start: 28 outliers final: 17 residues processed: 210 average time/residue: 0.2566 time to fit residues: 79.0576 Evaluate side-chains 204 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 756 LEU Chi-restraints excluded: chain A residue 782 CYS 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 12894 Z= 0.366 Angle : 0.618 7.906 17494 Z= 0.312 Chirality : 0.044 0.170 2042 Planarity : 0.005 0.058 2190 Dihedral : 5.382 58.749 1832 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 2.92 % Allowed : 16.84 % 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: 0.07 (0.22), residues: 1560 helix: 1.28 (0.19), residues: 828 sheet: 0.07 (0.57), residues: 76 loop : -1.62 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.008 0.001 HIS B 586 PHE 0.027 0.002 PHE A 827 TYR 0.017 0.001 TYR B 789 ARG 0.006 0.000 ARG A 680 *********************** 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 226 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 1042 MET cc_start: 0.7422 (mmm) cc_final: 0.6938 (tpt) REVERT: A 1137 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6852 (tp30) REVERT: B 399 HIS cc_start: 0.8439 (t70) cc_final: 0.8217 (t70) REVERT: B 421 ARG cc_start: 0.7880 (ptm-80) cc_final: 0.7493 (ptp90) REVERT: B 633 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7648 (ttp) REVERT: B 702 ASP cc_start: 0.8109 (t0) cc_final: 0.7582 (t0) REVERT: B 749 LEU cc_start: 0.8241 (tp) cc_final: 0.7888 (tp) REVERT: B 849 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: B 994 MET cc_start: 0.7958 (mmp) cc_final: 0.7588 (mmt) REVERT: B 1137 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6885 (mp0) REVERT: B 1142 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (mp) REVERT: B 1147 LYS cc_start: 0.8435 (mptt) cc_final: 0.8150 (pttt) outliers start: 40 outliers final: 26 residues processed: 208 average time/residue: 0.2700 time to fit residues: 82.2807 Evaluate side-chains 211 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 776 GLU Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 846 ILE 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 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 1194 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12894 Z= 0.196 Angle : 0.551 8.653 17494 Z= 0.274 Chirality : 0.040 0.177 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.303 57.590 1832 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 2.55 % Allowed : 17.06 % Favored : 80.39 % 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: 0.23 (0.22), residues: 1560 helix: 1.37 (0.19), residues: 836 sheet: 0.14 (0.57), residues: 76 loop : -1.51 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 340 HIS 0.007 0.001 HIS B 586 PHE 0.016 0.001 PHE A 827 TYR 0.015 0.001 TYR B 789 ARG 0.007 0.000 ARG A 680 *********************** 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 223 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 1042 MET cc_start: 0.7292 (mmm) cc_final: 0.6835 (tpt) REVERT: A 1137 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: B 399 HIS cc_start: 0.8414 (t70) cc_final: 0.8207 (t70) REVERT: B 421 ARG cc_start: 0.7910 (ptm-80) cc_final: 0.7557 (ptp90) REVERT: B 702 ASP cc_start: 0.8134 (t0) cc_final: 0.7622 (t0) REVERT: B 749 LEU cc_start: 0.8148 (tp) cc_final: 0.7827 (tp) REVERT: B 849 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5968 (mp0) REVERT: B 1142 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 1147 LYS cc_start: 0.8462 (mptt) cc_final: 0.8202 (pttt) outliers start: 35 outliers final: 27 residues processed: 206 average time/residue: 0.2496 time to fit residues: 75.0156 Evaluate side-chains 213 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 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 776 GLU Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 846 ILE 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 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 591 LEU Chi-restraints excluded: chain B residue 782 CYS Chi-restraints excluded: chain B residue 783 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 0.0370 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12894 Z= 0.175 Angle : 0.550 9.576 17494 Z= 0.269 Chirality : 0.040 0.176 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.172 58.614 1832 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 17.71 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1560 helix: 1.52 (0.19), residues: 836 sheet: 0.21 (0.57), residues: 76 loop : -1.45 (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 0.020 0.001 PHE A 557 TYR 0.013 0.001 TYR B 789 ARG 0.008 0.000 ARG A 680 *********************** 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 224 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.8338 (tpp) cc_final: 0.7712 (tpp) REVERT: A 1042 MET cc_start: 0.7305 (mmm) cc_final: 0.6874 (tpt) REVERT: A 1137 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6745 (tp30) REVERT: B 399 HIS cc_start: 0.8367 (t70) cc_final: 0.8167 (t70) REVERT: B 421 ARG cc_start: 0.7998 (ptm-80) cc_final: 0.7679 (ptp90) REVERT: B 702 ASP cc_start: 0.8120 (t0) cc_final: 0.7682 (t0) REVERT: B 749 LEU cc_start: 0.8123 (tp) cc_final: 0.7791 (tp) REVERT: B 849 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5850 (mp0) REVERT: B 1142 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 1147 LYS cc_start: 0.8397 (mptt) cc_final: 0.8124 (pttt) outliers start: 34 outliers final: 28 residues processed: 207 average time/residue: 0.2527 time to fit residues: 76.0655 Evaluate side-chains 216 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 MET 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 633 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 798 PHE 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 411 ILE 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 782 CYS Chi-restraints excluded: chain B residue 783 SER 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 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 148 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 0.031 12894 Z= 0.165 Angle : 0.548 10.181 17494 Z= 0.267 Chirality : 0.039 0.179 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.109 59.366 1832 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 2.48 % Allowed : 17.64 % Favored : 79.88 % 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: 1.62 (0.19), residues: 836 sheet: 0.31 (0.57), residues: 76 loop : -1.40 (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 0.018 0.001 PHE A 557 TYR 0.013 0.001 TYR B 789 ARG 0.008 0.000 ARG A 680 ********************** 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 225 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 532 MET cc_start: 0.8296 (tpp) cc_final: 0.7777 (tpp) REVERT: A 1022 LYS cc_start: 0.8820 (mptt) cc_final: 0.8545 (mppt) REVERT: A 1042 MET cc_start: 0.7275 (mmm) cc_final: 0.6867 (tpt) REVERT: A 1137 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: B 702 ASP cc_start: 0.8117 (t0) cc_final: 0.7697 (t0) REVERT: B 749 LEU cc_start: 0.8101 (tp) cc_final: 0.7736 (tp) REVERT: B 806 LEU cc_start: 0.8114 (tt) cc_final: 0.7902 (tt) REVERT: B 849 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5817 (mp0) REVERT: B 994 MET cc_start: 0.7607 (mmp) cc_final: 0.7170 (mmt) REVERT: B 1142 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 1147 LYS cc_start: 0.8400 (mptt) cc_final: 0.8122 (pttt) outliers start: 34 outliers final: 27 residues processed: 209 average time/residue: 0.2497 time to fit residues: 77.3863 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 : 1.440 ------------------------------------------------------------------------------- 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 551 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 782 CYS Chi-restraints excluded: chain A residue 798 PHE 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 411 ILE Chi-restraints excluded: chain B residue 420 LEU 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 782 CYS Chi-restraints excluded: chain B residue 783 SER 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 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 131 optimal weight: 0.0070 chunk 37 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.162304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115704 restraints weight = 14582.502| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.81 r_work: 0.3027 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2058 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= 0.219 Angle : 0.569 9.308 17494 Z= 0.278 Chirality : 0.040 0.174 2042 Planarity : 0.004 0.058 2190 Dihedral : 5.120 58.818 1832 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.17 % Rotamer: Outliers : 2.19 % Allowed : 18.08 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1560 helix: 1.59 (0.19), residues: 836 sheet: 0.33 (0.57), residues: 76 loop : -1.39 (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 0.022 0.001 PHE A1122 TYR 0.014 0.001 TYR B 789 ARG 0.007 0.000 ARG A 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.15 seconds wall clock time: 48 minutes 35.77 seconds (2915.77 seconds total)