Starting phenix.real_space_refine on Thu Mar 5 22:21:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybj_33723/03_2026/7ybj_33723.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 16419 2.51 5 N 4296 2.21 5 O 4887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25719 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8573 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 53, 'TRANS': 1040} Chain breaks: 5 Chain: "B" Number of atoms: 8573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8573 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 53, 'TRANS': 1040} Chain breaks: 5 Chain: "C" Number of atoms: 8573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8573 Classifications: {'peptide': 1094} Link IDs: {'PTRANS': 53, 'TRANS': 1040} Chain breaks: 5 Time building chain proxies: 5.56, per 1000 atoms: 0.22 Number of scatterers: 25719 At special positions: 0 Unit cell: (148.72, 146.64, 196.56, 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 117 16.00 O 4887 8.00 N 4296 7.00 C 16419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6156 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 44 sheets defined 27.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.624A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.995A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.182A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.288A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.963A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 639 removed outlier: 4.035A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.575A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.550A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.801A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.519A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.219A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.861A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.100A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.203A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.745A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.099A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.517A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.591A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.967A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.839A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.565A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.540A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.284A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.189A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.605A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.985A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 4.039A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.600A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.991A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.649A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.630A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.292A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.209A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 3.593A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.163A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 43 current: chain 'B' and resid 538 through 543 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 547 current: chain 'B' and resid 573 through 577 removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 85 current: chain 'A' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 126 through 131 current: chain 'A' and resid 152 through 160 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.609A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.265A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.585A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.862A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.541A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.555A pdb=" N ILE C 788 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.853A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.222A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.176A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.960A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 7.003A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.491A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 507 through 513 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.598A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.859A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.270A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.550A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.395A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.046A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 84 through 85 current: chain 'C' and resid 116 through 121 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 126 through 131 current: chain 'C' and resid 153 through 160 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.493A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.381A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.591A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.939A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.588A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.506A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.238A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.590A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 1004 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8314 1.34 - 1.47: 6489 1.47 - 1.59: 11366 1.59 - 1.71: 0 1.71 - 1.83: 147 Bond restraints: 26316 Sorted by residual: bond pdb=" C PRO C 25 " pdb=" N PRO C 26 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.12e-02 7.97e+03 1.41e+01 bond pdb=" CG1 ILE A 997 " pdb=" CD1 ILE A 997 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.67e+00 bond pdb=" CG1 ILE B 997 " pdb=" CD1 ILE B 997 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.70e+00 bond pdb=" CG1 ILE C 997 " pdb=" CD1 ILE C 997 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.55e+00 bond pdb=" C THR C 630 " pdb=" N PRO C 631 " ideal model delta sigma weight residual 1.335 1.351 -0.016 8.70e-03 1.32e+04 3.40e+00 ... (remaining 26311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 34931 1.89 - 3.79: 786 3.79 - 5.68: 60 5.68 - 7.58: 9 7.58 - 9.47: 7 Bond angle restraints: 35793 Sorted by residual: angle pdb=" C THR A 19 " pdb=" CA THR A 19 " pdb=" CB THR A 19 " ideal model delta sigma weight residual 116.54 109.40 7.14 1.15e+00 7.56e-01 3.85e+01 angle pdb=" C THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta sigma weight residual 116.54 109.59 6.95 1.15e+00 7.56e-01 3.66e+01 angle pdb=" C GLN C 23 " pdb=" CA GLN C 23 " pdb=" CB GLN C 23 " ideal model delta sigma weight residual 115.89 110.40 5.49 1.32e+00 5.74e-01 1.73e+01 angle pdb=" N ILE C 666 " pdb=" CA ILE C 666 " pdb=" C ILE C 666 " ideal model delta sigma weight residual 111.48 107.90 3.58 9.40e-01 1.13e+00 1.45e+01 angle pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" N THR A 20 " ideal model delta sigma weight residual 119.52 116.52 3.00 7.90e-01 1.60e+00 1.44e+01 ... (remaining 35788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14457 17.97 - 35.94: 1015 35.94 - 53.91: 169 53.91 - 71.88: 43 71.88 - 89.85: 24 Dihedral angle restraints: 15708 sinusoidal: 6144 harmonic: 9564 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 174.54 -81.54 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 146.39 33.61 0 5.00e+00 4.00e-02 4.52e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 36.31 56.69 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 15705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2504 0.034 - 0.068: 1017 0.068 - 0.103: 367 0.103 - 0.137: 137 0.137 - 0.171: 19 Chirality restraints: 4044 Sorted by residual: chirality pdb=" CB THR B 274 " pdb=" CA THR B 274 " pdb=" OG1 THR B 274 " pdb=" CG2 THR B 274 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA ILE B 95 " pdb=" N ILE B 95 " pdb=" C ILE B 95 " pdb=" CB ILE B 95 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 4041 not shown) Planarity restraints: 4644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 25 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 275 " 0.017 2.00e-02 2.50e+03 1.45e-02 3.69e+00 pdb=" CG PHE C 275 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 275 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 275 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 275 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 275 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 275 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 527 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.025 5.00e-02 4.00e+02 ... (remaining 4641 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 388 2.67 - 3.23: 25289 3.23 - 3.78: 39211 3.78 - 4.34: 54197 4.34 - 4.90: 88320 Nonbonded interactions: 207405 Sorted by model distance: nonbonded pdb=" OG SER A 31 " pdb=" OG SER A 60 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.183 3.040 nonbonded pdb=" OG SER C 31 " pdb=" OG SER C 60 " model vdw 2.204 3.040 ... (remaining 207400 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.020 Find NCS groups from input model: 0.460 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.084 26358 Z= 0.165 Angle : 0.674 9.473 35877 Z= 0.397 Chirality : 0.045 0.171 4044 Planarity : 0.004 0.065 4644 Dihedral : 13.012 89.848 9426 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3246 helix: 0.89 (0.20), residues: 714 sheet: 0.10 (0.21), residues: 615 loop : -0.88 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 357 TYR 0.022 0.001 TYR C 265 PHE 0.033 0.002 PHE C 275 TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00335 (26316) covalent geometry : angle 0.67264 (35793) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.00198 ( 84) hydrogen bonds : bond 0.14112 ( 1004) hydrogen bonds : angle 7.48090 ( 2715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: B 1017 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7325 (tm-30) REVERT: C 777 ASN cc_start: 0.7138 (m-40) cc_final: 0.6831 (m-40) REVERT: C 864 LEU cc_start: 0.8523 (tt) cc_final: 0.7841 (tp) REVERT: C 900 MET cc_start: 0.8104 (mtp) cc_final: 0.7819 (mtt) REVERT: C 1017 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7312 (tm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1487 time to fit residues: 69.8150 Evaluate side-chains 193 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 784 GLN B 913 GLN B1002 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 969 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.165278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123871 restraints weight = 48063.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120780 restraints weight = 37560.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122837 restraints weight = 38063.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.122851 restraints weight = 25015.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123381 restraints weight = 21824.708| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26358 Z= 0.137 Angle : 0.587 9.365 35877 Z= 0.305 Chirality : 0.045 0.177 4044 Planarity : 0.004 0.047 4644 Dihedral : 4.803 32.941 3516 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.84 % Allowed : 6.51 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3246 helix: 1.59 (0.20), residues: 729 sheet: 0.04 (0.20), residues: 675 loop : -0.89 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 158 TYR 0.023 0.001 TYR A 265 PHE 0.022 0.002 PHE A 817 TRP 0.010 0.001 TRP A 104 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (26316) covalent geometry : angle 0.58588 (35793) SS BOND : bond 0.00360 ( 42) SS BOND : angle 0.94941 ( 84) hydrogen bonds : bond 0.03929 ( 1004) hydrogen bonds : angle 5.78825 ( 2715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1118 ASP cc_start: 0.7973 (t0) cc_final: 0.7669 (t0) REVERT: B 777 ASN cc_start: 0.7630 (m-40) cc_final: 0.7312 (m-40) REVERT: B 1017 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 974 SER cc_start: 0.8680 (t) cc_final: 0.8465 (m) REVERT: C 1017 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7480 (tm-30) outliers start: 24 outliers final: 15 residues processed: 234 average time/residue: 0.1418 time to fit residues: 56.2847 Evaluate side-chains 199 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 227 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 145 ASN A 580 GLN A 804 GLN B 784 GLN B 901 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1088 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.166263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125078 restraints weight = 48200.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122605 restraints weight = 44521.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124352 restraints weight = 43870.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124551 restraints weight = 25356.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125625 restraints weight = 22934.688| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 26358 Z= 0.239 Angle : 0.651 10.106 35877 Z= 0.337 Chirality : 0.047 0.182 4044 Planarity : 0.005 0.058 4644 Dihedral : 5.004 31.747 3516 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.67 % Allowed : 10.96 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3246 helix: 1.38 (0.19), residues: 732 sheet: -0.13 (0.20), residues: 705 loop : -0.99 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 158 TYR 0.024 0.002 TYR A1067 PHE 0.037 0.002 PHE B 817 TRP 0.007 0.001 TRP C 633 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00558 (26316) covalent geometry : angle 0.64909 (35793) SS BOND : bond 0.00456 ( 42) SS BOND : angle 1.22962 ( 84) hydrogen bonds : bond 0.04160 ( 1004) hydrogen bonds : angle 5.82278 ( 2715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8063 (tp40) cc_final: 0.7843 (tp-100) REVERT: A 83 VAL cc_start: 0.7293 (OUTLIER) cc_final: 0.6933 (m) REVERT: B 83 VAL cc_start: 0.7067 (OUTLIER) cc_final: 0.6710 (m) REVERT: B 1017 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7740 (tm-30) REVERT: C 360 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 974 SER cc_start: 0.8728 (t) cc_final: 0.8499 (m) REVERT: C 1017 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7677 (tm-30) outliers start: 48 outliers final: 27 residues processed: 231 average time/residue: 0.1393 time to fit residues: 55.4687 Evaluate side-chains 210 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 278 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 211 optimal weight: 0.4980 chunk 162 optimal weight: 0.5980 chunk 305 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 254 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 969 ASN B 804 GLN B 957 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 777 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.168106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126128 restraints weight = 47672.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.122745 restraints weight = 37189.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124033 restraints weight = 41405.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124762 restraints weight = 25848.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126042 restraints weight = 22148.886| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26358 Z= 0.117 Angle : 0.547 9.405 35877 Z= 0.284 Chirality : 0.044 0.175 4044 Planarity : 0.004 0.050 4644 Dihedral : 4.713 30.060 3516 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.18 % Allowed : 12.21 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3246 helix: 1.59 (0.19), residues: 759 sheet: 0.01 (0.20), residues: 699 loop : -1.02 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.018 0.001 TYR A 265 PHE 0.025 0.001 PHE B 817 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.000 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00266 (26316) covalent geometry : angle 0.54529 (35793) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.11950 ( 84) hydrogen bonds : bond 0.03544 ( 1004) hydrogen bonds : angle 5.50450 ( 2715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6787 (m) REVERT: A 855 PHE cc_start: 0.7396 (m-10) cc_final: 0.7190 (m-80) REVERT: B 83 VAL cc_start: 0.6951 (OUTLIER) cc_final: 0.6655 (m) REVERT: B 212 LEU cc_start: 0.1422 (OUTLIER) cc_final: 0.1180 (tp) REVERT: B 524 VAL cc_start: 0.7636 (OUTLIER) cc_final: 0.7264 (t) REVERT: B 988 GLU cc_start: 0.7305 (tp30) cc_final: 0.7070 (tp30) REVERT: B 1017 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 221 SER cc_start: 0.5888 (t) cc_final: 0.5498 (p) REVERT: C 974 SER cc_start: 0.8652 (t) cc_final: 0.8449 (m) REVERT: C 1017 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 34 outliers final: 18 residues processed: 228 average time/residue: 0.1342 time to fit residues: 53.3285 Evaluate side-chains 201 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 233 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 149 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 213 optimal weight: 0.0870 chunk 126 optimal weight: 7.9990 overall best weight: 0.8758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 969 ASN B 804 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.162555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121724 restraints weight = 47635.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118393 restraints weight = 43088.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119884 restraints weight = 39852.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120780 restraints weight = 25978.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121349 restraints weight = 23051.309| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26358 Z= 0.118 Angle : 0.538 9.386 35877 Z= 0.278 Chirality : 0.043 0.180 4044 Planarity : 0.004 0.051 4644 Dihedral : 4.573 29.319 3516 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.91 % Allowed : 12.67 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.15), residues: 3246 helix: 1.80 (0.20), residues: 744 sheet: 0.08 (0.20), residues: 687 loop : -0.96 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 190 TYR 0.018 0.001 TYR A 265 PHE 0.024 0.001 PHE B 275 TRP 0.017 0.001 TRP A 104 HIS 0.003 0.000 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00268 (26316) covalent geometry : angle 0.53707 (35793) SS BOND : bond 0.00310 ( 42) SS BOND : angle 0.94176 ( 84) hydrogen bonds : bond 0.03456 ( 1004) hydrogen bonds : angle 5.32640 ( 2715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 196 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7241 (OUTLIER) cc_final: 0.6899 (m) REVERT: A 551 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7360 (m) REVERT: B 83 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6531 (m) REVERT: B 212 LEU cc_start: 0.1502 (OUTLIER) cc_final: 0.1259 (tp) REVERT: B 524 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7213 (t) REVERT: B 817 PHE cc_start: 0.6480 (t80) cc_final: 0.6207 (t80) REVERT: B 1017 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 106 PHE cc_start: 0.4616 (m-80) cc_final: 0.4343 (m-80) REVERT: C 974 SER cc_start: 0.8639 (t) cc_final: 0.8303 (m) REVERT: C 1017 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 1097 SER cc_start: 0.9144 (t) cc_final: 0.8775 (p) outliers start: 55 outliers final: 32 residues processed: 240 average time/residue: 0.1444 time to fit residues: 58.9610 Evaluate side-chains 214 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 210 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 223 optimal weight: 0.2980 chunk 131 optimal weight: 20.0000 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 969 ASN B 87 ASN B 448 ASN B 580 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.160309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120142 restraints weight = 47699.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116386 restraints weight = 43254.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118024 restraints weight = 40348.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118366 restraints weight = 26348.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.118634 restraints weight = 24783.116| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26358 Z= 0.165 Angle : 0.579 9.370 35877 Z= 0.299 Chirality : 0.044 0.176 4044 Planarity : 0.004 0.049 4644 Dihedral : 4.657 30.143 3516 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.51 % Allowed : 13.15 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3246 helix: 1.77 (0.19), residues: 735 sheet: 0.05 (0.21), residues: 669 loop : -1.04 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.020 0.001 TYR A 265 PHE 0.020 0.002 PHE B 392 TRP 0.005 0.001 TRP A 64 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00386 (26316) covalent geometry : angle 0.57775 (35793) SS BOND : bond 0.00410 ( 42) SS BOND : angle 1.07299 ( 84) hydrogen bonds : bond 0.03636 ( 1004) hydrogen bonds : angle 5.39589 ( 2715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7071 (m) REVERT: A 324 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7226 (pt0) REVERT: A 551 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7495 (m) REVERT: A 850 ILE cc_start: 0.5749 (OUTLIER) cc_final: 0.4891 (mt) REVERT: B 41 LYS cc_start: 0.7445 (mtmt) cc_final: 0.7110 (pttt) REVERT: B 83 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6742 (m) REVERT: B 212 LEU cc_start: 0.1458 (OUTLIER) cc_final: 0.1235 (tp) REVERT: B 448 ASN cc_start: 0.4061 (OUTLIER) cc_final: 0.3702 (t0) REVERT: B 1017 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 41 LYS cc_start: 0.7683 (mtmt) cc_final: 0.7379 (mttp) REVERT: C 106 PHE cc_start: 0.4798 (m-80) cc_final: 0.4431 (m-80) REVERT: C 221 SER cc_start: 0.6325 (t) cc_final: 0.5916 (p) REVERT: C 974 SER cc_start: 0.8701 (t) cc_final: 0.8484 (m) REVERT: C 1017 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 72 outliers final: 44 residues processed: 250 average time/residue: 0.1439 time to fit residues: 60.7083 Evaluate side-chains 236 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 64 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 183 optimal weight: 0.0770 chunk 317 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 87 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 901 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.161909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131339 restraints weight = 49055.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133386 restraints weight = 92994.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133679 restraints weight = 64574.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.134015 restraints weight = 42184.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134950 restraints weight = 35004.313| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 26358 Z= 0.219 Angle : 0.622 9.347 35877 Z= 0.320 Chirality : 0.046 0.192 4044 Planarity : 0.004 0.050 4644 Dihedral : 4.809 30.695 3516 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3246 helix: 1.58 (0.19), residues: 756 sheet: 0.05 (0.21), residues: 663 loop : -1.14 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 815 TYR 0.030 0.002 TYR B 449 PHE 0.025 0.002 PHE B 275 TRP 0.006 0.001 TRP B 633 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00514 (26316) covalent geometry : angle 0.61937 (35793) SS BOND : bond 0.00464 ( 42) SS BOND : angle 1.24445 ( 84) hydrogen bonds : bond 0.03764 ( 1004) hydrogen bonds : angle 5.51853 ( 2715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7190 (m) REVERT: A 195 LYS cc_start: 0.5830 (pptt) cc_final: 0.5549 (mtmm) REVERT: B 83 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.6840 (m) REVERT: B 212 LEU cc_start: 0.1379 (OUTLIER) cc_final: 0.1084 (tp) REVERT: B 1017 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 106 PHE cc_start: 0.4939 (m-80) cc_final: 0.4657 (m-80) REVERT: C 221 SER cc_start: 0.6487 (t) cc_final: 0.6214 (p) REVERT: C 629 LEU cc_start: -0.0750 (OUTLIER) cc_final: -0.1512 (mp) REVERT: C 742 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9246 (mp) REVERT: C 882 ILE cc_start: 0.9198 (pt) cc_final: 0.8953 (mt) REVERT: C 1017 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7613 (tm-30) outliers start: 70 outliers final: 49 residues processed: 243 average time/residue: 0.1429 time to fit residues: 58.9499 Evaluate side-chains 235 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 32 optimal weight: 9.9990 chunk 255 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 170 optimal weight: 0.7980 chunk 249 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 301 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 777 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 935 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.165441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.133600 restraints weight = 49249.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130531 restraints weight = 88276.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132295 restraints weight = 74080.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133941 restraints weight = 43239.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134208 restraints weight = 37839.040| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26358 Z= 0.114 Angle : 0.558 9.741 35877 Z= 0.287 Chirality : 0.044 0.181 4044 Planarity : 0.004 0.050 4644 Dihedral : 4.610 30.100 3516 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.50 % Allowed : 15.17 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3246 helix: 1.75 (0.19), residues: 759 sheet: 0.05 (0.20), residues: 693 loop : -1.02 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 905 TYR 0.017 0.001 TYR C 265 PHE 0.056 0.001 PHE B 275 TRP 0.005 0.001 TRP A 104 HIS 0.003 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00262 (26316) covalent geometry : angle 0.55642 (35793) SS BOND : bond 0.00311 ( 42) SS BOND : angle 0.97613 ( 84) hydrogen bonds : bond 0.03437 ( 1004) hydrogen bonds : angle 5.29769 ( 2715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7192 (m) REVERT: A 195 LYS cc_start: 0.5912 (pptt) cc_final: 0.5511 (ptmm) REVERT: A 324 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: B 83 VAL cc_start: 0.7211 (OUTLIER) cc_final: 0.6689 (m) REVERT: B 212 LEU cc_start: 0.1386 (OUTLIER) cc_final: 0.0749 (tp) REVERT: B 756 TYR cc_start: 0.8780 (m-80) cc_final: 0.8466 (m-80) REVERT: B 1017 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7670 (tm-30) REVERT: C 83 VAL cc_start: 0.7608 (OUTLIER) cc_final: 0.7175 (m) REVERT: C 106 PHE cc_start: 0.4811 (m-80) cc_final: 0.4480 (m-80) REVERT: C 221 SER cc_start: 0.6485 (t) cc_final: 0.6234 (p) REVERT: C 882 ILE cc_start: 0.9117 (pt) cc_final: 0.8915 (mt) REVERT: C 1017 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7712 (tm-30) REVERT: C 1097 SER cc_start: 0.8971 (t) cc_final: 0.8719 (p) outliers start: 43 outliers final: 32 residues processed: 238 average time/residue: 0.1397 time to fit residues: 57.1275 Evaluate side-chains 224 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 225 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 279 optimal weight: 0.3980 chunk 270 optimal weight: 0.0170 chunk 179 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 167 optimal weight: 0.2980 chunk 248 optimal weight: 9.9990 chunk 316 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 87 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 969 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.172382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139934 restraints weight = 49256.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138933 restraints weight = 75148.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140958 restraints weight = 65355.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141048 restraints weight = 39102.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142606 restraints weight = 34437.201| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 26358 Z= 0.106 Angle : 0.546 9.371 35877 Z= 0.280 Chirality : 0.043 0.175 4044 Planarity : 0.004 0.050 4644 Dihedral : 4.438 29.467 3516 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.64 % Allowed : 15.31 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3246 helix: 1.98 (0.20), residues: 744 sheet: 0.07 (0.21), residues: 666 loop : -0.95 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.016 0.001 TYR C 265 PHE 0.019 0.001 PHE B 817 TRP 0.007 0.001 TRP C 104 HIS 0.003 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00239 (26316) covalent geometry : angle 0.54459 (35793) SS BOND : bond 0.00308 ( 42) SS BOND : angle 0.92967 ( 84) hydrogen bonds : bond 0.03311 ( 1004) hydrogen bonds : angle 5.21171 ( 2715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7495 (OUTLIER) cc_final: 0.7051 (m) REVERT: A 195 LYS cc_start: 0.5948 (pptt) cc_final: 0.5603 (mtmm) REVERT: A 324 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: A 850 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.4965 (mt) REVERT: A 990 GLU cc_start: 0.7801 (tt0) cc_final: 0.7471 (tt0) REVERT: A 1055 SER cc_start: 0.9125 (t) cc_final: 0.8840 (p) REVERT: B 83 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6789 (t) REVERT: B 212 LEU cc_start: 0.1529 (OUTLIER) cc_final: 0.0994 (tp) REVERT: B 756 TYR cc_start: 0.8875 (m-80) cc_final: 0.8513 (m-80) REVERT: B 1017 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 83 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7160 (m) REVERT: C 106 PHE cc_start: 0.4728 (m-80) cc_final: 0.4386 (m-80) REVERT: C 629 LEU cc_start: -0.1109 (OUTLIER) cc_final: -0.1742 (mp) REVERT: C 724 THR cc_start: 0.9615 (t) cc_final: 0.9344 (m) REVERT: C 882 ILE cc_start: 0.9127 (pt) cc_final: 0.8899 (mt) REVERT: C 1017 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7630 (tm-30) REVERT: C 1097 SER cc_start: 0.8909 (t) cc_final: 0.8631 (p) outliers start: 47 outliers final: 31 residues processed: 261 average time/residue: 0.1458 time to fit residues: 64.5644 Evaluate side-chains 241 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 155 optimal weight: 9.9990 chunk 313 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 300 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN B 87 ASN B 969 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138723 restraints weight = 49053.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139977 restraints weight = 79695.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140868 restraints weight = 61230.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141168 restraints weight = 39253.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142319 restraints weight = 32843.747| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26358 Z= 0.137 Angle : 0.573 9.765 35877 Z= 0.294 Chirality : 0.044 0.185 4044 Planarity : 0.004 0.049 4644 Dihedral : 4.495 30.417 3516 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.57 % Allowed : 15.76 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3246 helix: 1.97 (0.19), residues: 744 sheet: 0.03 (0.21), residues: 681 loop : -0.96 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.001 PHE B 817 TRP 0.006 0.001 TRP C 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (26316) covalent geometry : angle 0.57158 (35793) SS BOND : bond 0.00408 ( 42) SS BOND : angle 1.08906 ( 84) hydrogen bonds : bond 0.03412 ( 1004) hydrogen bonds : angle 5.24376 ( 2715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6492 Ramachandran restraints generated. 3246 Oldfield, 0 Emsley, 3246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7561 (OUTLIER) cc_final: 0.7120 (m) REVERT: A 195 LYS cc_start: 0.6121 (pptt) cc_final: 0.5755 (mtmm) REVERT: A 850 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.4775 (mt) REVERT: A 990 GLU cc_start: 0.7892 (tt0) cc_final: 0.7550 (tt0) REVERT: B 83 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6852 (t) REVERT: B 212 LEU cc_start: 0.1506 (OUTLIER) cc_final: 0.1239 (tp) REVERT: B 756 TYR cc_start: 0.8899 (m-80) cc_final: 0.8548 (m-80) REVERT: B 1017 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7672 (tm-30) REVERT: C 83 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7273 (m) REVERT: C 106 PHE cc_start: 0.4875 (m-80) cc_final: 0.4534 (m-80) REVERT: C 629 LEU cc_start: -0.1105 (OUTLIER) cc_final: -0.1751 (mp) REVERT: C 777 ASN cc_start: 0.7349 (m-40) cc_final: 0.7102 (m-40) REVERT: C 1017 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 1097 SER cc_start: 0.9002 (t) cc_final: 0.8701 (p) outliers start: 45 outliers final: 35 residues processed: 246 average time/residue: 0.1473 time to fit residues: 61.8387 Evaluate side-chains 242 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 987 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 295 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 136 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.163252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130566 restraints weight = 48883.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132915 restraints weight = 78749.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133371 restraints weight = 55968.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.133638 restraints weight = 37707.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135094 restraints weight = 31343.468| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26358 Z= 0.156 Angle : 0.589 10.419 35877 Z= 0.303 Chirality : 0.044 0.218 4044 Planarity : 0.004 0.048 4644 Dihedral : 4.537 28.759 3516 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.60 % Allowed : 15.94 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3246 helix: 1.89 (0.19), residues: 744 sheet: -0.06 (0.20), residues: 705 loop : -0.98 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.019 0.001 TYR B1067 PHE 0.035 0.002 PHE B 855 TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00367 (26316) covalent geometry : angle 0.58717 (35793) SS BOND : bond 0.00386 ( 42) SS BOND : angle 1.15394 ( 84) hydrogen bonds : bond 0.03489 ( 1004) hydrogen bonds : angle 5.30985 ( 2715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.52 seconds wall clock time: 60 minutes 14.77 seconds (3614.77 seconds total)