Starting phenix.real_space_refine on Sat May 24 19:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ybj_33723/05_2025/7ybj_33723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ybj_33723/05_2025/7ybj_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_33723/05_2025/7ybj_33723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ybj_33723/05_2025/7ybj_33723.map" model { file = "/net/cci-nas-00/data/ceres_data/7ybj_33723/05_2025/7ybj_33723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ybj_33723/05_2025/7ybj_33723.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.42, per 1000 atoms: 0.56 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: 6.85 Conformation dependent library (CDL) restraints added in 3.6 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: 4.52 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: 10.97 Time building geometry restraints manager: 7.92 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: 0.09 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 60.620 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.050 ------------------------------------------------------------------------------- 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 : 9.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), 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 TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS C 245 PHE 0.033 0.002 PHE C 275 TYR 0.022 0.001 TYR C 265 ARG 0.009 0.001 ARG C 357 Details of bonding type rmsd hydrogen bonds : bond 0.14112 ( 1004) hydrogen bonds : angle 7.48090 ( 2715) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.00198 ( 84) covalent geometry : bond 0.00335 (26316) covalent geometry : angle 0.67264 (35793) *********************** 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 : 2.982 Fit side-chains revert: symmetry clash REVERT: B 1017 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 777 ASN cc_start: 0.7138 (m-40) cc_final: 0.6831 (m-40) REVERT: C 864 LEU cc_start: 0.8524 (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: 0.7311 (tm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3571 time to fit residues: 166.7261 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 : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.0170 chunk 247 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 190 optimal weight: 0.0170 chunk 296 optimal weight: 10.0000 overall best weight: 1.5860 ------------------------------------------------------------------------------- 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 564 GLN A 969 ASN B 564 GLN B 784 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.123544 restraints weight = 47924.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119251 restraints weight = 43604.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120996 restraints weight = 39959.287| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26358 Z= 0.170 Angle : 0.609 9.402 35877 Z= 0.316 Chirality : 0.045 0.180 4044 Planarity : 0.004 0.048 4644 Dihedral : 4.880 33.359 3516 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.90 % Allowed : 6.89 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3246 helix: 1.52 (0.19), residues: 729 sheet: 0.10 (0.20), residues: 645 loop : -0.92 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS C1064 PHE 0.023 0.002 PHE A 817 TYR 0.024 0.002 TYR A 265 ARG 0.017 0.001 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 1004) hydrogen bonds : angle 5.81434 ( 2715) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.02829 ( 84) covalent geometry : bond 0.00394 (26316) covalent geometry : angle 0.60728 (35793) *********************** 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: 26 poor density : 216 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1118 ASP cc_start: 0.7978 (t0) cc_final: 0.7708 (t0) REVERT: B 1017 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 974 SER cc_start: 0.8687 (t) cc_final: 0.8475 (m) REVERT: C 1017 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7319 (tm-30) outliers start: 26 outliers final: 16 residues processed: 232 average time/residue: 0.3229 time to fit residues: 126.2286 Evaluate side-chains 193 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 B residue 1097 SER 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 113 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 969 ASN B 784 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.157237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115400 restraints weight = 47885.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113496 restraints weight = 37126.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114010 restraints weight = 42243.720| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 26358 Z= 0.296 Angle : 0.722 12.129 35877 Z= 0.373 Chirality : 0.049 0.198 4044 Planarity : 0.005 0.063 4644 Dihedral : 5.282 32.243 3516 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.95 % Allowed : 11.52 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3246 helix: 1.15 (0.19), residues: 729 sheet: -0.11 (0.20), residues: 681 loop : -1.13 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 633 HIS 0.008 0.001 HIS C1064 PHE 0.031 0.003 PHE B 817 TYR 0.027 0.002 TYR A 265 ARG 0.009 0.001 ARG A 905 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 1004) hydrogen bonds : angle 6.03733 ( 2715) SS BOND : bond 0.00493 ( 42) SS BOND : angle 1.40859 ( 84) covalent geometry : bond 0.00691 (26316) covalent geometry : angle 0.72001 (35793) *********************** 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 260 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7172 (m) REVERT: A 158 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.6141 (ptp-170) REVERT: A 855 PHE cc_start: 0.7545 (m-10) cc_final: 0.7174 (m-80) REVERT: A 1118 ASP cc_start: 0.8195 (t0) cc_final: 0.7935 (t0) REVERT: B 83 VAL cc_start: 0.7218 (OUTLIER) cc_final: 0.6947 (m) REVERT: B 582 LEU cc_start: 0.8700 (mm) cc_final: 0.8204 (tp) REVERT: B 756 TYR cc_start: 0.9067 (m-80) cc_final: 0.8710 (m-80) REVERT: B 1017 GLU cc_start: 0.8220 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 41 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7257 (pttt) REVERT: C 83 VAL cc_start: 0.7234 (OUTLIER) cc_final: 0.6901 (m) REVERT: C 855 PHE cc_start: 0.7715 (m-80) cc_final: 0.7304 (m-80) REVERT: C 1017 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7799 (tm-30) outliers start: 56 outliers final: 31 residues processed: 243 average time/residue: 0.3356 time to fit residues: 134.9583 Evaluate side-chains 219 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 270 LEU 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 531 THR Chi-restraints excluded: chain B residue 734 THR 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 83 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 860 VAL 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 94 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 580 GLN B 804 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 969 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 777 ASN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115526 restraints weight = 48243.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111556 restraints weight = 41965.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113106 restraints weight = 35992.240| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26358 Z= 0.197 Angle : 0.614 9.423 35877 Z= 0.318 Chirality : 0.046 0.194 4044 Planarity : 0.004 0.052 4644 Dihedral : 5.070 31.081 3516 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.12 % Allowed : 13.15 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3246 helix: 1.31 (0.19), residues: 753 sheet: -0.19 (0.20), residues: 705 loop : -1.19 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 633 HIS 0.003 0.001 HIS C1064 PHE 0.034 0.002 PHE B 817 TYR 0.022 0.002 TYR A 265 ARG 0.006 0.001 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1004) hydrogen bonds : angle 5.79470 ( 2715) SS BOND : bond 0.00721 ( 42) SS BOND : angle 1.15363 ( 84) covalent geometry : bond 0.00458 (26316) covalent geometry : angle 0.61173 (35793) *********************** 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 263 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7425 (OUTLIER) cc_final: 0.7165 (m) REVERT: A 158 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.6039 (ptp-170) REVERT: A 195 LYS cc_start: 0.6211 (pptt) cc_final: 0.5712 (tttm) REVERT: A 855 PHE cc_start: 0.7554 (m-10) cc_final: 0.7191 (m-80) REVERT: B 83 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.7059 (m) REVERT: B 192 PHE cc_start: 0.5819 (m-80) cc_final: 0.5611 (m-80) REVERT: B 212 LEU cc_start: 0.1459 (OUTLIER) cc_final: 0.1231 (tp) REVERT: B 524 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7370 (t) REVERT: B 582 LEU cc_start: 0.8615 (mm) cc_final: 0.8082 (tp) REVERT: B 1017 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7965 (tm-30) REVERT: C 41 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7251 (pttt) REVERT: C 192 PHE cc_start: 0.5595 (m-80) cc_final: 0.5326 (m-80) REVERT: C 221 SER cc_start: 0.6628 (t) cc_final: 0.6189 (p) REVERT: C 855 PHE cc_start: 0.7743 (m-80) cc_final: 0.7443 (m-80) REVERT: C 974 SER cc_start: 0.8685 (t) cc_final: 0.8472 (m) REVERT: C 1017 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7721 (tm-30) outliers start: 61 outliers final: 32 residues processed: 250 average time/residue: 0.3299 time to fit residues: 139.2611 Evaluate side-chains 220 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 656 VAL 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 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 734 THR Chi-restraints excluded: chain B residue 804 GLN 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 546 LEU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 130 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 317 optimal weight: 0.9990 chunk 278 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 280 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 969 ASN B 196 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 613 GLN C1005 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119264 restraints weight = 47752.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116626 restraints weight = 40901.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117851 restraints weight = 37611.946| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26358 Z= 0.115 Angle : 0.552 9.369 35877 Z= 0.288 Chirality : 0.044 0.175 4044 Planarity : 0.004 0.051 4644 Dihedral : 4.767 29.545 3516 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.02 % Allowed : 13.85 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3246 helix: 1.52 (0.19), residues: 762 sheet: -0.06 (0.20), residues: 693 loop : -1.01 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.005 0.001 HIS C 207 PHE 0.035 0.001 PHE B 817 TYR 0.020 0.001 TYR A 265 ARG 0.005 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1004) hydrogen bonds : angle 5.46364 ( 2715) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.09005 ( 84) covalent geometry : bond 0.00256 (26316) covalent geometry : angle 0.54988 (35793) *********************** 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 270 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7493 (OUTLIER) cc_final: 0.7162 (m) REVERT: A 855 PHE cc_start: 0.7576 (m-10) cc_final: 0.7339 (m-80) REVERT: A 900 MET cc_start: 0.8235 (mtp) cc_final: 0.8033 (mtp) REVERT: B 83 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6907 (m) REVERT: B 212 LEU cc_start: 0.1362 (OUTLIER) cc_final: 0.1111 (tp) REVERT: B 1017 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 41 LYS cc_start: 0.7690 (mtmt) cc_final: 0.7245 (pttt) REVERT: C 83 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7185 (m) REVERT: C 106 PHE cc_start: 0.4746 (m-80) cc_final: 0.4397 (m-80) REVERT: C 221 SER cc_start: 0.6650 (t) cc_final: 0.6241 (p) REVERT: C 770 ILE cc_start: 0.9145 (mt) cc_final: 0.8781 (mt) REVERT: C 855 PHE cc_start: 0.7678 (m-80) cc_final: 0.7336 (m-80) REVERT: C 974 SER cc_start: 0.8610 (t) cc_final: 0.8270 (m) REVERT: C 1017 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 1097 SER cc_start: 0.9113 (t) cc_final: 0.8813 (p) outliers start: 58 outliers final: 35 residues processed: 259 average time/residue: 0.3302 time to fit residues: 142.8437 Evaluate side-chains 229 residues out of total 2874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 270 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 791 THR 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 118 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 546 LEU Chi-restraints excluded: chain B residue 590 CYS 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 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 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 430 THR 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 987 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2247 > 50: distance: 54 - 78: 32.421 distance: 57 - 75: 35.189 distance: 72 - 75: 33.610 distance: 75 - 76: 50.573 distance: 76 - 77: 49.340 distance: 76 - 79: 8.536 distance: 77 - 78: 65.808 distance: 79 - 80: 42.843 distance: 80 - 81: 43.600 distance: 80 - 82: 40.360 distance: 81 - 83: 38.758 distance: 82 - 84: 53.224 distance: 83 - 84: 40.521 distance: 85 - 86: 24.579 distance: 85 - 248: 34.813 distance: 86 - 87: 62.316 distance: 86 - 89: 18.609 distance: 87 - 88: 39.753 distance: 87 - 96: 39.456 distance: 88 - 245: 32.242 distance: 89 - 90: 58.803 distance: 90 - 91: 42.359 distance: 90 - 92: 39.555 distance: 91 - 93: 34.084 distance: 92 - 94: 43.064 distance: 93 - 95: 15.945 distance: 94 - 95: 22.419 distance: 96 - 97: 9.785 distance: 96 - 102: 39.046 distance: 97 - 98: 42.035 distance: 97 - 100: 10.950 distance: 98 - 99: 56.594 distance: 98 - 103: 61.576 distance: 100 - 101: 31.756 distance: 101 - 102: 40.955 distance: 103 - 104: 63.792 distance: 104 - 105: 63.050 distance: 104 - 107: 55.446 distance: 105 - 106: 52.133 distance: 105 - 114: 30.014 distance: 107 - 108: 13.001 distance: 108 - 109: 15.950 distance: 110 - 111: 12.434 distance: 111 - 112: 18.810 distance: 111 - 113: 19.327 distance: 114 - 115: 55.689 distance: 115 - 116: 70.075 distance: 115 - 118: 15.143 distance: 116 - 117: 39.268 distance: 116 - 123: 3.643 distance: 118 - 119: 37.607 distance: 119 - 120: 27.489 distance: 120 - 121: 49.649 distance: 120 - 122: 12.964 distance: 123 - 124: 39.359 distance: 124 - 125: 16.148 distance: 125 - 126: 43.009 distance: 125 - 127: 42.166 distance: 127 - 128: 40.349 distance: 127 - 206: 31.678 distance: 128 - 129: 67.973 distance: 128 - 131: 42.801 distance: 129 - 130: 70.225 distance: 129 - 134: 69.459 distance: 130 - 203: 32.456 distance: 131 - 132: 24.866 distance: 131 - 133: 13.866 distance: 135 - 136: 40.309 distance: 135 - 138: 41.256 distance: 136 - 137: 38.996 distance: 136 - 145: 40.972 distance: 138 - 139: 23.280 distance: 139 - 140: 25.480 distance: 139 - 141: 42.537 distance: 140 - 142: 18.576 distance: 141 - 143: 4.458 distance: 142 - 144: 40.194 distance: 143 - 144: 52.948 distance: 145 - 192: 33.470 distance: 146 - 149: 6.789 distance: 147 - 152: 7.889 distance: 148 - 189: 33.504 distance: 149 - 150: 51.371 distance: 149 - 151: 41.872 distance: 152 - 153: 52.600 distance: 153 - 154: 56.310 distance: 153 - 156: 52.635 distance: 154 - 155: 10.558 distance: 154 - 158: 33.552 distance: 156 - 157: 42.508