Starting phenix.real_space_refine on Tue Apr 7 03:07:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3i_62786/04_2026/9l3i_62786.map" } resolution = 3.1 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= 0.002 sd= 0.030 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 105 5.16 5 C 15150 2.51 5 N 3900 2.21 5 O 4515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23670 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7675 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 53, 'TRANS': 927} Chain breaks: 7 Chain: "B" Number of atoms: 7675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7675 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 53, 'TRANS': 927} Chain breaks: 7 Chain: "C" Number of atoms: 7675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7675 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 53, 'TRANS': 927} Chain breaks: 7 Chain: "Z" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'28J:plan-1': 1, 'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.76, per 1000 atoms: 0.20 Number of scatterers: 23670 At special positions: 0 Unit cell: (129.93, 133.48, 173.24, 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 105 16.00 O 4515 8.00 N 3900 7.00 C 15150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 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 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=2.03 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 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=6, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 963.2 milliseconds 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 28J Z 4 " pdb=" CB 28J D 4 " pdb=" CB 28J I 4 " Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 43 sheets defined 26.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.502A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.886A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.535A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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: 3.732A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 876 Processing helix chain 'A' and resid 878 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 914 through 919 Processing helix chain 'A' and resid 919 through 941 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: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (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 1033 removed outlier: 4.121A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.588A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.766A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.553A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.367A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.703A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.648A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 876 Processing helix chain 'B' and resid 878 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 919 through 941 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: 3.967A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (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 985 through 1033 removed outlier: 4.070A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B1005 " --> pdb=" O LEU B1001 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL B1008 " --> pdb=" O LEU B1004 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.584A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.875A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.542A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.252A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.606A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.668A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (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 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 876 Processing helix chain 'C' and resid 878 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 914 through 919 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: 3.941A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (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 1033 removed outlier: 4.119A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C1005 " --> pdb=" O LEU C1001 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.761A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.570A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 172 removed outlier: 3.789A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.639A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.708A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.562A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.990A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.827A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.573A 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: 6.902A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.827A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.659A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.529A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.985A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.527A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 168 through 172 removed outlier: 3.992A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.606A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.882A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.579A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) 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 removed outlier: 3.569A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.978A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.783A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.654A 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 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.027A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.908A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 172 removed outlier: 3.843A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.618A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.847A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.602A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.406A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.620A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.018A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.787A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.787A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.612A 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 1122 989 hydrogen bonds defined for protein. 2652 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: 4.75 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 3822 1.31 - 1.45: 6814 1.45 - 1.59: 13439 1.59 - 1.73: 9 1.73 - 1.87: 132 Bond restraints: 24216 Sorted by residual: bond pdb=" C LEU D 5 " pdb=" N THR D 6 " ideal model delta sigma weight residual 1.330 1.509 -0.179 1.28e-02 6.10e+03 1.95e+02 bond pdb=" C LEU Z 5 " pdb=" N THR Z 6 " ideal model delta sigma weight residual 1.330 1.509 -0.179 1.28e-02 6.10e+03 1.95e+02 bond pdb=" C LEU I 5 " pdb=" N THR I 6 " ideal model delta sigma weight residual 1.330 1.509 -0.179 1.28e-02 6.10e+03 1.95e+02 bond pdb=" C PHE I 10 " pdb=" N LYS I 11 " ideal model delta sigma weight residual 1.329 1.502 -0.173 1.40e-02 5.10e+03 1.52e+02 bond pdb=" C PHE Z 10 " pdb=" N LYS Z 11 " ideal model delta sigma weight residual 1.329 1.501 -0.172 1.40e-02 5.10e+03 1.51e+02 ... (remaining 24211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 32365 2.36 - 4.71: 509 4.71 - 7.07: 55 7.07 - 9.42: 8 9.42 - 11.78: 6 Bond angle restraints: 32943 Sorted by residual: angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 124.93 -7.00 1.20e+00 6.94e-01 3.40e+01 angle pdb=" C CYS B 432 " pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sigma weight residual 109.68 100.65 9.03 1.98e+00 2.55e-01 2.08e+01 angle pdb=" CA PHE D 10 " pdb=" C PHE D 10 " pdb=" N LYS D 11 " ideal model delta sigma weight residual 116.45 122.06 -5.61 1.23e+00 6.61e-01 2.08e+01 angle pdb=" CA PHE Z 10 " pdb=" C PHE Z 10 " pdb=" N LYS Z 11 " ideal model delta sigma weight residual 116.45 122.05 -5.60 1.23e+00 6.61e-01 2.07e+01 angle pdb=" CA PHE I 10 " pdb=" C PHE I 10 " pdb=" N LYS I 11 " ideal model delta sigma weight residual 116.45 122.03 -5.58 1.23e+00 6.61e-01 2.06e+01 ... (remaining 32938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13438 17.78 - 35.55: 1035 35.55 - 53.33: 198 53.33 - 71.10: 39 71.10 - 88.88: 23 Dihedral angle restraints: 14733 sinusoidal: 6072 harmonic: 8661 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.26 -75.74 1 1.00e+01 1.00e-02 7.24e+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 93.00 150.07 -57.07 1 1.00e+01 1.00e-02 4.38e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -30.84 -55.16 1 1.00e+01 1.00e-02 4.12e+01 ... (remaining 14730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3402 0.078 - 0.157: 368 0.157 - 0.235: 15 0.235 - 0.314: 13 0.314 - 0.392: 9 Chirality restraints: 3807 Sorted by residual: chirality pdb=" CA LEU Z 5 " pdb=" N LEU Z 5 " pdb=" C LEU Z 5 " pdb=" CB LEU Z 5 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU I 5 " pdb=" N LEU I 5 " pdb=" C LEU I 5 " pdb=" CB LEU I 5 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LEU D 5 " pdb=" N LEU D 5 " pdb=" C LEU D 5 " pdb=" CB LEU D 5 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 3804 not shown) Planarity restraints: 4233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO B 561 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO A 561 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO C 561 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.030 5.00e-02 4.00e+02 ... (remaining 4230 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4837 2.78 - 3.31: 20770 3.31 - 3.84: 35914 3.84 - 4.37: 40629 4.37 - 4.90: 73039 Nonbonded interactions: 175189 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.248 3.040 nonbonded pdb=" NH2 ARG B 346 " pdb=" OH TYR B 451 " model vdw 2.262 3.120 nonbonded pdb=" O VAL C 445 " pdb=" NH1 ARG C 498 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR A 912 " pdb=" OE1 GLN A1106 " model vdw 2.289 3.040 ... (remaining 175184 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.570 Set stop_for_unknowns flag: 0.000 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: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.250 Find NCS groups from input model: 0.270 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.179 24282 Z= 0.517 Angle : 0.679 11.778 33087 Z= 0.363 Chirality : 0.051 0.392 3807 Planarity : 0.005 0.074 4221 Dihedral : 13.046 88.879 9057 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.19 % Favored : 96.53 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.19 % Cbeta Deviations : 0.25 % 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: 0.39 (0.15), residues: 2913 helix: 1.47 (0.21), residues: 660 sheet: 0.84 (0.19), residues: 660 loop : -0.49 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 273 TYR 0.019 0.001 TYR A1067 PHE 0.025 0.001 PHE A 429 TRP 0.020 0.001 TRP A1102 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00841 (24216) covalent geometry : angle 0.67415 (32943) SS BOND : bond 0.00299 ( 36) SS BOND : angle 1.68327 ( 72) hydrogen bonds : bond 0.13697 ( 960) hydrogen bonds : angle 6.12047 ( 2652) Misc. bond : bond 0.05335 ( 6) link_BETA1-4 : bond 0.00298 ( 12) link_BETA1-4 : angle 0.83547 ( 36) link_NAG-ASN : bond 0.00175 ( 12) link_NAG-ASN : angle 1.41971 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 860 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.8553 (mt) cc_final: 0.8314 (mt) REVERT: A 324 GLU cc_start: 0.6722 (mp0) cc_final: 0.6465 (mp0) REVERT: A 336 CYS cc_start: 0.5316 (m) cc_final: 0.4723 (m) REVERT: A 390 LEU cc_start: 0.8322 (mt) cc_final: 0.8110 (mt) REVERT: A 406 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7160 (mt-10) REVERT: A 457 ARG cc_start: 0.7858 (ttt-90) cc_final: 0.7456 (ttt-90) REVERT: A 465 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6304 (tm-30) REVERT: A 516 GLU cc_start: 0.6755 (tt0) cc_final: 0.6459 (tt0) REVERT: A 578 ASP cc_start: 0.7550 (t70) cc_final: 0.7074 (t70) REVERT: A 586 ASP cc_start: 0.7189 (m-30) cc_final: 0.6907 (m-30) REVERT: A 773 GLU cc_start: 0.7416 (pt0) cc_final: 0.7190 (pt0) REVERT: A 904 TYR cc_start: 0.7999 (m-10) cc_final: 0.7798 (m-10) REVERT: A 933 LYS cc_start: 0.8256 (mttp) cc_final: 0.7988 (mtpp) REVERT: A 1045 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7959 (tmtt) REVERT: B 190 ARG cc_start: 0.7340 (mpt180) cc_final: 0.6931 (mpt180) REVERT: B 235 ILE cc_start: 0.6753 (mt) cc_final: 0.6456 (mp) REVERT: B 239 GLN cc_start: 0.6955 (mp10) cc_final: 0.6633 (mp10) REVERT: B 324 GLU cc_start: 0.6355 (mp0) cc_final: 0.6097 (mp0) REVERT: B 336 CYS cc_start: 0.5346 (m) cc_final: 0.4804 (m) REVERT: B 406 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 420 ASP cc_start: 0.7274 (m-30) cc_final: 0.6930 (m-30) REVERT: B 440 LYS cc_start: 0.8661 (mmpt) cc_final: 0.8450 (mmpt) REVERT: B 453 TYR cc_start: 0.6959 (p90) cc_final: 0.6464 (p90) REVERT: B 462 LYS cc_start: 0.8255 (mtmm) cc_final: 0.8004 (mtmm) REVERT: B 465 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6505 (tm-30) REVERT: B 467 ASP cc_start: 0.7258 (t0) cc_final: 0.6910 (t0) REVERT: B 493 GLN cc_start: 0.6686 (mp10) cc_final: 0.5540 (mp10) REVERT: B 564 GLN cc_start: 0.7708 (tp40) cc_final: 0.7272 (tp40) REVERT: B 675 GLN cc_start: 0.7361 (pp30) cc_final: 0.7031 (pp30) REVERT: B 868 GLU cc_start: 0.7110 (mp0) cc_final: 0.6897 (mp0) REVERT: B 1125 ASN cc_start: 0.7684 (p0) cc_final: 0.7408 (p0) REVERT: C 189 LEU cc_start: 0.7869 (tp) cc_final: 0.7407 (tp) REVERT: C 190 ARG cc_start: 0.7208 (mpt180) cc_final: 0.6826 (mpt180) REVERT: C 336 CYS cc_start: 0.5391 (m) cc_final: 0.4829 (m) REVERT: C 340 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 364 ASP cc_start: 0.7622 (t0) cc_final: 0.7332 (t0) REVERT: C 402 ILE cc_start: 0.8442 (pt) cc_final: 0.8201 (pt) REVERT: C 455 LEU cc_start: 0.8246 (tp) cc_final: 0.7981 (tp) REVERT: C 465 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6502 (tm-30) REVERT: C 532 ASN cc_start: 0.8001 (m-40) cc_final: 0.7775 (m-40) REVERT: C 675 GLN cc_start: 0.7688 (pp30) cc_final: 0.7297 (pp30) REVERT: C 776 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8063 (ttmm) REVERT: C 795 LYS cc_start: 0.8294 (mptt) cc_final: 0.7987 (mmtm) REVERT: C 864 LEU cc_start: 0.8990 (tp) cc_final: 0.8772 (tt) REVERT: C 990 GLU cc_start: 0.6686 (mp0) cc_final: 0.6481 (mp0) outliers start: 10 outliers final: 6 residues processed: 864 average time/residue: 0.1637 time to fit residues: 219.0319 Evaluate side-chains 752 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 746 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain Z residue 11 LYS Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain I residue 11 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0670 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.0570 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 339 HIS A 613 GLN A 913 GLN A1005 GLN B 207 HIS B 616 ASN B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 409 GLN C 616 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.131050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113812 restraints weight = 37838.784| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.93 r_work: 0.3360 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24282 Z= 0.122 Angle : 0.570 11.691 33087 Z= 0.291 Chirality : 0.044 0.158 3807 Planarity : 0.005 0.061 4221 Dihedral : 5.893 56.528 3715 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.61 % Allowed : 11.19 % Favored : 87.20 % 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: 0.51 (0.15), residues: 2913 helix: 1.62 (0.20), residues: 708 sheet: 0.99 (0.19), residues: 642 loop : -0.54 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR C1067 PHE 0.023 0.001 PHE I 10 TRP 0.011 0.001 TRP A1102 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00268 (24216) covalent geometry : angle 0.56387 (32943) SS BOND : bond 0.00513 ( 36) SS BOND : angle 1.64516 ( 72) hydrogen bonds : bond 0.05011 ( 960) hydrogen bonds : angle 4.87585 ( 2652) Misc. bond : bond 0.00053 ( 6) link_BETA1-4 : bond 0.00407 ( 12) link_BETA1-4 : angle 0.84029 ( 36) link_NAG-ASN : bond 0.00186 ( 12) link_NAG-ASN : angle 1.34596 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 797 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7985 (mpt180) cc_final: 0.7493 (mmt180) REVERT: A 324 GLU cc_start: 0.7155 (mp0) cc_final: 0.6814 (mp0) REVERT: A 336 CYS cc_start: 0.6055 (m) cc_final: 0.5846 (m) REVERT: A 364 ASP cc_start: 0.8066 (t0) cc_final: 0.7778 (t0) REVERT: A 390 LEU cc_start: 0.8459 (mt) cc_final: 0.8198 (mt) REVERT: A 467 ASP cc_start: 0.7672 (t0) cc_final: 0.7410 (t0) REVERT: A 516 GLU cc_start: 0.7328 (tt0) cc_final: 0.6966 (tt0) REVERT: A 578 ASP cc_start: 0.7940 (t70) cc_final: 0.7341 (t70) REVERT: A 586 ASP cc_start: 0.7658 (m-30) cc_final: 0.7383 (m-30) REVERT: A 740 MET cc_start: 0.8504 (tpt) cc_final: 0.8292 (tpp) REVERT: A 773 GLU cc_start: 0.7825 (pt0) cc_final: 0.7538 (pt0) REVERT: A 1045 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8036 (tmtt) REVERT: A 1082 CYS cc_start: 0.7058 (t) cc_final: 0.6682 (t) REVERT: B 195 LYS cc_start: 0.7738 (tttm) cc_final: 0.7510 (tttm) REVERT: B 235 ILE cc_start: 0.6648 (mt) cc_final: 0.6306 (mp) REVERT: B 239 GLN cc_start: 0.7298 (mp10) cc_final: 0.6875 (mp10) REVERT: B 273 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7968 (ttm110) REVERT: B 336 CYS cc_start: 0.6150 (m) cc_final: 0.5685 (m) REVERT: B 357 ARG cc_start: 0.8635 (mtp85) cc_final: 0.8431 (mtp85) REVERT: B 379 CYS cc_start: 0.6794 (m) cc_final: 0.6509 (m) REVERT: B 406 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 420 ASP cc_start: 0.7725 (m-30) cc_final: 0.7320 (m-30) REVERT: B 440 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8569 (mmpt) REVERT: B 456 PHE cc_start: 0.8516 (m-10) cc_final: 0.8283 (m-10) REVERT: B 462 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8199 (mtmm) REVERT: B 465 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7004 (tm-30) REVERT: B 493 GLN cc_start: 0.6958 (mp10) cc_final: 0.6547 (mp10) REVERT: B 564 GLN cc_start: 0.8091 (tp40) cc_final: 0.7497 (tp40) REVERT: B 578 ASP cc_start: 0.7887 (t70) cc_final: 0.7583 (t70) REVERT: B 675 GLN cc_start: 0.7641 (pp30) cc_final: 0.7208 (pp30) REVERT: B 725 GLU cc_start: 0.7965 (tt0) cc_final: 0.7458 (tt0) REVERT: B 733 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8576 (mtmt) REVERT: B 808 ASP cc_start: 0.8032 (t0) cc_final: 0.7498 (t0) REVERT: B 868 GLU cc_start: 0.7647 (mp0) cc_final: 0.7381 (mp0) REVERT: B 921 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7592 (mmmm) REVERT: B 1125 ASN cc_start: 0.7707 (p0) cc_final: 0.7296 (p0) REVERT: C 340 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 364 ASP cc_start: 0.7944 (t0) cc_final: 0.7616 (t0) REVERT: C 402 ILE cc_start: 0.8542 (pt) cc_final: 0.8316 (pt) REVERT: C 455 LEU cc_start: 0.8224 (tp) cc_final: 0.7945 (tp) REVERT: C 465 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7047 (tm-30) REVERT: C 467 ASP cc_start: 0.7677 (t0) cc_final: 0.7368 (t0) REVERT: C 532 ASN cc_start: 0.8454 (m-40) cc_final: 0.8240 (m-40) REVERT: C 552 LEU cc_start: 0.8906 (mm) cc_final: 0.8604 (mp) REVERT: C 578 ASP cc_start: 0.7949 (t70) cc_final: 0.7593 (t70) REVERT: C 675 GLN cc_start: 0.7904 (pp30) cc_final: 0.7451 (pp30) REVERT: C 740 MET cc_start: 0.8737 (tpp) cc_final: 0.8525 (tpp) REVERT: C 795 LYS cc_start: 0.8446 (mptt) cc_final: 0.8064 (mptt) REVERT: C 864 LEU cc_start: 0.9043 (tp) cc_final: 0.8820 (tt) REVERT: C 990 GLU cc_start: 0.7320 (mp0) cc_final: 0.6895 (mp0) REVERT: C 1028 LYS cc_start: 0.8893 (ttmm) cc_final: 0.8690 (ttmm) REVERT: C 1045 LYS cc_start: 0.8413 (tmtt) cc_final: 0.8133 (tmtt) REVERT: C 1082 CYS cc_start: 0.7363 (t) cc_final: 0.6966 (t) REVERT: C 1100 THR cc_start: 0.8699 (p) cc_final: 0.8462 (t) REVERT: C 1101 HIS cc_start: 0.8086 (m-70) cc_final: 0.7880 (m-70) REVERT: I 11 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (mmtp) outliers start: 42 outliers final: 24 residues processed: 810 average time/residue: 0.1673 time to fit residues: 205.9454 Evaluate side-chains 787 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 762 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain I residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 180 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 196 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 784 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 = 0.3766 r_free = 0.3766 target = 0.131029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113796 restraints weight = 38001.360| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.93 r_work: 0.3368 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24282 Z= 0.112 Angle : 0.544 12.571 33087 Z= 0.275 Chirality : 0.043 0.177 3807 Planarity : 0.004 0.057 4221 Dihedral : 5.104 54.535 3704 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.38 % Allowed : 14.49 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.15), residues: 2913 helix: 1.88 (0.21), residues: 702 sheet: 0.94 (0.19), residues: 657 loop : -0.54 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1014 TYR 0.022 0.001 TYR B1138 PHE 0.019 0.001 PHE B 541 TRP 0.010 0.001 TRP A1102 HIS 0.010 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00251 (24216) covalent geometry : angle 0.53621 (32943) SS BOND : bond 0.00555 ( 36) SS BOND : angle 1.73045 ( 72) hydrogen bonds : bond 0.04594 ( 960) hydrogen bonds : angle 4.71066 ( 2652) Misc. bond : bond 0.00015 ( 6) link_BETA1-4 : bond 0.00345 ( 12) link_BETA1-4 : angle 0.92877 ( 36) link_NAG-ASN : bond 0.00138 ( 12) link_NAG-ASN : angle 1.34494 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 759 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7544 (mmt180) REVERT: A 324 GLU cc_start: 0.7084 (mp0) cc_final: 0.6735 (mp0) REVERT: A 362 VAL cc_start: 0.8549 (m) cc_final: 0.8173 (m) REVERT: A 364 ASP cc_start: 0.8015 (t0) cc_final: 0.7739 (t0) REVERT: A 390 LEU cc_start: 0.8548 (mt) cc_final: 0.8301 (mt) REVERT: A 457 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.8169 (ttt-90) REVERT: A 467 ASP cc_start: 0.7737 (t0) cc_final: 0.7360 (t0) REVERT: A 501 TYR cc_start: 0.8416 (m-80) cc_final: 0.8071 (m-80) REVERT: A 516 GLU cc_start: 0.7241 (tt0) cc_final: 0.6874 (tt0) REVERT: A 578 ASP cc_start: 0.7923 (t70) cc_final: 0.7315 (t70) REVERT: A 586 ASP cc_start: 0.7651 (m-30) cc_final: 0.7374 (m-30) REVERT: A 773 GLU cc_start: 0.7825 (pt0) cc_final: 0.7559 (pt0) REVERT: A 950 ASP cc_start: 0.7691 (m-30) cc_final: 0.7375 (m-30) REVERT: A 1045 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7965 (tmtt) REVERT: A 1082 CYS cc_start: 0.7003 (t) cc_final: 0.6635 (t) REVERT: B 235 ILE cc_start: 0.6610 (mt) cc_final: 0.6269 (mp) REVERT: B 273 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7910 (ttm110) REVERT: B 304 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: B 324 GLU cc_start: 0.6854 (mp0) cc_final: 0.6518 (mp0) REVERT: B 362 VAL cc_start: 0.8454 (m) cc_final: 0.8158 (m) REVERT: B 379 CYS cc_start: 0.6735 (m) cc_final: 0.6457 (m) REVERT: B 406 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7949 (mt-10) REVERT: B 420 ASP cc_start: 0.7756 (m-30) cc_final: 0.7372 (m-30) REVERT: B 440 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8551 (mmpt) REVERT: B 456 PHE cc_start: 0.8534 (m-10) cc_final: 0.8297 (m-10) REVERT: B 462 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8204 (mtmm) REVERT: B 465 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 493 GLN cc_start: 0.7108 (mp10) cc_final: 0.6754 (mp10) REVERT: B 501 TYR cc_start: 0.8505 (m-80) cc_final: 0.7529 (m-80) REVERT: B 529 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7999 (mmmm) REVERT: B 564 GLN cc_start: 0.8100 (tp40) cc_final: 0.7508 (tp40) REVERT: B 578 ASP cc_start: 0.7863 (t70) cc_final: 0.7548 (t70) REVERT: B 675 GLN cc_start: 0.7633 (pp30) cc_final: 0.7335 (pp30) REVERT: B 719 THR cc_start: 0.8689 (m) cc_final: 0.8350 (p) REVERT: B 725 GLU cc_start: 0.7966 (tt0) cc_final: 0.7485 (tt0) REVERT: B 808 ASP cc_start: 0.8033 (t0) cc_final: 0.7476 (t0) REVERT: B 868 GLU cc_start: 0.7694 (mp0) cc_final: 0.7389 (mp0) REVERT: B 1010 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: C 340 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7964 (mt-10) REVERT: C 361 CYS cc_start: 0.6657 (p) cc_final: 0.6418 (p) REVERT: C 364 ASP cc_start: 0.7915 (t0) cc_final: 0.7571 (t0) REVERT: C 402 ILE cc_start: 0.8525 (pt) cc_final: 0.8304 (pt) REVERT: C 455 LEU cc_start: 0.8174 (tp) cc_final: 0.7876 (tp) REVERT: C 465 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7077 (tm-30) REVERT: C 467 ASP cc_start: 0.7757 (t0) cc_final: 0.7396 (t0) REVERT: C 532 ASN cc_start: 0.8432 (m-40) cc_final: 0.8221 (m-40) REVERT: C 537 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7906 (mtpp) REVERT: C 552 LEU cc_start: 0.8900 (mm) cc_final: 0.8659 (mp) REVERT: C 564 GLN cc_start: 0.8243 (tp40) cc_final: 0.8031 (tp40) REVERT: C 578 ASP cc_start: 0.7947 (t70) cc_final: 0.7573 (t70) REVERT: C 675 GLN cc_start: 0.7921 (pp30) cc_final: 0.7538 (pp30) REVERT: C 740 MET cc_start: 0.8735 (tpp) cc_final: 0.8524 (tpp) REVERT: C 990 GLU cc_start: 0.7333 (mp0) cc_final: 0.6923 (mp0) REVERT: C 1045 LYS cc_start: 0.8438 (tmtt) cc_final: 0.8169 (tmtt) REVERT: C 1101 HIS cc_start: 0.8076 (m-70) cc_final: 0.7850 (m-70) REVERT: C 1125 ASN cc_start: 0.8023 (p0) cc_final: 0.7792 (p0) REVERT: C 1139 ASP cc_start: 0.8034 (t0) cc_final: 0.7683 (t0) outliers start: 62 outliers final: 44 residues processed: 777 average time/residue: 0.1634 time to fit residues: 195.7315 Evaluate side-chains 764 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 718 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 173 optimal weight: 0.6980 chunk 216 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 257 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 180 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 HIS A 409 GLN A 913 GLN B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.130616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.113381 restraints weight = 37805.826| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.94 r_work: 0.3350 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 24282 Z= 0.132 Angle : 0.566 12.576 33087 Z= 0.285 Chirality : 0.044 0.159 3807 Planarity : 0.004 0.056 4221 Dihedral : 4.774 50.767 3700 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.69 % Allowed : 15.57 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.60 (0.15), residues: 2913 helix: 1.92 (0.21), residues: 702 sheet: 0.86 (0.19), residues: 627 loop : -0.48 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR B1138 PHE 0.022 0.001 PHE B 377 TRP 0.010 0.001 TRP A1102 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00302 (24216) covalent geometry : angle 0.55491 (32943) SS BOND : bond 0.00527 ( 36) SS BOND : angle 2.17737 ( 72) hydrogen bonds : bond 0.04863 ( 960) hydrogen bonds : angle 4.67993 ( 2652) Misc. bond : bond 0.00027 ( 6) link_BETA1-4 : bond 0.00285 ( 12) link_BETA1-4 : angle 0.94391 ( 36) link_NAG-ASN : bond 0.00170 ( 12) link_NAG-ASN : angle 1.42775 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 745 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7095 (mp0) cc_final: 0.6685 (mp0) REVERT: A 364 ASP cc_start: 0.7955 (t0) cc_final: 0.7694 (t0) REVERT: A 467 ASP cc_start: 0.7801 (t0) cc_final: 0.7429 (t0) REVERT: A 501 TYR cc_start: 0.8443 (m-80) cc_final: 0.8111 (m-80) REVERT: A 516 GLU cc_start: 0.7206 (tt0) cc_final: 0.6857 (tt0) REVERT: A 578 ASP cc_start: 0.7925 (t70) cc_final: 0.7316 (t70) REVERT: A 586 ASP cc_start: 0.7649 (m-30) cc_final: 0.7338 (m-30) REVERT: A 615 VAL cc_start: 0.8957 (p) cc_final: 0.8698 (m) REVERT: A 773 GLU cc_start: 0.7861 (pt0) cc_final: 0.7620 (pt0) REVERT: A 808 ASP cc_start: 0.7936 (t0) cc_final: 0.7370 (t0) REVERT: A 950 ASP cc_start: 0.7658 (m-30) cc_final: 0.7337 (m-30) REVERT: A 1045 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7985 (tmtt) REVERT: A 1082 CYS cc_start: 0.7071 (t) cc_final: 0.6675 (t) REVERT: B 54 LEU cc_start: 0.8750 (mm) cc_final: 0.8499 (mp) REVERT: B 235 ILE cc_start: 0.6596 (mt) cc_final: 0.6263 (mp) REVERT: B 273 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7864 (ttm110) REVERT: B 287 ASP cc_start: 0.8041 (t0) cc_final: 0.7813 (t0) REVERT: B 304 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8677 (mtmm) REVERT: B 324 GLU cc_start: 0.6929 (mp0) cc_final: 0.6624 (mp0) REVERT: B 379 CYS cc_start: 0.6790 (m) cc_final: 0.6495 (m) REVERT: B 406 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7985 (mt-10) REVERT: B 420 ASP cc_start: 0.7757 (m-30) cc_final: 0.7373 (m-30) REVERT: B 440 LYS cc_start: 0.8822 (mmpt) cc_final: 0.8530 (mmpt) REVERT: B 456 PHE cc_start: 0.8559 (m-10) cc_final: 0.8300 (m-10) REVERT: B 462 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8171 (mtmm) REVERT: B 465 GLU cc_start: 0.7452 (tm-30) cc_final: 0.6994 (tm-30) REVERT: B 493 GLN cc_start: 0.7106 (mp10) cc_final: 0.6708 (mp-120) REVERT: B 501 TYR cc_start: 0.8509 (m-80) cc_final: 0.7506 (m-80) REVERT: B 525 CYS cc_start: 0.6309 (m) cc_final: 0.6058 (m) REVERT: B 529 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8002 (mmmm) REVERT: B 564 GLN cc_start: 0.8109 (tp40) cc_final: 0.7499 (tp40) REVERT: B 578 ASP cc_start: 0.7885 (t70) cc_final: 0.7536 (t70) REVERT: B 675 GLN cc_start: 0.7647 (pp30) cc_final: 0.7091 (pp30) REVERT: B 719 THR cc_start: 0.8697 (m) cc_final: 0.8371 (p) REVERT: B 725 GLU cc_start: 0.7995 (tt0) cc_final: 0.7527 (tt0) REVERT: B 808 ASP cc_start: 0.8040 (t0) cc_final: 0.7504 (t0) REVERT: B 868 GLU cc_start: 0.7695 (mp0) cc_final: 0.7366 (mp0) REVERT: B 921 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7660 (mmmm) REVERT: B 1010 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: C 206 LYS cc_start: 0.8244 (tptt) cc_final: 0.7917 (tppt) REVERT: C 340 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 364 ASP cc_start: 0.7946 (t0) cc_final: 0.7611 (t0) REVERT: C 441 LEU cc_start: 0.9079 (mm) cc_final: 0.8838 (mm) REVERT: C 455 LEU cc_start: 0.8208 (tp) cc_final: 0.7905 (tp) REVERT: C 465 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7072 (tm-30) REVERT: C 467 ASP cc_start: 0.7757 (t0) cc_final: 0.7401 (t0) REVERT: C 532 ASN cc_start: 0.8429 (m-40) cc_final: 0.8216 (m-40) REVERT: C 537 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7877 (mtpp) REVERT: C 564 GLN cc_start: 0.8260 (tp40) cc_final: 0.8053 (tp40) REVERT: C 578 ASP cc_start: 0.7983 (t70) cc_final: 0.7591 (t70) REVERT: C 675 GLN cc_start: 0.7919 (pp30) cc_final: 0.7536 (pp30) REVERT: C 780 GLU cc_start: 0.8080 (tt0) cc_final: 0.7828 (tt0) REVERT: C 790 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8335 (mtmm) REVERT: C 864 LEU cc_start: 0.8870 (tt) cc_final: 0.8657 (tp) REVERT: C 990 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6987 (mp0) REVERT: C 1010 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: C 1045 LYS cc_start: 0.8394 (tmtt) cc_final: 0.8173 (tmtt) REVERT: C 1101 HIS cc_start: 0.8090 (m-70) cc_final: 0.7866 (m-70) REVERT: C 1107 ARG cc_start: 0.8147 (mpt180) cc_final: 0.7924 (mpt180) REVERT: C 1139 ASP cc_start: 0.8053 (t0) cc_final: 0.7653 (t0) outliers start: 70 outliers final: 49 residues processed: 767 average time/residue: 0.1628 time to fit residues: 192.6244 Evaluate side-chains 774 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 722 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 339 HIS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.079 > 50: distance: 64 - 66: 33.940 distance: 65 - 87: 23.784 distance: 66 - 67: 10.920 distance: 67 - 68: 11.914 distance: 67 - 70: 37.367 distance: 68 - 74: 23.449 distance: 69 - 95: 35.235 distance: 70 - 71: 23.520 distance: 71 - 72: 7.713 distance: 71 - 73: 42.183 distance: 74 - 75: 10.076 distance: 75 - 76: 22.377 distance: 75 - 78: 27.298 distance: 76 - 77: 41.098 distance: 76 - 82: 21.080 distance: 77 - 107: 36.110 distance: 78 - 79: 31.009 distance: 78 - 80: 23.826 distance: 79 - 81: 8.593 distance: 82 - 83: 43.079 distance: 83 - 84: 64.825 distance: 84 - 85: 6.647 distance: 84 - 87: 39.267 distance: 87 - 88: 26.592 distance: 88 - 89: 35.236 distance: 88 - 91: 17.067 distance: 89 - 90: 11.557 distance: 89 - 95: 16.038 distance: 91 - 92: 26.040 distance: 92 - 93: 29.806 distance: 92 - 94: 47.482 distance: 95 - 96: 22.688 distance: 96 - 97: 19.440 distance: 96 - 99: 22.265 distance: 97 - 107: 26.723 distance: 99 - 100: 13.748 distance: 100 - 101: 9.891 distance: 100 - 102: 29.146 distance: 101 - 103: 13.537 distance: 102 - 104: 17.816 distance: 103 - 105: 20.490 distance: 104 - 105: 17.741 distance: 105 - 106: 5.744 distance: 107 - 108: 18.170 distance: 108 - 109: 16.732 distance: 108 - 111: 20.502 distance: 109 - 110: 30.079 distance: 109 - 115: 16.434 distance: 111 - 112: 36.716 distance: 112 - 113: 12.826 distance: 112 - 114: 10.355 distance: 115 - 116: 31.373 distance: 116 - 117: 33.538 distance: 116 - 119: 24.980 distance: 117 - 118: 28.587 distance: 117 - 127: 44.989 distance: 119 - 120: 25.959 distance: 120 - 121: 14.599 distance: 120 - 122: 23.895 distance: 121 - 123: 24.371 distance: 122 - 124: 4.647 distance: 123 - 125: 21.327 distance: 124 - 125: 30.309 distance: 125 - 126: 13.819 distance: 127 - 128: 3.518 distance: 128 - 129: 51.120 distance: 128 - 131: 21.308 distance: 129 - 130: 32.709 distance: 129 - 136: 24.933 distance: 131 - 132: 29.103 distance: 132 - 133: 32.069 distance: 133 - 134: 41.846 distance: 134 - 135: 31.686 distance: 136 - 137: 40.763 distance: 137 - 138: 54.793 distance: 137 - 140: 38.395 distance: 138 - 139: 22.281 distance: 138 - 144: 9.401 distance: 140 - 141: 14.242 distance: 141 - 142: 22.071 distance: 141 - 143: 30.548 distance: 144 - 145: 11.545 distance: 144 - 150: 8.547 distance: 145 - 146: 6.336 distance: 145 - 148: 41.167 distance: 146 - 147: 10.902 distance: 146 - 151: 28.888 distance: 148 - 149: 30.600 distance: 149 - 150: 47.008