Starting phenix.real_space_refine on Sat Mar 7 14:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xu5_33459/03_2026/7xu5_33459_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xu5_33459/03_2026/7xu5_33459.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/7xu5_33459/03_2026/7xu5_33459_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xu5_33459/03_2026/7xu5_33459_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xu5_33459/03_2026/7xu5_33459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xu5_33459/03_2026/7xu5_33459.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= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 99 5.16 5 C 14532 2.51 5 N 3717 2.21 5 O 4395 1.98 5 H 21549 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44292 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 Chain: "A" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 Chain: "C" Number of atoms: 14525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 14525 Classifications: {'peptide': 938} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 45, 'TRANS': 892} Chain breaks: 14 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: "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: "Z" 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: "b" 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: "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: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 183 Unusual residues: {'BLA': 1, 'NAG': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 7.92, per 1000 atoms: 0.18 Number of scatterers: 44292 At special positions: 0 Unit cell: (126.259, 134.747, 158.089, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 O 4395 8.00 N 3717 7.00 C 14532 6.00 H 21549 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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 427 " - pdb=" SG CYS C 987 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS A 427 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " 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=2.04 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 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 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=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " NAG-ASN " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 282 " " NAG A1404 " - " ASN A 331 " " NAG A1405 " - " ASN A 343 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1074 " " NAG A1410 " - " ASN A1098 " " NAG A1411 " - " ASN A1134 " " NAG B1402 " - " ASN B 61 " " NAG B1403 " - " ASN B 282 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1074 " " NAG B1410 " - " ASN B1098 " " NAG B1411 " - " ASN B1134 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 282 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 343 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 709 " " NAG C1409 " - " ASN C1074 " " NAG C1410 " - " ASN C1098 " " NAG C1411 " - " ASN C1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG Z 1 " - " ASN A 717 " " NAG b 1 " - " ASN A 801 " " NAG o 1 " - " ASN C 717 " " NAG q 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.4 seconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5292 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 27.2% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.025A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.221A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.286A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 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 removed outlier: 3.660A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.727A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.739A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 3.847A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.024A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.222A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.286A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 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: 3.660A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.727A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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: 3.739A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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: 3.847A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (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: 4.024A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.221A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.287A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 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: 3.660A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.728A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) 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: 3.739A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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: 3.846A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.599A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.861A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.847A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.214A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.860A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.224A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.937A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.060A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.373A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.483A pdb=" N ILE B 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 'B' and resid 1120 through 1125 removed outlier: 4.788A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 29 through 30 removed outlier: 3.598A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.847A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AC2, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.214A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.860A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.224A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.936A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.060A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.789A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.598A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.327A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.847A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.214A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.225A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.936A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.060A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.374A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.788A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2553 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: 11.74 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21546 1.03 - 1.23: 558 1.23 - 1.43: 9491 1.43 - 1.63: 13057 1.63 - 1.83: 123 Bond restraints: 44775 Sorted by residual: bond pdb=" C4C BLA B1401 " pdb=" NC BLA B1401 " ideal model delta sigma weight residual 1.375 1.542 -0.167 2.00e-02 2.50e+03 6.96e+01 bond pdb=" C4C BLA A1401 " pdb=" NC BLA A1401 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C4C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.375 1.541 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C1C BLA C1401 " pdb=" NC BLA C1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C1C BLA B1401 " pdb=" NC BLA B1401 " ideal model delta sigma weight residual 1.368 1.530 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 44770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 79511 2.35 - 4.71: 742 4.71 - 7.06: 88 7.06 - 9.41: 4 9.41 - 11.76: 4 Bond angle restraints: 80349 Sorted by residual: angle pdb=" C1B BLA A1401 " pdb=" CHB BLA A1401 " pdb=" C4A BLA A1401 " ideal model delta sigma weight residual 128.06 116.30 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C1B BLA B1401 " pdb=" CHB BLA B1401 " pdb=" C4A BLA B1401 " ideal model delta sigma weight residual 128.06 116.32 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C1B BLA C1401 " pdb=" CHB BLA C1401 " pdb=" C4A BLA C1401 " ideal model delta sigma weight residual 128.06 116.37 11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" SD MET B 740 " pdb=" CE MET B 740 " pdb=" HE1 MET B 740 " ideal model delta sigma weight residual 109.00 120.24 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C3B BLA B1401 " pdb=" CAB BLA B1401 " pdb=" CBB BLA B1401 " ideal model delta sigma weight residual 126.95 118.30 8.65 3.00e+00 1.11e-01 8.32e+00 ... (remaining 80344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 19924 17.95 - 35.90: 1610 35.90 - 53.84: 368 53.84 - 71.79: 124 71.79 - 89.74: 27 Dihedral angle restraints: 22053 sinusoidal: 12210 harmonic: 9843 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.26 -89.74 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.29 -89.71 1 1.00e+01 1.00e-02 9.55e+01 ... (remaining 22050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3241 0.073 - 0.146: 449 0.146 - 0.220: 12 0.220 - 0.293: 0 0.293 - 0.366: 9 Chirality restraints: 3711 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.55e+00 chirality pdb=" C1 NAG o 2 " pdb=" O4 NAG o 1 " pdb=" C2 NAG o 2 " pdb=" O5 NAG o 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.52e+00 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.24e+00 ... (remaining 3708 not shown) Planarity restraints: 6666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA A1401 " -0.032 2.00e-02 2.50e+03 4.75e-02 5.64e+01 pdb=" C1A BLA A1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA A1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA A1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA A1401 " -0.015 2.00e-02 2.50e+03 pdb=" C4D BLA A1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA A1401 " 0.011 2.00e-02 2.50e+03 pdb=" CHA BLA A1401 " -0.077 2.00e-02 2.50e+03 pdb=" CHD BLA A1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA A1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1401 " -0.032 2.00e-02 2.50e+03 4.75e-02 5.64e+01 pdb=" C1A BLA B1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA B1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA B1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA B1401 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA B1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA B1401 " 0.011 2.00e-02 2.50e+03 pdb=" CHA BLA B1401 " -0.076 2.00e-02 2.50e+03 pdb=" CHD BLA B1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA B1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1401 " -0.032 2.00e-02 2.50e+03 4.74e-02 5.63e+01 pdb=" C1A BLA C1401 " 0.107 2.00e-02 2.50e+03 pdb=" C1D BLA C1401 " -0.007 2.00e-02 2.50e+03 pdb=" C2D BLA C1401 " 0.008 2.00e-02 2.50e+03 pdb=" C3D BLA C1401 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA C1401 " -0.037 2.00e-02 2.50e+03 pdb=" CAD BLA C1401 " 0.012 2.00e-02 2.50e+03 pdb=" CHA BLA C1401 " -0.076 2.00e-02 2.50e+03 pdb=" CHD BLA C1401 " -0.006 2.00e-02 2.50e+03 pdb=" CMD BLA C1401 " 0.048 2.00e-02 2.50e+03 ... (remaining 6663 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 5642 2.25 - 2.84: 97091 2.84 - 3.43: 110294 3.43 - 4.01: 160563 4.01 - 4.60: 240126 Nonbonded interactions: 613716 Sorted by model distance: nonbonded pdb=" HZ2 LYS C 825 " pdb=" O LEU C 938 " model vdw 1.663 2.450 nonbonded pdb=" HZ2 LYS B 825 " pdb=" O LEU B 938 " model vdw 1.663 2.450 nonbonded pdb=" HZ2 LYS A 825 " pdb=" O LEU A 938 " model vdw 1.663 2.450 nonbonded pdb=" O GLN A 957 " pdb=" HG1 THR A 961 " model vdw 1.668 2.450 nonbonded pdb=" O GLN C 957 " pdb=" HG1 THR C 961 " model vdw 1.669 2.450 ... (remaining 613711 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'Z' selection = chain 'b' selection = chain 'o' selection = chain 'q' } 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=0.00 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: 3.090 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 40.480 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.167 23307 Z= 0.389 Angle : 0.795 11.763 31767 Z= 0.388 Chirality : 0.050 0.366 3711 Planarity : 0.005 0.059 3993 Dihedral : 13.698 88.024 8988 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.17 (0.15), residues: 2724 helix: 0.52 (0.20), residues: 654 sheet: -0.65 (0.19), residues: 642 loop : -1.46 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 319 TYR 0.013 0.001 TYR C1067 PHE 0.028 0.002 PHE C 906 TRP 0.011 0.002 TRP C 436 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00836 (23226) covalent geometry : angle 0.76331 (31569) SS BOND : bond 0.00624 ( 36) SS BOND : angle 2.68116 ( 72) hydrogen bonds : bond 0.15408 ( 935) hydrogen bonds : angle 8.04008 ( 2553) Misc. bond : bond 0.00122 ( 3) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.24799 ( 18) link_NAG-ASN : bond 0.00758 ( 36) link_NAG-ASN : angle 3.23712 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.190 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.4691 time to fit residues: 37.9856 Evaluate side-chains 42 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062808 restraints weight = 162034.397| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.80 r_work: 0.2925 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23307 Z= 0.174 Angle : 0.557 8.492 31767 Z= 0.289 Chirality : 0.046 0.344 3711 Planarity : 0.004 0.056 3993 Dihedral : 7.568 64.788 3957 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.20 % Allowed : 1.79 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.82 (0.15), residues: 2724 helix: 1.36 (0.21), residues: 636 sheet: -0.70 (0.18), residues: 678 loop : -1.37 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 328 TYR 0.015 0.001 TYR A 170 PHE 0.012 0.001 PHE A 906 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00390 (23226) covalent geometry : angle 0.52875 (31569) SS BOND : bond 0.00471 ( 36) SS BOND : angle 2.01273 ( 72) hydrogen bonds : bond 0.04615 ( 935) hydrogen bonds : angle 6.27702 ( 2553) Misc. bond : bond 0.00039 ( 3) link_BETA1-4 : bond 0.00207 ( 6) link_BETA1-4 : angle 0.98917 ( 18) link_NAG-ASN : bond 0.00541 ( 36) link_NAG-ASN : angle 2.58337 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 1.063 Fit side-chains REVERT: B 740 MET cc_start: 0.9180 (tpt) cc_final: 0.8934 (tpt) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.5534 time to fit residues: 40.0808 Evaluate side-chains 46 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 136 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 3 optimal weight: 0.0170 chunk 107 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 271 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.086690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.063006 restraints weight = 162155.075| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.78 r_work: 0.2928 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23307 Z= 0.148 Angle : 0.514 8.647 31767 Z= 0.263 Chirality : 0.045 0.321 3711 Planarity : 0.004 0.053 3993 Dihedral : 7.004 61.500 3957 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.12 % Allowed : 2.85 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.69 (0.16), residues: 2724 helix: 1.54 (0.21), residues: 639 sheet: -0.81 (0.18), residues: 684 loop : -1.22 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.012 0.001 TYR A1067 PHE 0.012 0.001 PHE C 898 TRP 0.006 0.001 TRP B 104 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00335 (23226) covalent geometry : angle 0.48576 (31569) SS BOND : bond 0.00417 ( 36) SS BOND : angle 1.84214 ( 72) hydrogen bonds : bond 0.04198 ( 935) hydrogen bonds : angle 5.94543 ( 2553) Misc. bond : bond 0.00025 ( 3) link_BETA1-4 : bond 0.00187 ( 6) link_BETA1-4 : angle 1.08354 ( 18) link_NAG-ASN : bond 0.00535 ( 36) link_NAG-ASN : angle 2.50733 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 1.111 Fit side-chains REVERT: B 740 MET cc_start: 0.9229 (tpt) cc_final: 0.8994 (tpt) REVERT: B 902 MET cc_start: 0.9070 (tpp) cc_final: 0.8784 (mmt) REVERT: A 902 MET cc_start: 0.9016 (tpp) cc_final: 0.8702 (tpt) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.5575 time to fit residues: 37.6910 Evaluate side-chains 48 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 213 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 226 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062928 restraints weight = 162216.459| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.81 r_work: 0.2920 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23307 Z= 0.131 Angle : 0.490 8.342 31767 Z= 0.250 Chirality : 0.045 0.300 3711 Planarity : 0.003 0.048 3993 Dihedral : 6.434 58.198 3957 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.45 % Allowed : 2.89 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.47 (0.16), residues: 2724 helix: 1.85 (0.21), residues: 639 sheet: -0.75 (0.19), residues: 660 loop : -1.10 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.012 0.001 TYR A1067 PHE 0.012 0.001 PHE C 898 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00296 (23226) covalent geometry : angle 0.46364 (31569) SS BOND : bond 0.00368 ( 36) SS BOND : angle 1.71720 ( 72) hydrogen bonds : bond 0.03655 ( 935) hydrogen bonds : angle 5.58344 ( 2553) Misc. bond : bond 0.00006 ( 3) link_BETA1-4 : bond 0.00253 ( 6) link_BETA1-4 : angle 1.03120 ( 18) link_NAG-ASN : bond 0.00530 ( 36) link_NAG-ASN : angle 2.38874 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: B 740 MET cc_start: 0.9261 (tpt) cc_final: 0.8987 (tpt) REVERT: B 902 MET cc_start: 0.9065 (tpp) cc_final: 0.8790 (mmt) REVERT: A 902 MET cc_start: 0.8988 (tpp) cc_final: 0.8650 (tpt) outliers start: 11 outliers final: 5 residues processed: 55 average time/residue: 0.5587 time to fit residues: 43.3547 Evaluate side-chains 50 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN A 920 GLN C 394 ASN C 920 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.085311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.061182 restraints weight = 164291.471| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.81 r_work: 0.2870 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 23307 Z= 0.301 Angle : 0.574 8.293 31767 Z= 0.296 Chirality : 0.047 0.291 3711 Planarity : 0.004 0.053 3993 Dihedral : 6.498 57.069 3957 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.61 % Allowed : 3.62 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.75 (0.16), residues: 2724 helix: 1.65 (0.21), residues: 639 sheet: -0.97 (0.18), residues: 690 loop : -1.27 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.015 0.002 TYR A1067 PHE 0.020 0.002 PHE A 906 TRP 0.007 0.001 TRP C 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00682 (23226) covalent geometry : angle 0.54251 (31569) SS BOND : bond 0.00383 ( 36) SS BOND : angle 2.53059 ( 72) hydrogen bonds : bond 0.04344 ( 935) hydrogen bonds : angle 5.71557 ( 2553) Misc. bond : bond 0.00040 ( 3) link_BETA1-4 : bond 0.00097 ( 6) link_BETA1-4 : angle 1.24458 ( 18) link_NAG-ASN : bond 0.00535 ( 36) link_NAG-ASN : angle 2.50499 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9301 (tpt) cc_final: 0.9067 (tpt) REVERT: B 902 MET cc_start: 0.9122 (tpp) cc_final: 0.8821 (mmt) REVERT: A 902 MET cc_start: 0.9053 (tpp) cc_final: 0.8743 (tpt) outliers start: 15 outliers final: 8 residues processed: 60 average time/residue: 0.5049 time to fit residues: 43.6275 Evaluate side-chains 56 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 246 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN A 920 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.085720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061944 restraints weight = 163375.979| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.78 r_work: 0.2889 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23307 Z= 0.174 Angle : 0.512 8.202 31767 Z= 0.263 Chirality : 0.045 0.285 3711 Planarity : 0.004 0.052 3993 Dihedral : 6.245 58.236 3957 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.57 % Allowed : 4.88 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.67 (0.16), residues: 2724 helix: 1.79 (0.21), residues: 636 sheet: -0.90 (0.18), residues: 678 loop : -1.26 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.014 0.001 TYR A1067 PHE 0.013 0.001 PHE C 898 TRP 0.006 0.001 TRP B 104 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00395 (23226) covalent geometry : angle 0.48332 (31569) SS BOND : bond 0.00385 ( 36) SS BOND : angle 2.05041 ( 72) hydrogen bonds : bond 0.03909 ( 935) hydrogen bonds : angle 5.56786 ( 2553) Misc. bond : bond 0.00046 ( 3) link_BETA1-4 : bond 0.00223 ( 6) link_BETA1-4 : angle 1.13045 ( 18) link_NAG-ASN : bond 0.00529 ( 36) link_NAG-ASN : angle 2.39549 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.9267 (tpt) cc_final: 0.9044 (tpt) REVERT: B 902 MET cc_start: 0.9111 (tpp) cc_final: 0.8862 (mmt) REVERT: A 902 MET cc_start: 0.9048 (tpp) cc_final: 0.8744 (tpt) outliers start: 14 outliers final: 6 residues processed: 61 average time/residue: 0.5582 time to fit residues: 47.8973 Evaluate side-chains 53 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 209 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 237 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN C 394 ASN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061961 restraints weight = 163408.506| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.78 r_work: 0.2890 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23307 Z= 0.191 Angle : 0.515 8.192 31767 Z= 0.264 Chirality : 0.045 0.288 3711 Planarity : 0.004 0.050 3993 Dihedral : 6.109 59.674 3957 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.53 % Allowed : 5.00 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.67 (0.16), residues: 2724 helix: 1.84 (0.21), residues: 636 sheet: -1.05 (0.18), residues: 696 loop : -1.20 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 319 TYR 0.014 0.001 TYR A1067 PHE 0.012 0.001 PHE C 898 TRP 0.006 0.001 TRP B 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00437 (23226) covalent geometry : angle 0.48386 (31569) SS BOND : bond 0.00453 ( 36) SS BOND : angle 2.32978 ( 72) hydrogen bonds : bond 0.03851 ( 935) hydrogen bonds : angle 5.49344 ( 2553) Misc. bond : bond 0.00048 ( 3) link_BETA1-4 : bond 0.00106 ( 6) link_BETA1-4 : angle 1.06501 ( 18) link_NAG-ASN : bond 0.00535 ( 36) link_NAG-ASN : angle 2.39723 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.9104 (tpp) cc_final: 0.8877 (mmt) REVERT: A 902 MET cc_start: 0.9050 (tpp) cc_final: 0.8728 (tpt) outliers start: 13 outliers final: 11 residues processed: 58 average time/residue: 0.4951 time to fit residues: 41.6391 Evaluate side-chains 58 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 901 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 9 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.061237 restraints weight = 164525.099| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.77 r_work: 0.2885 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23307 Z= 0.275 Angle : 0.547 8.177 31767 Z= 0.282 Chirality : 0.046 0.293 3711 Planarity : 0.004 0.053 3993 Dihedral : 6.168 54.774 3957 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.53 % Allowed : 5.33 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.78 (0.16), residues: 2724 helix: 1.79 (0.21), residues: 636 sheet: -1.10 (0.18), residues: 696 loop : -1.29 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 357 TYR 0.015 0.001 TYR A1067 PHE 0.016 0.001 PHE C 898 TRP 0.006 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00628 (23226) covalent geometry : angle 0.51724 (31569) SS BOND : bond 0.00402 ( 36) SS BOND : angle 2.36666 ( 72) hydrogen bonds : bond 0.04072 ( 935) hydrogen bonds : angle 5.53712 ( 2553) Misc. bond : bond 0.00063 ( 3) link_BETA1-4 : bond 0.00100 ( 6) link_BETA1-4 : angle 1.14997 ( 18) link_NAG-ASN : bond 0.00535 ( 36) link_NAG-ASN : angle 2.42273 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.9073 (tpp) cc_final: 0.8758 (tpt) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.4231 time to fit residues: 36.3125 Evaluate side-chains 55 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 134 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062630 restraints weight = 163684.581| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.80 r_work: 0.2900 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23307 Z= 0.124 Angle : 0.488 8.129 31767 Z= 0.250 Chirality : 0.044 0.287 3711 Planarity : 0.004 0.049 3993 Dihedral : 5.888 53.136 3957 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.41 % Allowed : 5.45 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.16), residues: 2724 helix: 1.96 (0.21), residues: 636 sheet: -0.97 (0.18), residues: 690 loop : -1.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.012 0.001 TYR A1067 PHE 0.012 0.001 PHE B 898 TRP 0.006 0.001 TRP B 104 HIS 0.002 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00283 (23226) covalent geometry : angle 0.45955 (31569) SS BOND : bond 0.00396 ( 36) SS BOND : angle 1.98634 ( 72) hydrogen bonds : bond 0.03611 ( 935) hydrogen bonds : angle 5.39978 ( 2553) Misc. bond : bond 0.00042 ( 3) link_BETA1-4 : bond 0.00175 ( 6) link_BETA1-4 : angle 1.03421 ( 18) link_NAG-ASN : bond 0.00546 ( 36) link_NAG-ASN : angle 2.36301 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.4693 time to fit residues: 35.1503 Evaluate side-chains 55 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 275 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 203 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.086581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062845 restraints weight = 163148.874| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.80 r_work: 0.2906 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23307 Z= 0.116 Angle : 0.481 8.129 31767 Z= 0.246 Chirality : 0.044 0.288 3711 Planarity : 0.003 0.048 3993 Dihedral : 5.775 53.509 3957 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.41 % Allowed : 5.45 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.16), residues: 2724 helix: 2.03 (0.21), residues: 636 sheet: -0.95 (0.18), residues: 690 loop : -1.13 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.012 0.001 TYR A1067 PHE 0.012 0.001 PHE B 898 TRP 0.006 0.001 TRP A 104 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00264 (23226) covalent geometry : angle 0.45286 (31569) SS BOND : bond 0.00391 ( 36) SS BOND : angle 1.90705 ( 72) hydrogen bonds : bond 0.03531 ( 935) hydrogen bonds : angle 5.34066 ( 2553) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00178 ( 6) link_BETA1-4 : angle 0.99727 ( 18) link_NAG-ASN : bond 0.00548 ( 36) link_NAG-ASN : angle 2.34835 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.3773 time to fit residues: 29.6959 Evaluate side-chains 56 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 552 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 248 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.085565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.061886 restraints weight = 165117.546| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.79 r_work: 0.2888 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23307 Z= 0.197 Angle : 0.506 8.112 31767 Z= 0.259 Chirality : 0.045 0.290 3711 Planarity : 0.004 0.051 3993 Dihedral : 5.761 54.394 3957 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.37 % Allowed : 5.53 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.58 (0.16), residues: 2724 helix: 2.02 (0.21), residues: 636 sheet: -1.04 (0.18), residues: 696 loop : -1.17 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 357 TYR 0.014 0.001 TYR A1067 PHE 0.014 0.001 PHE B 898 TRP 0.005 0.001 TRP C 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00450 (23226) covalent geometry : angle 0.47765 (31569) SS BOND : bond 0.00387 ( 36) SS BOND : angle 2.09742 ( 72) hydrogen bonds : bond 0.03752 ( 935) hydrogen bonds : angle 5.35479 ( 2553) Misc. bond : bond 0.00045 ( 3) link_BETA1-4 : bond 0.00131 ( 6) link_BETA1-4 : angle 1.06386 ( 18) link_NAG-ASN : bond 0.00530 ( 36) link_NAG-ASN : angle 2.35925 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9066.91 seconds wall clock time: 154 minutes 42.04 seconds (9282.04 seconds total)