Starting phenix.real_space_refine on Sun Jun 22 20:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.map" model { file = "/net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vrv_32107/06_2025/7vrv_32107.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16623 2.51 5 N 4277 2.21 5 O 5137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26151 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.55, per 1000 atoms: 0.63 Number of scatterers: 26151 At special positions: 0 Unit cell: (154.96, 160.16, 193.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5137 8.00 N 4277 7.00 C 16623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.04 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 702 " " NAG A1310 " - " ASN A1067 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 702 " " NAG B1309 " - " ASN B 710 " " NAG B1310 " - " ASN B1067 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 702 " " NAG C1310 " - " ASN C1067 " " NAG C1311 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 710 " " NAG F 1 " - " ASN A 794 " " NAG G 1 " - " ASN A1091 " " NAG H 1 " - " ASN A1127 " " NAG I 1 " - " ASN B 282 " " NAG J 1 " - " ASN B 794 " " NAG K 1 " - " ASN B1091 " " NAG L 1 " - " ASN B1127 " " NAG M 1 " - " ASN C 710 " " NAG N 1 " - " ASN C 794 " " NAG O 1 " - " ASN C1091 " " NAG P 1 " - " ASN C1127 " Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.2 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 23.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.722A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.898A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.387A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.576A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.298A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 751 through 776 removed outlier: 3.869A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 3.896A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.673A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 911 removed outlier: 3.973A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.657A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.102A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.828A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.673A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.839A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.641A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.786A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 749 removed outlier: 3.733A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.716A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.535A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.715A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 848 " --> pdb=" O CYS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 848' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 879 through 883 removed outlier: 3.900A pdb=" N GLY B 882 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.712A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.020A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.859A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 3.987A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.689A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 818 removed outlier: 4.124A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.091A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.347A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.100A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.534A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.701A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1139 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.521A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.642A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.270A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.666A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.406A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.823A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.930A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 553 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 697 Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 720 removed outlier: 6.825A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 728 through 729 Processing sheet with id=AB9, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.590A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.812A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.510A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.640A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 327 removed outlier: 6.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.205A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.665A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 704 through 713 removed outlier: 6.360A pdb=" N GLN B1064 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE B 711 " --> pdb=" O PRO B1062 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 713 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B1060 " --> pdb=" O ILE B 713 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 720 removed outlier: 4.174A pdb=" N THR B1069 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE B1088 " --> pdb=" O ALA B1071 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.004A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 29 through 30 removed outlier: 5.146A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.571A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.507A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.549A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.896A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.419A pdb=" N THR C 689 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 704 through 713 removed outlier: 7.147A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AE7, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AE8, first strand: chain 'C' and resid 1087 through 1089 913 hydrogen bonds defined for protein. 2499 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: 11.61 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8334 1.34 - 1.47: 6757 1.47 - 1.59: 11513 1.59 - 1.71: 0 1.71 - 1.83: 144 Bond restraints: 26748 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.64e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 ... (remaining 26743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 35253 1.72 - 3.44: 1064 3.44 - 5.16: 90 5.16 - 6.88: 19 6.88 - 8.60: 3 Bond angle restraints: 36429 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 112.29 106.77 5.52 9.40e-01 1.13e+00 3.44e+01 angle pdb=" N VAL C 213 " pdb=" CA VAL C 213 " pdb=" C VAL C 213 " ideal model delta sigma weight residual 112.96 109.50 3.46 1.00e+00 1.00e+00 1.19e+01 angle pdb=" N VAL C 722 " pdb=" CA VAL C 722 " pdb=" C VAL C 722 " ideal model delta sigma weight residual 113.71 110.60 3.11 9.50e-01 1.11e+00 1.07e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA CYS A 525 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " ideal model delta sigma weight residual 114.40 120.53 -6.13 2.30e+00 1.89e-01 7.11e+00 ... (remaining 36424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15050 17.47 - 34.95: 1269 34.95 - 52.42: 225 52.42 - 69.89: 68 69.89 - 87.37: 27 Dihedral angle restraints: 16639 sinusoidal: 7158 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -0.49 -85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.96 -80.04 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " pdb=" SG CYS B 742 " pdb=" CB CYS B 742 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 ... (remaining 16636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3831 0.079 - 0.159: 440 0.159 - 0.238: 12 0.238 - 0.318: 6 0.318 - 0.397: 4 Chirality restraints: 4293 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 4290 not shown) Planarity restraints: 4697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 664 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO B 665 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO B 665 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 665 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.031 2.00e-02 2.50e+03 3.07e-02 1.18e+01 pdb=" CG ASN B 603 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B1049 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO B1050 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B1050 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B1050 " -0.033 5.00e-02 4.00e+02 ... (remaining 4694 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 424 2.64 - 3.20: 25246 3.20 - 3.77: 39970 3.77 - 4.33: 54712 4.33 - 4.90: 87006 Nonbonded interactions: 207358 Sorted by model distance: nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.071 3.040 nonbonded pdb=" OG SER B 751 " pdb=" OG1 THR B 754 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.140 3.040 nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.143 3.040 nonbonded pdb=" O ASP B 290 " pdb=" OG SER B 297 " model vdw 2.156 3.040 ... (remaining 207353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1140 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1140 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1140 or resid 1301 thro \ ugh 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.030 Extract box with map and model: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 63.550 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.160 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 : 0.004 0.051 26844 Z= 0.197 Angle : 0.710 11.087 36678 Z= 0.372 Chirality : 0.048 0.397 4293 Planarity : 0.005 0.103 4653 Dihedral : 13.403 87.365 10432 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3239 helix: 0.61 (0.21), residues: 645 sheet: -1.12 (0.20), residues: 636 loop : -2.19 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 436 HIS 0.011 0.001 HIS A 66 PHE 0.035 0.002 PHE C 392 TYR 0.019 0.001 TYR A 866 ARG 0.009 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 44) link_NAG-ASN : angle 3.20162 ( 132) link_BETA1-4 : bond 0.00566 ( 13) link_BETA1-4 : angle 2.62092 ( 39) hydrogen bonds : bond 0.13690 ( 899) hydrogen bonds : angle 7.28067 ( 2499) SS BOND : bond 0.00398 ( 39) SS BOND : angle 1.92737 ( 78) covalent geometry : bond 0.00406 (26748) covalent geometry : angle 0.67443 (36429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.5670 (mtt180) cc_final: 0.5417 (mtt180) REVERT: A 237 ARG cc_start: 0.8303 (mtt180) cc_final: 0.7979 (mtp85) REVERT: A 516 GLU cc_start: 0.7566 (pm20) cc_final: 0.7359 (pm20) REVERT: C 700 TYR cc_start: 0.8375 (t80) cc_final: 0.8091 (t80) REVERT: C 848 PHE cc_start: 0.6649 (t80) cc_final: 0.6397 (t80) REVERT: C 1043 MET cc_start: 0.7802 (ptp) cc_final: 0.7483 (ptp) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3364 time to fit residues: 143.3805 Evaluate side-chains 153 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 253 optimal weight: 0.0040 chunk 98 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 294 optimal weight: 5.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 239 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS B1094 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079266 restraints weight = 87058.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079537 restraints weight = 67954.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080054 restraints weight = 51339.335| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26844 Z= 0.118 Angle : 0.604 10.751 36678 Z= 0.307 Chirality : 0.046 0.376 4293 Planarity : 0.004 0.070 4653 Dihedral : 7.456 59.814 4690 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3239 helix: 1.06 (0.21), residues: 663 sheet: -0.94 (0.20), residues: 645 loop : -1.99 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.010 0.001 HIS A 66 PHE 0.023 0.001 PHE C 238 TYR 0.018 0.001 TYR A1060 ARG 0.004 0.000 ARG A1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 44) link_NAG-ASN : angle 2.80317 ( 132) link_BETA1-4 : bond 0.00696 ( 13) link_BETA1-4 : angle 2.26694 ( 39) hydrogen bonds : bond 0.04288 ( 899) hydrogen bonds : angle 6.03307 ( 2499) SS BOND : bond 0.00501 ( 39) SS BOND : angle 1.33766 ( 78) covalent geometry : bond 0.00255 (26748) covalent geometry : angle 0.57396 (36429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8249 (mtt180) cc_final: 0.8041 (mtp85) REVERT: A 490 PHE cc_start: 0.7580 (t80) cc_final: 0.7224 (t80) REVERT: B 723 SER cc_start: 0.9018 (t) cc_final: 0.8539 (t) REVERT: C 392 PHE cc_start: 0.7881 (m-10) cc_final: 0.7565 (m-80) REVERT: C 849 ASN cc_start: 0.8657 (m110) cc_final: 0.8454 (m110) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.3268 time to fit residues: 136.4389 Evaluate side-chains 162 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 179 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 274 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 563 GLN C 894 GLN C 948 ASN C 958 GLN ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.098886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078004 restraints weight = 87925.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077877 restraints weight = 75805.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.078435 restraints weight = 59823.857| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26844 Z= 0.180 Angle : 0.630 10.742 36678 Z= 0.320 Chirality : 0.046 0.376 4293 Planarity : 0.004 0.064 4653 Dihedral : 7.188 59.792 4690 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.11 % Allowed : 4.42 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3239 helix: 1.01 (0.21), residues: 662 sheet: -0.90 (0.20), residues: 654 loop : -2.01 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 879 HIS 0.009 0.001 HIS A 66 PHE 0.022 0.001 PHE B 374 TYR 0.024 0.001 TYR B 897 ARG 0.004 0.000 ARG A 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 44) link_NAG-ASN : angle 2.75658 ( 132) link_BETA1-4 : bond 0.00641 ( 13) link_BETA1-4 : angle 2.28859 ( 39) hydrogen bonds : bond 0.04389 ( 899) hydrogen bonds : angle 5.93991 ( 2499) SS BOND : bond 0.00421 ( 39) SS BOND : angle 1.53149 ( 78) covalent geometry : bond 0.00401 (26748) covalent geometry : angle 0.60110 (36429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 241 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6677 (ptp) cc_final: 0.6292 (ptp) REVERT: A 983 GLU cc_start: 0.6598 (tm-30) cc_final: 0.5998 (tp30) REVERT: A 987 ASP cc_start: 0.8511 (m-30) cc_final: 0.8260 (m-30) REVERT: C 317 ASN cc_start: 0.8177 (t0) cc_final: 0.7754 (t0) REVERT: C 571 ASP cc_start: 0.7596 (t70) cc_final: 0.7262 (t0) REVERT: C 998 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7923 (mm-40) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.3403 time to fit residues: 139.3305 Evaluate side-chains 158 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 217 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 306 optimal weight: 0.5980 chunk 205 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.096903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075692 restraints weight = 89079.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075804 restraints weight = 74136.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076260 restraints weight = 57136.028| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26844 Z= 0.258 Angle : 0.705 10.251 36678 Z= 0.358 Chirality : 0.048 0.401 4293 Planarity : 0.005 0.065 4653 Dihedral : 7.320 59.150 4690 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 3239 helix: 0.74 (0.21), residues: 668 sheet: -1.01 (0.20), residues: 681 loop : -2.09 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 104 HIS 0.010 0.002 HIS C 66 PHE 0.023 0.002 PHE B 374 TYR 0.024 0.002 TYR A1060 ARG 0.005 0.001 ARG A1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 44) link_NAG-ASN : angle 2.75204 ( 132) link_BETA1-4 : bond 0.00628 ( 13) link_BETA1-4 : angle 2.34768 ( 39) hydrogen bonds : bond 0.04661 ( 899) hydrogen bonds : angle 6.08636 ( 2499) SS BOND : bond 0.00535 ( 39) SS BOND : angle 1.74378 ( 78) covalent geometry : bond 0.00571 (26748) covalent geometry : angle 0.67876 (36429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7962 (mtp85) REVERT: A 490 PHE cc_start: 0.7652 (t80) cc_final: 0.7405 (t80) REVERT: A 983 GLU cc_start: 0.6611 (tm-30) cc_final: 0.5921 (tp30) REVERT: A 987 ASP cc_start: 0.8541 (m-30) cc_final: 0.8255 (m-30) REVERT: C 317 ASN cc_start: 0.8260 (t0) cc_final: 0.7786 (t0) REVERT: C 360 ASN cc_start: 0.8560 (m-40) cc_final: 0.8313 (p0) REVERT: C 571 ASP cc_start: 0.7637 (t70) cc_final: 0.7247 (t0) REVERT: C 895 MET cc_start: 0.8756 (tpp) cc_final: 0.8275 (tpt) REVERT: C 998 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7807 (mm-40) REVERT: C 1043 MET cc_start: 0.8419 (ptp) cc_final: 0.7797 (ptp) outliers start: 2 outliers final: 1 residues processed: 228 average time/residue: 0.3200 time to fit residues: 123.9934 Evaluate side-chains 145 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 310 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 995 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077857 restraints weight = 87615.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078263 restraints weight = 69205.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078613 restraints weight = 53543.492| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26844 Z= 0.142 Angle : 0.621 10.169 36678 Z= 0.314 Chirality : 0.046 0.382 4293 Planarity : 0.004 0.059 4653 Dihedral : 6.938 59.870 4690 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3239 helix: 1.00 (0.21), residues: 664 sheet: -0.87 (0.20), residues: 666 loop : -1.99 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 879 HIS 0.021 0.001 HIS B1041 PHE 0.022 0.001 PHE B 374 TYR 0.022 0.001 TYR B 897 ARG 0.004 0.000 ARG A1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 44) link_NAG-ASN : angle 2.70086 ( 132) link_BETA1-4 : bond 0.00636 ( 13) link_BETA1-4 : angle 2.32792 ( 39) hydrogen bonds : bond 0.04191 ( 899) hydrogen bonds : angle 5.78822 ( 2499) SS BOND : bond 0.00407 ( 39) SS BOND : angle 1.71270 ( 78) covalent geometry : bond 0.00318 (26748) covalent geometry : angle 0.59094 (36429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6685 (ptp) cc_final: 0.6425 (ptp) REVERT: A 516 GLU cc_start: 0.7382 (pm20) cc_final: 0.7048 (pm20) REVERT: A 983 GLU cc_start: 0.6599 (tm-30) cc_final: 0.5833 (tp30) REVERT: A 987 ASP cc_start: 0.8568 (m-30) cc_final: 0.8244 (m-30) REVERT: C 317 ASN cc_start: 0.7975 (t0) cc_final: 0.7404 (t0) REVERT: C 571 ASP cc_start: 0.7501 (t70) cc_final: 0.7085 (t0) REVERT: C 754 THR cc_start: 0.7911 (p) cc_final: 0.7640 (t) REVERT: C 895 MET cc_start: 0.8812 (tpp) cc_final: 0.8269 (tpt) REVERT: C 1043 MET cc_start: 0.8366 (ptp) cc_final: 0.7752 (ptp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3266 time to fit residues: 141.7861 Evaluate side-chains 159 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 123 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.100150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079290 restraints weight = 87783.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.079413 restraints weight = 74143.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079928 restraints weight = 58391.788| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26844 Z= 0.128 Angle : 0.598 9.893 36678 Z= 0.302 Chirality : 0.045 0.369 4293 Planarity : 0.004 0.055 4653 Dihedral : 6.610 59.709 4690 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3239 helix: 1.12 (0.21), residues: 665 sheet: -0.78 (0.20), residues: 691 loop : -1.93 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.013 0.001 HIS C 66 PHE 0.039 0.001 PHE B 816 TYR 0.017 0.001 TYR A1060 ARG 0.004 0.000 ARG A 976 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 44) link_NAG-ASN : angle 2.56859 ( 132) link_BETA1-4 : bond 0.00674 ( 13) link_BETA1-4 : angle 2.29471 ( 39) hydrogen bonds : bond 0.04008 ( 899) hydrogen bonds : angle 5.62821 ( 2499) SS BOND : bond 0.00506 ( 39) SS BOND : angle 1.50992 ( 78) covalent geometry : bond 0.00288 (26748) covalent geometry : angle 0.57100 (36429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6670 (ptp) cc_final: 0.6431 (ptp) REVERT: A 983 GLU cc_start: 0.6599 (tm-30) cc_final: 0.5881 (tp30) REVERT: C 317 ASN cc_start: 0.7917 (t0) cc_final: 0.7493 (t0) REVERT: C 571 ASP cc_start: 0.7503 (t70) cc_final: 0.7093 (t0) REVERT: C 754 THR cc_start: 0.7960 (p) cc_final: 0.7630 (t) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3217 time to fit residues: 139.2719 Evaluate side-chains 160 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 270 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 221 optimal weight: 30.0000 chunk 256 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 755 GLN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.096361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075433 restraints weight = 89078.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.075040 restraints weight = 79558.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075651 restraints weight = 66458.724| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 26844 Z= 0.300 Angle : 0.773 10.586 36678 Z= 0.391 Chirality : 0.049 0.383 4293 Planarity : 0.005 0.063 4653 Dihedral : 7.223 59.971 4690 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3239 helix: 0.46 (0.20), residues: 682 sheet: -1.09 (0.19), residues: 714 loop : -2.05 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 104 HIS 0.011 0.002 HIS C 66 PHE 0.028 0.002 PHE B 374 TYR 0.035 0.002 TYR B 897 ARG 0.009 0.001 ARG B 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 44) link_NAG-ASN : angle 2.78804 ( 132) link_BETA1-4 : bond 0.00621 ( 13) link_BETA1-4 : angle 2.45791 ( 39) hydrogen bonds : bond 0.04858 ( 899) hydrogen bonds : angle 6.06511 ( 2499) SS BOND : bond 0.00626 ( 39) SS BOND : angle 2.22679 ( 78) covalent geometry : bond 0.00665 (26748) covalent geometry : angle 0.74573 (36429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6611 (ptp) cc_final: 0.6356 (ptp) REVERT: B 911 GLU cc_start: 0.8345 (pp20) cc_final: 0.7772 (pp20) REVERT: C 317 ASN cc_start: 0.8283 (t0) cc_final: 0.7616 (t0) REVERT: C 552 LEU cc_start: 0.9137 (mm) cc_final: 0.8556 (mp) REVERT: C 571 ASP cc_start: 0.7653 (t70) cc_final: 0.7253 (t0) REVERT: C 1043 MET cc_start: 0.8448 (ptp) cc_final: 0.8089 (ptp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.4328 time to fit residues: 160.0347 Evaluate side-chains 138 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 33 optimal weight: 0.0060 chunk 137 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 865 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 894 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.100048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.078855 restraints weight = 87285.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.079871 restraints weight = 69168.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.080230 restraints weight = 49681.342| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26844 Z= 0.123 Angle : 0.622 10.157 36678 Z= 0.316 Chirality : 0.046 0.387 4293 Planarity : 0.004 0.055 4653 Dihedral : 6.682 59.954 4690 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3239 helix: 1.00 (0.21), residues: 666 sheet: -0.79 (0.20), residues: 684 loop : -1.93 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 633 HIS 0.009 0.001 HIS C 66 PHE 0.023 0.002 PHE C 392 TYR 0.020 0.001 TYR B 265 ARG 0.005 0.000 ARG A1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 44) link_NAG-ASN : angle 2.61988 ( 132) link_BETA1-4 : bond 0.00653 ( 13) link_BETA1-4 : angle 2.32927 ( 39) hydrogen bonds : bond 0.04074 ( 899) hydrogen bonds : angle 5.62427 ( 2499) SS BOND : bond 0.00368 ( 39) SS BOND : angle 1.83245 ( 78) covalent geometry : bond 0.00276 (26748) covalent geometry : angle 0.59314 (36429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 983 GLU cc_start: 0.6909 (tp30) cc_final: 0.6647 (tp30) REVERT: C 317 ASN cc_start: 0.8024 (t0) cc_final: 0.7414 (t0) REVERT: C 534 VAL cc_start: 0.8520 (t) cc_final: 0.8284 (t) REVERT: C 552 LEU cc_start: 0.9113 (mm) cc_final: 0.8496 (mp) REVERT: C 571 ASP cc_start: 0.7432 (t70) cc_final: 0.6988 (t0) REVERT: C 690 MET cc_start: 0.8197 (tmm) cc_final: 0.7845 (tmm) REVERT: C 848 PHE cc_start: 0.6575 (t80) cc_final: 0.6299 (t80) REVERT: C 978 ASP cc_start: 0.7042 (m-30) cc_final: 0.6542 (m-30) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.4391 time to fit residues: 186.9766 Evaluate side-chains 162 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 3.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 217 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 139 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.099226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.078787 restraints weight = 88192.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078048 restraints weight = 80441.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078771 restraints weight = 64478.834| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26844 Z= 0.161 Angle : 0.632 10.358 36678 Z= 0.320 Chirality : 0.046 0.379 4293 Planarity : 0.004 0.056 4653 Dihedral : 6.634 58.798 4690 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3239 helix: 0.95 (0.21), residues: 670 sheet: -0.78 (0.20), residues: 681 loop : -1.94 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 104 HIS 0.010 0.001 HIS A 66 PHE 0.027 0.002 PHE C 392 TYR 0.018 0.001 TYR B 866 ARG 0.004 0.000 ARG A1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 44) link_NAG-ASN : angle 2.56561 ( 132) link_BETA1-4 : bond 0.00644 ( 13) link_BETA1-4 : angle 2.33499 ( 39) hydrogen bonds : bond 0.04163 ( 899) hydrogen bonds : angle 5.66391 ( 2499) SS BOND : bond 0.00353 ( 39) SS BOND : angle 1.75608 ( 78) covalent geometry : bond 0.00367 (26748) covalent geometry : angle 0.60523 (36429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.7639 (t80) cc_final: 0.7399 (t80) REVERT: A 724 MET cc_start: 0.8549 (ptm) cc_final: 0.8272 (ptm) REVERT: A 733 MET cc_start: 0.8490 (tpp) cc_final: 0.7948 (tpt) REVERT: C 317 ASN cc_start: 0.8102 (t0) cc_final: 0.7493 (t0) REVERT: C 534 VAL cc_start: 0.8576 (t) cc_final: 0.8361 (t) REVERT: C 552 LEU cc_start: 0.9096 (mm) cc_final: 0.8516 (mp) REVERT: C 571 ASP cc_start: 0.7483 (t70) cc_final: 0.7060 (t0) REVERT: C 690 MET cc_start: 0.8237 (tmm) cc_final: 0.7919 (tmm) REVERT: C 754 THR cc_start: 0.8031 (p) cc_final: 0.7758 (t) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3432 time to fit residues: 138.8456 Evaluate side-chains 157 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 279 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 239 optimal weight: 40.0000 chunk 110 optimal weight: 0.9980 chunk 306 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 0.0870 chunk 320 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 overall best weight: 1.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 GLN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.099463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078636 restraints weight = 87733.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.078125 restraints weight = 77465.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.078712 restraints weight = 63192.034| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26844 Z= 0.144 Angle : 0.619 10.179 36678 Z= 0.314 Chirality : 0.046 0.373 4293 Planarity : 0.004 0.059 4653 Dihedral : 6.552 59.274 4690 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3239 helix: 0.96 (0.21), residues: 676 sheet: -0.73 (0.20), residues: 667 loop : -1.95 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.011 0.001 HIS A 66 PHE 0.024 0.001 PHE A 275 TYR 0.019 0.001 TYR B 866 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 44) link_NAG-ASN : angle 2.47283 ( 132) link_BETA1-4 : bond 0.00627 ( 13) link_BETA1-4 : angle 2.30522 ( 39) hydrogen bonds : bond 0.04022 ( 899) hydrogen bonds : angle 5.59457 ( 2499) SS BOND : bond 0.00396 ( 39) SS BOND : angle 1.77495 ( 78) covalent geometry : bond 0.00327 (26748) covalent geometry : angle 0.59260 (36429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.9006 (pt) cc_final: 0.8774 (tt) REVERT: A 724 MET cc_start: 0.8469 (ptm) cc_final: 0.8157 (ptm) REVERT: A 733 MET cc_start: 0.8545 (tpp) cc_final: 0.8022 (tpt) REVERT: A 983 GLU cc_start: 0.6830 (tp30) cc_final: 0.6550 (tp30) REVERT: B 912 ASN cc_start: 0.8394 (p0) cc_final: 0.8021 (p0) REVERT: B 1040 TYR cc_start: 0.7922 (m-80) cc_final: 0.7668 (m-80) REVERT: C 317 ASN cc_start: 0.8115 (t0) cc_final: 0.7564 (t0) REVERT: C 534 VAL cc_start: 0.8567 (t) cc_final: 0.8340 (t) REVERT: C 552 LEU cc_start: 0.9120 (mm) cc_final: 0.8543 (mp) REVERT: C 571 ASP cc_start: 0.7484 (t70) cc_final: 0.7094 (t0) REVERT: C 690 MET cc_start: 0.8232 (tmm) cc_final: 0.7927 (tmm) REVERT: C 754 THR cc_start: 0.8073 (p) cc_final: 0.7786 (t) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3480 time to fit residues: 137.6307 Evaluate side-chains 159 residues out of total 2839 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5588 > 50: distance: 40 - 98: 10.949 distance: 43 - 95: 13.950 distance: 53 - 85: 10.920 distance: 69 - 75: 5.079 distance: 75 - 76: 14.157 distance: 76 - 77: 7.055 distance: 76 - 79: 13.552 distance: 77 - 78: 11.609 distance: 77 - 82: 15.834 distance: 79 - 80: 4.971 distance: 79 - 81: 23.298 distance: 82 - 83: 3.089 distance: 83 - 84: 8.114 distance: 84 - 85: 5.752 distance: 84 - 90: 8.304 distance: 86 - 87: 4.643 distance: 87 - 88: 8.661 distance: 87 - 89: 8.394 distance: 91 - 92: 7.441 distance: 91 - 94: 3.599 distance: 92 - 93: 9.684 distance: 92 - 95: 5.842 distance: 95 - 96: 10.706 distance: 96 - 97: 16.753 distance: 96 - 99: 21.342 distance: 97 - 98: 14.919 distance: 97 - 102: 13.415 distance: 99 - 100: 5.181 distance: 99 - 101: 6.137 distance: 102 - 103: 7.059 distance: 103 - 104: 9.343 distance: 103 - 106: 14.919 distance: 104 - 105: 8.051 distance: 104 - 110: 4.558 distance: 106 - 107: 6.411 distance: 107 - 108: 14.700 distance: 107 - 109: 10.907 distance: 111 - 114: 5.309 distance: 112 - 113: 3.438 distance: 112 - 116: 3.304 distance: 114 - 115: 11.053 distance: 115 - 180: 14.468 distance: 116 - 117: 12.514 distance: 117 - 118: 15.734 distance: 117 - 120: 12.413 distance: 118 - 119: 21.782 distance: 118 - 121: 21.309 distance: 121 - 122: 10.606 distance: 122 - 123: 19.100 distance: 122 - 125: 20.514 distance: 123 - 124: 23.877 distance: 123 - 129: 5.469 distance: 125 - 126: 6.874 distance: 126 - 127: 3.743 distance: 129 - 130: 8.074 distance: 130 - 131: 5.965 distance: 130 - 133: 9.935 distance: 131 - 137: 4.879 distance: 132 - 157: 12.234 distance: 133 - 134: 9.158 distance: 134 - 136: 4.733 distance: 137 - 138: 3.002 distance: 137 - 143: 5.083 distance: 138 - 139: 8.728 distance: 138 - 141: 4.840 distance: 139 - 144: 4.613 distance: 140 - 166: 5.610 distance: 141 - 142: 12.186 distance: 142 - 143: 11.146