Starting phenix.real_space_refine on Fri Sep 19 08:53:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.cif Found real_map, /net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.map" model { file = "/net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8epq_28533/09_2025/8epq_28533.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 15464 2.51 5 N 3962 2.21 5 O 4760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24287 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7937 Classifications: {'peptide': 1014} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 50, 'TRANS': 962} Chain breaks: 8 Chain: "B" Number of atoms: 7622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7622 Classifications: {'peptide': 973} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 47, 'TRANS': 923} Chain breaks: 10 Chain: "C" Number of atoms: 7816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7816 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 49, 'TRANS': 946} Chain breaks: 9 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 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 Time building chain proxies: 6.35, per 1000 atoms: 0.26 Number of scatterers: 24287 At special positions: 0 Unit cell: (138.69, 135.34, 185.59, 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 101 16.00 O 4760 8.00 N 3962 7.00 C 15464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1201 " - " ASN A 122 " " NAG A1202 " - " ASN A 616 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 234 " " NAG A1206 " - " ASN A 331 " " NAG A1207 " - " ASN A 709 " " NAG A1208 " - " ASN A 61 " " NAG A1209 " - " ASN A 165 " " NAG A1210 " - " ASN A 603 " " NAG A1211 " - " ASN A1098 " " NAG A1212 " - " ASN A1134 " " NAG B1201 " - " ASN B 709 " " NAG B1202 " - " ASN B 343 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B1098 " " NAG B1205 " - " ASN B 61 " " NAG B1206 " - " ASN B 616 " " NAG B1207 " - " ASN B 657 " " NAG B1208 " - " ASN B 331 " " NAG B1209 " - " ASN B 603 " " NAG B1210 " - " ASN B1074 " " NAG C1201 " - " ASN C1074 " " NAG C1202 " - " ASN C 331 " " NAG C1203 " - " ASN C 657 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 165 " " NAG C1206 " - " ASN C1098 " " NAG C1207 " - " ASN C 234 " " NAG C1208 " - " ASN C 603 " " NAG C1209 " - " ASN C 343 " " NAG C1210 " - " ASN C 709 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 616 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5608 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 26.1% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.284A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.507A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.683A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.576A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.728A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 946 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.473A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.376A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.556A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 854 through 856 No H-bonds generated for 'chain 'B' and resid 854 through 856' Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.544A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 888 No H-bonds generated for 'chain 'B' and resid 886 through 888' Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.656A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.387A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.833A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.543A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.670A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.344A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.540A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.701A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.656A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.569A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.588A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 828 removed outlier: 3.543A pdb=" N LEU C 821 " --> pdb=" O ALA C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.561A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.618A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.155A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 941 " --> pdb=" O GLY C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.056A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.963A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.593A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.945A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.951A 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 removed outlier: 5.858A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.558A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.145A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.875A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.846A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.276A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.328A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.328A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.244A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.918A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.534A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.750A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.124A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.599A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.798A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.363A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.027A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.529A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 9.050A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.057A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.311A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.002A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.504A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.544A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.767A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.683A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 973 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3926 1.32 - 1.45: 6976 1.45 - 1.57: 13783 1.57 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 24810 Sorted by residual: bond pdb=" C PRO C1069 " pdb=" O PRO C1069 " ideal model delta sigma weight residual 1.233 1.194 0.040 1.12e-02 7.97e+03 1.24e+01 bond pdb=" CA SER B 708 " pdb=" CB SER B 708 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" CA SER A 708 " pdb=" CB SER A 708 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.61e-02 3.86e+03 8.97e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 bond pdb=" CA ALA B 706 " pdb=" CB ALA B 706 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.50e-02 4.44e+03 6.42e+00 ... (remaining 24805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 33637 3.69 - 7.38: 90 7.38 - 11.07: 7 11.07 - 14.76: 2 14.76 - 18.45: 2 Bond angle restraints: 33738 Sorted by residual: angle pdb=" C ASN B 540 " pdb=" N PHE B 541 " pdb=" CA PHE B 541 " ideal model delta sigma weight residual 121.70 140.15 -18.45 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C PHE C 186 " pdb=" N LYS C 187 " pdb=" CA LYS C 187 " ideal model delta sigma weight residual 121.70 138.07 -16.37 1.80e+00 3.09e-01 8.27e+01 angle pdb=" C CYS A 525 " pdb=" N GLY A 526 " pdb=" CA GLY A 526 " ideal model delta sigma weight residual 121.70 133.21 -11.51 1.80e+00 3.09e-01 4.09e+01 angle pdb=" C ASN C 87 " pdb=" CA ASN C 87 " pdb=" CB ASN C 87 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 angle pdb=" C ASN A 544 " pdb=" CA ASN A 544 " pdb=" CB ASN A 544 " ideal model delta sigma weight residual 117.23 110.63 6.60 1.36e+00 5.41e-01 2.35e+01 ... (remaining 33733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 14681 22.10 - 44.20: 730 44.20 - 66.30: 141 66.30 - 88.40: 57 88.40 - 110.50: 21 Dihedral angle restraints: 15630 sinusoidal: 6938 harmonic: 8692 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.51 70.51 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -150.80 64.80 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -149.59 63.59 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 15627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 3961 0.123 - 0.246: 47 0.246 - 0.369: 10 0.369 - 0.492: 2 0.492 - 0.615: 5 Chirality restraints: 4025 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.22e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.70e+00 ... (remaining 4022 not shown) Planarity restraints: 4329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO B 527 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 703 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C ASN A 703 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 703 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 704 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " -0.019 2.00e-02 2.50e+03 1.84e-02 4.21e+00 pdb=" CG ASN A1098 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A1211 " -0.019 2.00e-02 2.50e+03 ... (remaining 4326 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 470 2.67 - 3.23: 22402 3.23 - 3.79: 35920 3.79 - 4.34: 48153 4.34 - 4.90: 80344 Nonbonded interactions: 187289 Sorted by model distance: nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR A 95 " pdb=" O PHE A 186 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR A 29 " pdb=" OD1 ASP A 215 " model vdw 2.215 3.040 nonbonded pdb=" O VAL C 367 " pdb=" OG SER C 371 " model vdw 2.221 3.040 ... (remaining 187284 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 435 or resid 451 through 468 or resid 493 throu \ gh 498 or resid 506 through 1210)) selection = (chain 'B' and (resid 27 through 825 or resid 853 through 1210)) selection = (chain 'C' and (resid 27 through 435 or resid 451 through 468 or resid 493 throu \ gh 498 or resid 506 through 825 or resid 853 through 1210)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.110 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 0.054 24909 Z= 0.207 Angle : 0.760 19.631 34000 Z= 0.381 Chirality : 0.053 0.615 4025 Planarity : 0.004 0.060 4282 Dihedral : 14.306 110.497 9926 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 0.12 % Allowed : 7.15 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 2924 helix: 2.05 (0.21), residues: 679 sheet: 0.49 (0.20), residues: 610 loop : -1.09 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 905 TYR 0.016 0.001 TYR C 674 PHE 0.014 0.001 PHE C1075 TRP 0.028 0.002 TRP A 64 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00390 (24810) covalent geometry : angle 0.67592 (33738) SS BOND : bond 0.00350 ( 32) SS BOND : angle 1.24174 ( 64) hydrogen bonds : bond 0.20981 ( 962) hydrogen bonds : angle 8.12003 ( 2685) Misc. bond : bond 0.00061 ( 1) link_BETA1-4 : bond 0.00737 ( 19) link_BETA1-4 : angle 2.29651 ( 57) link_NAG-ASN : bond 0.00920 ( 47) link_NAG-ASN : angle 5.21780 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 55 average time/residue: 0.1598 time to fit residues: 15.5814 Evaluate side-chains 49 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 965 GLN ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 437 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053365 restraints weight = 141283.860| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 5.62 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 24909 Z= 0.340 Angle : 0.853 18.710 34000 Z= 0.411 Chirality : 0.054 0.473 4025 Planarity : 0.005 0.065 4282 Dihedral : 8.918 64.542 4569 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 1.77 % Allowed : 7.69 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 2924 helix: 1.78 (0.20), residues: 687 sheet: 0.34 (0.20), residues: 600 loop : -1.34 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1019 TYR 0.035 0.002 TYR A 266 PHE 0.021 0.002 PHE A 855 TRP 0.020 0.002 TRP A 64 HIS 0.008 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00793 (24810) covalent geometry : angle 0.76991 (33738) SS BOND : bond 0.00532 ( 32) SS BOND : angle 1.38225 ( 64) hydrogen bonds : bond 0.07822 ( 962) hydrogen bonds : angle 6.39511 ( 2685) Misc. bond : bond 0.00080 ( 1) link_BETA1-4 : bond 0.00446 ( 19) link_BETA1-4 : angle 2.59504 ( 57) link_NAG-ASN : bond 0.00839 ( 47) link_NAG-ASN : angle 5.48936 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 47 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8331 (m-90) cc_final: 0.7986 (m-90) REVERT: A 238 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6899 (t80) REVERT: A 266 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: A 895 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: B 740 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7979 (tmm) REVERT: C 819 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6311 (pt0) REVERT: C 1118 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8531 (p0) outliers start: 46 outliers final: 22 residues processed: 90 average time/residue: 0.1519 time to fit residues: 23.9321 Evaluate side-chains 71 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 43 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 216 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 130 optimal weight: 20.0000 chunk 240 optimal weight: 0.0040 chunk 231 optimal weight: 40.0000 chunk 125 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 overall best weight: 3.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047276 restraints weight = 144117.009| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 5.47 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24909 Z= 0.179 Angle : 0.696 19.097 34000 Z= 0.331 Chirality : 0.050 0.472 4025 Planarity : 0.004 0.052 4282 Dihedral : 7.561 58.708 4569 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.46 % Allowed : 9.03 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 2924 helix: 2.05 (0.20), residues: 692 sheet: 0.40 (0.20), residues: 595 loop : -1.25 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.022 0.001 TYR A 266 PHE 0.014 0.001 PHE C 133 TRP 0.013 0.001 TRP B 64 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00404 (24810) covalent geometry : angle 0.59816 (33738) SS BOND : bond 0.00555 ( 32) SS BOND : angle 1.17219 ( 64) hydrogen bonds : bond 0.06684 ( 962) hydrogen bonds : angle 5.88862 ( 2685) Misc. bond : bond 0.00042 ( 1) link_BETA1-4 : bond 0.00673 ( 19) link_BETA1-4 : angle 2.46538 ( 57) link_NAG-ASN : bond 0.00857 ( 47) link_NAG-ASN : angle 5.29736 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 50 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8350 (m-90) cc_final: 0.8057 (m-90) REVERT: B 740 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8009 (tmm) REVERT: C 1118 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8500 (p0) outliers start: 38 outliers final: 24 residues processed: 84 average time/residue: 0.1445 time to fit residues: 21.6346 Evaluate side-chains 70 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 44 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 57 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.067756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.047350 restraints weight = 144464.546| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 5.49 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24909 Z= 0.161 Angle : 0.671 18.953 34000 Z= 0.318 Chirality : 0.049 0.474 4025 Planarity : 0.004 0.053 4282 Dihedral : 6.733 54.807 4569 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.00 % Allowed : 9.15 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.15), residues: 2924 helix: 2.20 (0.20), residues: 686 sheet: 0.46 (0.20), residues: 597 loop : -1.24 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1019 TYR 0.022 0.001 TYR A 266 PHE 0.012 0.001 PHE A 855 TRP 0.023 0.002 TRP A 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00364 (24810) covalent geometry : angle 0.57430 (33738) SS BOND : bond 0.00314 ( 32) SS BOND : angle 1.48128 ( 64) hydrogen bonds : bond 0.06192 ( 962) hydrogen bonds : angle 5.68261 ( 2685) Misc. bond : bond 0.00156 ( 1) link_BETA1-4 : bond 0.00543 ( 19) link_BETA1-4 : angle 2.27287 ( 57) link_NAG-ASN : bond 0.00749 ( 47) link_NAG-ASN : angle 5.15588 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 49 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8355 (m-90) cc_final: 0.8053 (m-90) REVERT: A 238 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6862 (t80) REVERT: A 266 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: A 1116 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8087 (m) REVERT: B 740 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: C 386 LYS cc_start: 0.8253 (mttt) cc_final: 0.7964 (mtpt) REVERT: C 398 ASP cc_start: -0.1722 (OUTLIER) cc_final: -0.2068 (m-30) REVERT: C 1118 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8470 (p0) outliers start: 52 outliers final: 30 residues processed: 98 average time/residue: 0.1502 time to fit residues: 25.4758 Evaluate side-chains 79 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 43 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 213 optimal weight: 30.0000 chunk 111 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 234 optimal weight: 40.0000 chunk 81 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.066966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046598 restraints weight = 143946.661| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 5.43 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24909 Z= 0.214 Angle : 0.710 18.693 34000 Z= 0.338 Chirality : 0.050 0.451 4025 Planarity : 0.004 0.049 4282 Dihedral : 6.452 58.719 4569 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 2.11 % Allowed : 9.84 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 2924 helix: 2.11 (0.20), residues: 685 sheet: 0.32 (0.20), residues: 594 loop : -1.32 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 509 TYR 0.024 0.001 TYR A 266 PHE 0.018 0.001 PHE A 855 TRP 0.023 0.002 TRP A 64 HIS 0.006 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00498 (24810) covalent geometry : angle 0.61670 (33738) SS BOND : bond 0.00316 ( 32) SS BOND : angle 1.58186 ( 64) hydrogen bonds : bond 0.06697 ( 962) hydrogen bonds : angle 5.67835 ( 2685) Misc. bond : bond 0.00124 ( 1) link_BETA1-4 : bond 0.00586 ( 19) link_BETA1-4 : angle 2.25455 ( 57) link_NAG-ASN : bond 0.00755 ( 47) link_NAG-ASN : angle 5.21553 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 49 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8300 (m-90) cc_final: 0.8004 (m-90) REVERT: A 238 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6922 (t80) REVERT: A 266 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: A 1116 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (m) REVERT: B 392 PHE cc_start: 0.6457 (m-80) cc_final: 0.6254 (m-80) REVERT: B 565 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: B 740 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8158 (tmm) REVERT: C 386 LYS cc_start: 0.8298 (mttt) cc_final: 0.7992 (mtpt) REVERT: C 398 ASP cc_start: -0.1611 (OUTLIER) cc_final: -0.1897 (m-30) REVERT: C 402 ILE cc_start: 0.5958 (tp) cc_final: 0.5746 (tp) REVERT: C 1118 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8535 (p0) outliers start: 55 outliers final: 37 residues processed: 98 average time/residue: 0.1402 time to fit residues: 24.3240 Evaluate side-chains 90 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 46 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 252 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.070492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048020 restraints weight = 133435.302| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 5.00 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24909 Z= 0.118 Angle : 0.623 19.150 34000 Z= 0.295 Chirality : 0.048 0.472 4025 Planarity : 0.004 0.048 4282 Dihedral : 5.918 59.160 4569 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.46 % Allowed : 10.72 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 2924 helix: 2.40 (0.20), residues: 684 sheet: 0.52 (0.20), residues: 593 loop : -1.21 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 214 TYR 0.015 0.001 TYR A 266 PHE 0.013 0.001 PHE B 168 TRP 0.015 0.001 TRP B 64 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00249 (24810) covalent geometry : angle 0.52938 (33738) SS BOND : bond 0.00254 ( 32) SS BOND : angle 1.34114 ( 64) hydrogen bonds : bond 0.05388 ( 962) hydrogen bonds : angle 5.30409 ( 2685) Misc. bond : bond 0.00105 ( 1) link_BETA1-4 : bond 0.00619 ( 19) link_BETA1-4 : angle 1.92675 ( 57) link_NAG-ASN : bond 0.00771 ( 47) link_NAG-ASN : angle 4.93369 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 52 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8364 (m-90) cc_final: 0.8102 (m-90) REVERT: A 238 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6860 (t80) REVERT: A 1116 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8066 (m) REVERT: B 738 CYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 740 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8219 (tmm) REVERT: C 386 LYS cc_start: 0.8388 (mttt) cc_final: 0.8091 (mtpt) REVERT: C 398 ASP cc_start: -0.0764 (OUTLIER) cc_final: -0.1099 (m-30) REVERT: C 1118 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8536 (p0) outliers start: 38 outliers final: 22 residues processed: 87 average time/residue: 0.1446 time to fit residues: 22.7112 Evaluate side-chains 73 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 45 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 213 optimal weight: 8.9990 chunk 165 optimal weight: 0.0670 chunk 18 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 151 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.067519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047006 restraints weight = 144129.855| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.68 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24909 Z= 0.154 Angle : 0.647 18.890 34000 Z= 0.305 Chirality : 0.048 0.451 4025 Planarity : 0.004 0.049 4282 Dihedral : 5.810 59.904 4569 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 10.95 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 2924 helix: 2.50 (0.20), residues: 681 sheet: 0.55 (0.20), residues: 587 loop : -1.22 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.020 0.001 TYR A 266 PHE 0.013 0.001 PHE A 855 TRP 0.027 0.002 TRP A 64 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00349 (24810) covalent geometry : angle 0.55286 (33738) SS BOND : bond 0.00284 ( 32) SS BOND : angle 1.35624 ( 64) hydrogen bonds : bond 0.05707 ( 962) hydrogen bonds : angle 5.31137 ( 2685) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00543 ( 19) link_BETA1-4 : angle 1.96345 ( 57) link_NAG-ASN : bond 0.00731 ( 47) link_NAG-ASN : angle 5.02980 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 48 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8375 (m-90) cc_final: 0.8098 (m-90) REVERT: A 238 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 266 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: A 1116 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8122 (m) REVERT: B 738 CYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 740 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8247 (tmm) REVERT: C 386 LYS cc_start: 0.8319 (mttt) cc_final: 0.8025 (mtpt) REVERT: C 398 ASP cc_start: -0.1499 (OUTLIER) cc_final: -0.1782 (m-30) REVERT: C 1118 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8546 (p0) outliers start: 41 outliers final: 28 residues processed: 86 average time/residue: 0.1437 time to fit residues: 22.0136 Evaluate side-chains 79 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 44 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 289 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 256 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.069105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.048130 restraints weight = 142968.123| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.76 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24909 Z= 0.107 Angle : 0.603 19.202 34000 Z= 0.283 Chirality : 0.047 0.460 4025 Planarity : 0.004 0.046 4282 Dihedral : 5.451 59.948 4569 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.42 % Allowed : 11.15 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.15), residues: 2924 helix: 2.60 (0.21), residues: 683 sheet: 0.60 (0.20), residues: 603 loop : -1.16 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.013 0.001 TYR B1067 PHE 0.008 0.001 PHE C 329 TRP 0.021 0.002 TRP A 64 HIS 0.002 0.000 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00225 (24810) covalent geometry : angle 0.51141 (33738) SS BOND : bond 0.00245 ( 32) SS BOND : angle 1.19361 ( 64) hydrogen bonds : bond 0.04841 ( 962) hydrogen bonds : angle 5.06844 ( 2685) Misc. bond : bond 0.00100 ( 1) link_BETA1-4 : bond 0.00625 ( 19) link_BETA1-4 : angle 1.80395 ( 57) link_NAG-ASN : bond 0.00778 ( 47) link_NAG-ASN : angle 4.80169 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 50 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8374 (m-90) cc_final: 0.8087 (m-90) REVERT: A 238 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6815 (t80) REVERT: A 1116 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7975 (m) REVERT: B 565 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: C 386 LYS cc_start: 0.8393 (mttt) cc_final: 0.7820 (mtmt) REVERT: C 398 ASP cc_start: -0.0966 (OUTLIER) cc_final: -0.1196 (m-30) REVERT: C 1118 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8516 (p0) outliers start: 37 outliers final: 23 residues processed: 83 average time/residue: 0.1464 time to fit residues: 21.5162 Evaluate side-chains 74 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 58 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 224 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.071126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.048358 restraints weight = 129645.764| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 5.12 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24909 Z= 0.167 Angle : 0.640 18.915 34000 Z= 0.303 Chirality : 0.048 0.444 4025 Planarity : 0.004 0.051 4282 Dihedral : 5.564 58.741 4569 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.38 % Allowed : 11.18 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.15), residues: 2924 helix: 2.53 (0.21), residues: 687 sheet: 0.56 (0.20), residues: 597 loop : -1.14 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.019 0.001 TYR A 266 PHE 0.013 0.001 PHE C 318 TRP 0.018 0.002 TRP B 353 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00384 (24810) covalent geometry : angle 0.54942 (33738) SS BOND : bond 0.00414 ( 32) SS BOND : angle 1.61788 ( 64) hydrogen bonds : bond 0.05627 ( 962) hydrogen bonds : angle 5.22126 ( 2685) Misc. bond : bond 0.00056 ( 1) link_BETA1-4 : bond 0.00496 ( 19) link_BETA1-4 : angle 1.87804 ( 57) link_NAG-ASN : bond 0.00730 ( 47) link_NAG-ASN : angle 4.89230 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 46 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8348 (m-90) cc_final: 0.8114 (m-90) REVERT: A 238 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6870 (t80) REVERT: A 1116 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8056 (m) REVERT: B 565 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: C 386 LYS cc_start: 0.8284 (mttt) cc_final: 0.7947 (mtmt) REVERT: C 1118 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8607 (p0) outliers start: 36 outliers final: 26 residues processed: 80 average time/residue: 0.1480 time to fit residues: 21.0768 Evaluate side-chains 75 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 70 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN B 762 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.070401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047760 restraints weight = 129888.886| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 5.06 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24909 Z= 0.176 Angle : 0.660 18.866 34000 Z= 0.315 Chirality : 0.048 0.439 4025 Planarity : 0.004 0.048 4282 Dihedral : 5.835 58.054 4569 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.19 % Allowed : 11.41 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 2924 helix: 2.36 (0.20), residues: 693 sheet: 0.49 (0.20), residues: 598 loop : -1.18 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 355 TYR 0.019 0.001 TYR A 266 PHE 0.011 0.001 PHE C 318 TRP 0.019 0.002 TRP C 353 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00403 (24810) covalent geometry : angle 0.56931 (33738) SS BOND : bond 0.00392 ( 32) SS BOND : angle 1.84325 ( 64) hydrogen bonds : bond 0.06098 ( 962) hydrogen bonds : angle 5.33510 ( 2685) Misc. bond : bond 0.00059 ( 1) link_BETA1-4 : bond 0.00547 ( 19) link_BETA1-4 : angle 1.94800 ( 57) link_NAG-ASN : bond 0.00734 ( 47) link_NAG-ASN : angle 4.93944 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5848 Ramachandran restraints generated. 2924 Oldfield, 0 Emsley, 2924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8334 (m-90) cc_final: 0.8083 (m-90) REVERT: A 238 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 266 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6247 (m-80) REVERT: A 1116 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8115 (m) REVERT: B 565 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7969 (m-80) REVERT: C 386 LYS cc_start: 0.8287 (mttt) cc_final: 0.8028 (mtpt) REVERT: C 398 ASP cc_start: -0.0484 (OUTLIER) cc_final: -0.0835 (m-30) REVERT: C 1118 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8549 (p0) outliers start: 31 outliers final: 25 residues processed: 78 average time/residue: 0.1504 time to fit residues: 20.7128 Evaluate side-chains 75 residues out of total 2602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 44 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 217 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.070443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.048510 restraints weight = 131457.958| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.56 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24909 Z= 0.136 Angle : 0.630 19.002 34000 Z= 0.298 Chirality : 0.048 0.440 4025 Planarity : 0.004 0.049 4282 Dihedral : 5.661 56.330 4569 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.38 % Allowed : 11.30 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 2924 helix: 2.47 (0.21), residues: 689 sheet: 0.55 (0.21), residues: 593 loop : -1.15 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.016 0.001 TYR A 266 PHE 0.012 0.001 PHE A 855 TRP 0.033 0.002 TRP A 64 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00303 (24810) covalent geometry : angle 0.53826 (33738) SS BOND : bond 0.00348 ( 32) SS BOND : angle 1.80570 ( 64) hydrogen bonds : bond 0.05596 ( 962) hydrogen bonds : angle 5.20160 ( 2685) Misc. bond : bond 0.00068 ( 1) link_BETA1-4 : bond 0.00561 ( 19) link_BETA1-4 : angle 1.89396 ( 57) link_NAG-ASN : bond 0.00745 ( 47) link_NAG-ASN : angle 4.84647 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5914.92 seconds wall clock time: 102 minutes 26.61 seconds (6146.61 seconds total)