Starting phenix.real_space_refine on Fri Mar 6 12:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.map" model { file = "/net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uz4_26878/03_2026/7uz4_26878.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 135 5.16 5 C 19575 2.51 5 N 5037 2.21 5 O 6015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30762 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8247 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1005} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "P" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 946 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 7.25, per 1000 atoms: 0.24 Number of scatterers: 30762 At special positions: 0 Unit cell: (154.752, 165.568, 194.688, 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 135 16.00 O 6015 8.00 N 5037 7.00 C 19575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.02 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 122 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 234 " " NAG A1314 " - " ASN A 282 " " NAG A1315 " - " ASN A 801 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 122 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 234 " " NAG B1314 " - " ASN B 282 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 343 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 234 " " NAG C1314 " - " ASN C 282 " " NAG C1315 " - " ASN C 801 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 66 sheets defined 22.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.827A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.952A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.995A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.834A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.594A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.599A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.536A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 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: 4.241A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.470A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.847A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.622A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.808A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 3.657A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.532A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 966 Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.592A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.693A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.527A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.577A pdb=" N ALA C 352 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.001A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.699A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.990A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.709A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.536A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.559A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 removed outlier: 3.542A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.319A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.641A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 84 No H-bonds generated for 'chain 'H' and resid 82 through 84' Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.876A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 85 Processing helix chain 'M' and resid 95 through 99 removed outlier: 3.535A pdb=" N ASP M 98 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER M 99 " --> pdb=" O SER M 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 95 through 99' Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.505A pdb=" N ASN P 36 " --> pdb=" O THR P 29 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR P 37 " --> pdb=" O PHE P 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 29 through 37' Processing helix chain 'P' and resid 69 through 72 removed outlier: 4.298A pdb=" N LYS P 72 " --> pdb=" O GLN P 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 69 through 72' Processing helix chain 'P' and resid 82 through 85 Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'Q' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.356A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.872A 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: 3.940A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.340A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.938A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 9.926A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.216A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.631A 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 314 removed outlier: 3.517A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.529A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 removed outlier: 4.178A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 395 removed outlier: 4.178A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.772A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.531A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1047 through 1048 Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.391A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.878A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.129A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.858A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.551A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.565A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.565A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.599A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.510A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.530A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.144A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.640A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.540A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.540A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.177A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.534A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.534A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.804A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AF5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.575A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.733A pdb=" N LYS H 24 " --> pdb=" O GLN H 5 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL H 19 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU H 91 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.088A pdb=" N TRP H 118 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG H 106 " --> pdb=" O TRP H 118 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN H 120 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS H 104 " --> pdb=" O GLN H 120 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET H 39 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.077A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.978A pdb=" N MET L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'L' and resid 51 through 52 removed outlier: 3.509A pdb=" N TYR L 42 " --> pdb=" O HIS L 103 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS L 103 " --> pdb=" O TYR L 42 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.647A pdb=" N VAL M 13 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS M 40 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET M 39 " --> pdb=" O GLU M 55 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLU M 55 " --> pdb=" O MET M 39 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TRP M 41 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS M 66 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 19 through 21 removed outlier: 3.866A pdb=" N VAL M 19 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU M 91 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.521A pdb=" N HIS N 103 " --> pdb=" O TYR N 42 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.894A pdb=" N VAL N 19 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR N 87 " --> pdb=" O CYS N 23 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR N 88 " --> pdb=" O SER N 79 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER N 79 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AG8, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.651A pdb=" N THR P 125 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL P 42 " --> pdb=" O TYR P 103 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS P 40 " --> pdb=" O ALA P 105 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LYS P 43 " --> pdb=" O TRP P 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP P 52 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG P 45 " --> pdb=" O LEU P 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU P 50 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS P 66 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 11 through 12 removed outlier: 3.651A pdb=" N THR P 125 " --> pdb=" O GLU P 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR P 117 " --> pdb=" O ARG P 106 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 18 through 21 removed outlier: 3.651A pdb=" N LEU P 91 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR P 86 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 4 through 5 removed outlier: 3.540A pdb=" N VAL Q 19 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR Q 90 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 50 through 54 removed outlier: 6.823A pdb=" N TRP Q 41 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR Q 117 " --> pdb=" O GLN Q 106 " (cutoff:3.500A) 1151 hydrogen bonds defined for protein. 3057 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: 8.03 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9771 1.34 - 1.47: 8121 1.47 - 1.59: 13428 1.59 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 31497 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 31492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 41779 1.61 - 3.22: 1008 3.22 - 4.83: 104 4.83 - 6.45: 20 6.45 - 8.06: 1 Bond angle restraints: 42912 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.68 -3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" CA GLY C 219 " pdb=" C GLY C 219 " pdb=" N PHE C 220 " ideal model delta sigma weight residual 114.66 117.95 -3.29 1.10e+00 8.26e-01 8.93e+00 angle pdb=" CA GLY A 667 " pdb=" C GLY A 667 " pdb=" N ALA A 668 " ideal model delta sigma weight residual 114.23 116.59 -2.36 8.80e-01 1.29e+00 7.22e+00 angle pdb=" CA ARG A 237 " pdb=" CB ARG A 237 " pdb=" CG ARG A 237 " ideal model delta sigma weight residual 114.10 119.45 -5.35 2.00e+00 2.50e-01 7.16e+00 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.99e+00 ... (remaining 42907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 17557 17.12 - 34.24: 1377 34.24 - 51.35: 280 51.35 - 68.47: 68 68.47 - 85.59: 26 Dihedral angle restraints: 19308 sinusoidal: 8067 harmonic: 11241 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -151.69 65.69 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 155.76 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 153.91 -60.91 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 19305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4407 0.076 - 0.151: 557 0.151 - 0.227: 10 0.227 - 0.303: 3 0.303 - 0.379: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1 NAG C1315 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1315 " pdb=" O5 NAG C1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 4977 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.001 2.00e-02 2.50e+03 1.96e-02 4.79e+00 pdb=" CG ASN C 801 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1315 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " -0.017 2.00e-02 2.50e+03 1.56e-02 4.27e+00 pdb=" CG PHE A 906 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.003 2.00e-02 2.50e+03 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 641 2.68 - 3.23: 29411 3.23 - 3.79: 47537 3.79 - 4.34: 64036 4.34 - 4.90: 107184 Nonbonded interactions: 248809 Sorted by model distance: nonbonded pdb=" O TYR P 114 " pdb=" OH TYR Q 42 " model vdw 2.122 3.040 nonbonded pdb=" O PHE H 71 " pdb=" OG SER H 76 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR C 369 " pdb=" O SER P 110 " model vdw 2.177 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.177 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.196 3.040 ... (remaining 248804 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 30.500 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.005 0.064 31590 Z= 0.223 Angle : 0.614 11.469 43149 Z= 0.314 Chirality : 0.046 0.379 4980 Planarity : 0.004 0.053 5475 Dihedral : 12.867 85.591 11976 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.06 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.13), residues: 3819 helix: 2.21 (0.20), residues: 613 sheet: -0.35 (0.18), residues: 885 loop : -0.85 (0.12), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 815 TYR 0.024 0.002 TYR B1138 PHE 0.036 0.002 PHE A 906 TRP 0.034 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00503 (31497) covalent geometry : angle 0.59392 (42912) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.25333 ( 84) hydrogen bonds : bond 0.21694 ( 1106) hydrogen bonds : angle 9.10896 ( 3057) link_BETA1-4 : bond 0.00498 ( 3) link_BETA1-4 : angle 1.84145 ( 9) link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 2.60420 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.5089 (ppp) cc_final: 0.4861 (ppp) REVERT: A 237 ARG cc_start: 0.7735 (tpt170) cc_final: 0.7192 (tpt170) REVERT: A 950 ASP cc_start: 0.7695 (t0) cc_final: 0.7430 (t0) REVERT: B 1141 LEU cc_start: 0.7942 (mt) cc_final: 0.7703 (tt) REVERT: C 574 ASP cc_start: 0.7503 (t70) cc_final: 0.7136 (t70) outliers start: 2 outliers final: 1 residues processed: 179 average time/residue: 0.1675 time to fit residues: 53.0668 Evaluate side-chains 134 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 658 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.5848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A1088 HIS B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 658 ASN C 239 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN C1101 HIS H 6 GLN ** M 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.206327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126962 restraints weight = 49686.064| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.76 r_work: 0.3389 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31590 Z= 0.149 Angle : 0.559 10.613 43149 Z= 0.287 Chirality : 0.046 0.371 4980 Planarity : 0.004 0.048 5475 Dihedral : 6.345 57.539 5225 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.30 % Allowed : 5.30 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3819 helix: 2.19 (0.20), residues: 650 sheet: -0.19 (0.17), residues: 923 loop : -0.89 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.023 0.001 TYR A 170 PHE 0.022 0.001 PHE A 400 TRP 0.019 0.001 TRP A 886 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00338 (31497) covalent geometry : angle 0.54149 (42912) SS BOND : bond 0.00334 ( 42) SS BOND : angle 0.98030 ( 84) hydrogen bonds : bond 0.04610 ( 1106) hydrogen bonds : angle 6.83885 ( 3057) link_BETA1-4 : bond 0.00401 ( 3) link_BETA1-4 : angle 1.31746 ( 9) link_NAG-ASN : bond 0.00545 ( 48) link_NAG-ASN : angle 2.39079 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.5580 (m90) cc_final: 0.5314 (m90) REVERT: A 238 PHE cc_start: 0.4973 (p90) cc_final: 0.4741 (p90) REVERT: A 950 ASP cc_start: 0.8306 (t0) cc_final: 0.7944 (t0) REVERT: B 1141 LEU cc_start: 0.8086 (mt) cc_final: 0.7687 (tt) REVERT: C 562 PHE cc_start: 0.7808 (p90) cc_final: 0.7579 (p90) REVERT: H 89 MET cc_start: 0.2275 (mtt) cc_final: 0.1730 (mmp) REVERT: N 105 GLN cc_start: 0.0849 (tm-30) cc_final: 0.0455 (mm-40) outliers start: 10 outliers final: 10 residues processed: 166 average time/residue: 0.1715 time to fit residues: 49.3610 Evaluate side-chains 148 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 975 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 246 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 153 optimal weight: 6.9990 chunk 352 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 341 optimal weight: 30.0000 chunk 87 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN M 36 ASN M 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.205600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.125925 restraints weight = 49699.160| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.74 r_work: 0.3375 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31590 Z= 0.176 Angle : 0.552 10.414 43149 Z= 0.280 Chirality : 0.046 0.342 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.977 57.973 5223 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.60 % Allowed : 8.22 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3819 helix: 2.14 (0.20), residues: 649 sheet: -0.28 (0.16), residues: 935 loop : -0.91 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 815 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.002 PHE A1121 TRP 0.018 0.001 TRP B 886 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00411 (31497) covalent geometry : angle 0.53373 (42912) SS BOND : bond 0.00397 ( 42) SS BOND : angle 0.87271 ( 84) hydrogen bonds : bond 0.04132 ( 1106) hydrogen bonds : angle 6.34115 ( 3057) link_BETA1-4 : bond 0.00215 ( 3) link_BETA1-4 : angle 1.24376 ( 9) link_NAG-ASN : bond 0.00561 ( 48) link_NAG-ASN : angle 2.40792 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5034 (p90) cc_final: 0.4688 (p90) REVERT: A 950 ASP cc_start: 0.8299 (t0) cc_final: 0.7904 (t0) REVERT: A 1144 GLU cc_start: 0.7749 (mp0) cc_final: 0.7509 (mp0) REVERT: B 1141 LEU cc_start: 0.8063 (mt) cc_final: 0.7565 (tt) REVERT: C 65 PHE cc_start: 0.7059 (m-80) cc_final: 0.6473 (m-10) REVERT: C 780 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8063 (mm-30) REVERT: N 105 GLN cc_start: 0.0855 (tm-30) cc_final: 0.0472 (mm-40) REVERT: N 116 TYR cc_start: 0.3198 (m-10) cc_final: 0.2991 (m-10) outliers start: 20 outliers final: 11 residues processed: 176 average time/residue: 0.1722 time to fit residues: 52.9939 Evaluate side-chains 157 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 274 optimal weight: 0.9990 chunk 225 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 319 optimal weight: 0.0770 chunk 107 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 345 optimal weight: 7.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.207054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130223 restraints weight = 49361.255| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.13 r_work: 0.3397 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31590 Z= 0.104 Angle : 0.499 9.839 43149 Z= 0.252 Chirality : 0.044 0.392 4980 Planarity : 0.003 0.047 5475 Dihedral : 5.516 54.284 5223 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 9.49 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3819 helix: 2.41 (0.20), residues: 656 sheet: -0.25 (0.17), residues: 910 loop : -0.88 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.014 0.001 TYR B 170 PHE 0.017 0.001 PHE A 400 TRP 0.015 0.001 TRP A 353 HIS 0.003 0.000 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00226 (31497) covalent geometry : angle 0.48150 (42912) SS BOND : bond 0.00186 ( 42) SS BOND : angle 0.66881 ( 84) hydrogen bonds : bond 0.03523 ( 1106) hydrogen bonds : angle 5.89580 ( 3057) link_BETA1-4 : bond 0.00483 ( 3) link_BETA1-4 : angle 0.98926 ( 9) link_NAG-ASN : bond 0.00489 ( 48) link_NAG-ASN : angle 2.27075 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5322 (p90) cc_final: 0.4893 (p90) REVERT: A 950 ASP cc_start: 0.8243 (t0) cc_final: 0.7823 (t0) REVERT: A 1144 GLU cc_start: 0.7755 (mp0) cc_final: 0.7499 (mp0) REVERT: B 1141 LEU cc_start: 0.8042 (mt) cc_final: 0.7487 (tt) REVERT: C 65 PHE cc_start: 0.7002 (m-80) cc_final: 0.6380 (m-10) REVERT: C 780 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7983 (mm-30) REVERT: H 89 MET cc_start: 0.2196 (mtt) cc_final: 0.1778 (mmp) REVERT: M 39 MET cc_start: 0.3931 (tpt) cc_final: -0.0025 (mpp) outliers start: 30 outliers final: 20 residues processed: 202 average time/residue: 0.1650 time to fit residues: 58.1665 Evaluate side-chains 162 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 357 optimal weight: 30.0000 chunk 149 optimal weight: 0.0370 chunk 291 optimal weight: 3.9990 chunk 366 optimal weight: 8.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.205608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127388 restraints weight = 49550.270| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.13 r_work: 0.3354 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31590 Z= 0.170 Angle : 0.536 11.134 43149 Z= 0.271 Chirality : 0.045 0.407 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.510 58.141 5223 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.29 % Allowed : 10.30 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3819 helix: 2.25 (0.20), residues: 649 sheet: -0.33 (0.17), residues: 916 loop : -0.89 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 34 TYR 0.018 0.001 TYR A1067 PHE 0.020 0.001 PHE A1121 TRP 0.016 0.001 TRP L 56 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00399 (31497) covalent geometry : angle 0.51599 (42912) SS BOND : bond 0.00383 ( 42) SS BOND : angle 1.41450 ( 84) hydrogen bonds : bond 0.03734 ( 1106) hydrogen bonds : angle 5.87905 ( 3057) link_BETA1-4 : bond 0.00191 ( 3) link_BETA1-4 : angle 1.13302 ( 9) link_NAG-ASN : bond 0.00512 ( 48) link_NAG-ASN : angle 2.34833 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5451 (p90) cc_final: 0.4958 (p90) REVERT: A 737 ASP cc_start: 0.7794 (t0) cc_final: 0.7384 (t0) REVERT: A 902 MET cc_start: 0.8791 (tpt) cc_final: 0.8464 (mmt) REVERT: A 950 ASP cc_start: 0.8317 (t0) cc_final: 0.7894 (t0) REVERT: B 34 ARG cc_start: 0.8032 (mmt180) cc_final: 0.7767 (mmt180) REVERT: B 1141 LEU cc_start: 0.8027 (mt) cc_final: 0.7484 (tt) REVERT: C 65 PHE cc_start: 0.7095 (m-80) cc_final: 0.6479 (m-10) REVERT: C 1138 TYR cc_start: 0.7121 (t80) cc_final: 0.6898 (t80) REVERT: M 39 MET cc_start: 0.4066 (tpt) cc_final: 0.0101 (mpp) REVERT: N 105 GLN cc_start: 0.0774 (tm-30) cc_final: 0.0350 (mm-40) outliers start: 43 outliers final: 31 residues processed: 189 average time/residue: 0.1706 time to fit residues: 56.5243 Evaluate side-chains 179 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 316 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 239 GLN C 703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.205975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.126870 restraints weight = 49469.713| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.72 r_work: 0.3391 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31590 Z= 0.145 Angle : 0.526 11.186 43149 Z= 0.265 Chirality : 0.045 0.336 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.389 56.943 5223 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.39 % Allowed : 10.81 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 3819 helix: 2.29 (0.20), residues: 649 sheet: -0.36 (0.16), residues: 923 loop : -0.91 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE A1121 TRP 0.018 0.001 TRP A 353 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00337 (31497) covalent geometry : angle 0.50560 (42912) SS BOND : bond 0.00307 ( 42) SS BOND : angle 0.93983 ( 84) hydrogen bonds : bond 0.03599 ( 1106) hydrogen bonds : angle 5.76221 ( 3057) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.07928 ( 9) link_NAG-ASN : bond 0.00607 ( 48) link_NAG-ASN : angle 2.49567 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5405 (p90) cc_final: 0.4905 (p90) REVERT: A 902 MET cc_start: 0.8757 (tpt) cc_final: 0.8426 (mmt) REVERT: A 950 ASP cc_start: 0.8289 (t0) cc_final: 0.7860 (t0) REVERT: B 935 GLN cc_start: 0.8204 (tp40) cc_final: 0.7734 (tp40) REVERT: B 1141 LEU cc_start: 0.8027 (mt) cc_final: 0.7467 (tt) REVERT: C 65 PHE cc_start: 0.7135 (m-80) cc_final: 0.6432 (m-10) REVERT: C 1050 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: C 1138 TYR cc_start: 0.7164 (t80) cc_final: 0.6953 (t80) REVERT: H 89 MET cc_start: 0.2005 (mtt) cc_final: 0.1638 (mmp) REVERT: M 39 MET cc_start: 0.4059 (tpt) cc_final: 0.0091 (mpp) REVERT: N 105 GLN cc_start: 0.0835 (tm-30) cc_final: 0.0448 (mm-40) REVERT: P 89 MET cc_start: 0.0010 (tmm) cc_final: -0.0472 (ttt) outliers start: 46 outliers final: 34 residues processed: 191 average time/residue: 0.1686 time to fit residues: 56.3554 Evaluate side-chains 181 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 1.9990 chunk 280 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 355 optimal weight: 20.0000 chunk 191 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 159 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.204099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126495 restraints weight = 49420.385| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 3.13 r_work: 0.3330 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31590 Z= 0.212 Angle : 0.572 13.208 43149 Z= 0.287 Chirality : 0.046 0.345 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.610 59.965 5223 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.60 % Allowed : 11.53 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 3819 helix: 2.15 (0.20), residues: 644 sheet: -0.55 (0.16), residues: 918 loop : -0.93 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.021 0.001 TYR A1067 PHE 0.024 0.002 PHE A1121 TRP 0.026 0.001 TRP A 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00501 (31497) covalent geometry : angle 0.55071 (42912) SS BOND : bond 0.00470 ( 42) SS BOND : angle 0.93506 ( 84) hydrogen bonds : bond 0.03840 ( 1106) hydrogen bonds : angle 5.84687 ( 3057) link_BETA1-4 : bond 0.00195 ( 3) link_BETA1-4 : angle 1.19895 ( 9) link_NAG-ASN : bond 0.00584 ( 48) link_NAG-ASN : angle 2.67865 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5424 (ppp) cc_final: 0.5194 (ppp) REVERT: A 238 PHE cc_start: 0.5445 (p90) cc_final: 0.4897 (p90) REVERT: A 636 TYR cc_start: 0.4863 (m-10) cc_final: 0.4640 (m-80) REVERT: A 737 ASP cc_start: 0.7853 (t0) cc_final: 0.7507 (t0) REVERT: A 902 MET cc_start: 0.8823 (tpt) cc_final: 0.8445 (mmt) REVERT: A 950 ASP cc_start: 0.8396 (t0) cc_final: 0.7941 (t0) REVERT: B 1141 LEU cc_start: 0.8148 (mt) cc_final: 0.7594 (tt) REVERT: C 65 PHE cc_start: 0.7064 (m-80) cc_final: 0.6444 (m-10) REVERT: C 636 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.5053 (m-10) REVERT: C 1050 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8487 (mtp) REVERT: H 89 MET cc_start: 0.1886 (mtt) cc_final: 0.1513 (mmp) REVERT: M 39 MET cc_start: 0.4077 (tpt) cc_final: 0.0188 (mpp) REVERT: N 105 GLN cc_start: 0.0823 (tm-30) cc_final: 0.0505 (mm-40) REVERT: P 89 MET cc_start: 0.0094 (tmm) cc_final: -0.0307 (ttt) outliers start: 53 outliers final: 39 residues processed: 195 average time/residue: 0.1612 time to fit residues: 55.7514 Evaluate side-chains 185 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 73 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 184 optimal weight: 0.4980 chunk 149 optimal weight: 0.4980 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 351 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN B 239 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN H 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.205937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127675 restraints weight = 49624.732| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.70 r_work: 0.3412 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31590 Z= 0.116 Angle : 0.510 9.806 43149 Z= 0.257 Chirality : 0.045 0.498 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.285 55.370 5223 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.29 % Allowed : 12.26 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 3819 helix: 2.49 (0.20), residues: 636 sheet: -0.45 (0.16), residues: 946 loop : -0.86 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.016 0.001 TYR B1138 PHE 0.017 0.001 PHE A 192 TRP 0.035 0.001 TRP A 104 HIS 0.003 0.000 HIS N 103 Details of bonding type rmsd covalent geometry : bond 0.00262 (31497) covalent geometry : angle 0.49212 (42912) SS BOND : bond 0.00259 ( 42) SS BOND : angle 0.79260 ( 84) hydrogen bonds : bond 0.03433 ( 1106) hydrogen bonds : angle 5.58217 ( 3057) link_BETA1-4 : bond 0.00384 ( 3) link_BETA1-4 : angle 0.99200 ( 9) link_NAG-ASN : bond 0.00480 ( 48) link_NAG-ASN : angle 2.32472 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.2304 (p0) cc_final: 0.2094 (p0) REVERT: A 238 PHE cc_start: 0.5479 (p90) cc_final: 0.4950 (p90) REVERT: A 239 GLN cc_start: 0.6817 (tt0) cc_final: 0.6395 (tm-30) REVERT: A 636 TYR cc_start: 0.4816 (m-10) cc_final: 0.4561 (m-10) REVERT: A 950 ASP cc_start: 0.8254 (t0) cc_final: 0.7797 (t0) REVERT: C 65 PHE cc_start: 0.7066 (m-80) cc_final: 0.6383 (m-10) REVERT: M 39 MET cc_start: 0.4176 (tpt) cc_final: 0.0296 (mpp) REVERT: N 4 MET cc_start: 0.3085 (mmp) cc_final: 0.2860 (mmp) REVERT: P 89 MET cc_start: 0.0252 (tmm) cc_final: -0.0194 (ttt) outliers start: 43 outliers final: 34 residues processed: 196 average time/residue: 0.1582 time to fit residues: 54.7548 Evaluate side-chains 183 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 338 optimal weight: 20.0000 chunk 309 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 261 optimal weight: 0.0000 chunk 199 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 158 optimal weight: 0.1980 chunk 218 optimal weight: 9.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 218 GLN B 239 GLN B 644 GLN B 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.207604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.129691 restraints weight = 49547.883| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.73 r_work: 0.3435 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 31590 Z= 0.098 Angle : 0.494 10.290 43149 Z= 0.249 Chirality : 0.044 0.390 4980 Planarity : 0.003 0.046 5475 Dihedral : 5.046 54.915 5223 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.26 % Allowed : 12.53 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.13), residues: 3819 helix: 2.65 (0.20), residues: 645 sheet: -0.27 (0.17), residues: 912 loop : -0.82 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 237 TYR 0.014 0.001 TYR C1067 PHE 0.017 0.001 PHE A 192 TRP 0.037 0.001 TRP A 104 HIS 0.002 0.000 HIS N 103 Details of bonding type rmsd covalent geometry : bond 0.00212 (31497) covalent geometry : angle 0.47705 (42912) SS BOND : bond 0.00167 ( 42) SS BOND : angle 0.70046 ( 84) hydrogen bonds : bond 0.03255 ( 1106) hydrogen bonds : angle 5.33329 ( 3057) link_BETA1-4 : bond 0.00557 ( 3) link_BETA1-4 : angle 0.96983 ( 9) link_NAG-ASN : bond 0.00511 ( 48) link_NAG-ASN : angle 2.24848 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.5420 (p90) cc_final: 0.4900 (p90) REVERT: A 239 GLN cc_start: 0.6532 (tt0) cc_final: 0.6136 (tm-30) REVERT: A 796 ASP cc_start: 0.8070 (t0) cc_final: 0.7763 (t0) REVERT: A 950 ASP cc_start: 0.8208 (t0) cc_final: 0.7752 (t0) REVERT: C 65 PHE cc_start: 0.7087 (m-80) cc_final: 0.6414 (m-10) REVERT: C 902 MET cc_start: 0.8781 (tpt) cc_final: 0.8252 (tpt) REVERT: H 89 MET cc_start: 0.2028 (mtt) cc_final: 0.1759 (mmp) REVERT: M 39 MET cc_start: 0.3834 (tpt) cc_final: -0.0043 (mpp) REVERT: P 89 MET cc_start: 0.0129 (tmm) cc_final: -0.0296 (ttt) outliers start: 42 outliers final: 39 residues processed: 198 average time/residue: 0.1669 time to fit residues: 58.2242 Evaluate side-chains 190 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 201 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 339 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 342 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 957 GLN C 914 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.205851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127152 restraints weight = 49204.254| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.71 r_work: 0.3398 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31590 Z= 0.150 Angle : 0.531 10.950 43149 Z= 0.266 Chirality : 0.045 0.407 4980 Planarity : 0.004 0.046 5475 Dihedral : 5.123 57.194 5223 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.32 % Allowed : 12.77 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3819 helix: 2.49 (0.20), residues: 643 sheet: -0.36 (0.17), residues: 930 loop : -0.86 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.020 0.001 TYR A 170 PHE 0.018 0.001 PHE A1121 TRP 0.036 0.001 TRP A 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00350 (31497) covalent geometry : angle 0.51397 (42912) SS BOND : bond 0.00325 ( 42) SS BOND : angle 0.77352 ( 84) hydrogen bonds : bond 0.03457 ( 1106) hydrogen bonds : angle 5.41540 ( 3057) link_BETA1-4 : bond 0.00220 ( 3) link_BETA1-4 : angle 1.06533 ( 9) link_NAG-ASN : bond 0.00508 ( 48) link_NAG-ASN : angle 2.31514 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7638 Ramachandran restraints generated. 3819 Oldfield, 0 Emsley, 3819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7547 (t80) cc_final: 0.6961 (t80) REVERT: A 176 LEU cc_start: 0.6654 (tt) cc_final: 0.6454 (tt) REVERT: A 237 ARG cc_start: 0.7003 (tpt170) cc_final: 0.6772 (tpt170) REVERT: A 239 GLN cc_start: 0.6618 (tt0) cc_final: 0.6225 (tm-30) REVERT: A 796 ASP cc_start: 0.8155 (t0) cc_final: 0.7819 (t0) REVERT: A 902 MET cc_start: 0.8816 (tpt) cc_final: 0.8418 (mmt) REVERT: A 950 ASP cc_start: 0.8266 (t0) cc_final: 0.7824 (t0) REVERT: A 1144 GLU cc_start: 0.7907 (mp0) cc_final: 0.7634 (mp0) REVERT: C 65 PHE cc_start: 0.7099 (m-80) cc_final: 0.6420 (m-10) REVERT: H 89 MET cc_start: 0.1998 (mtt) cc_final: 0.1623 (mmp) REVERT: M 39 MET cc_start: 0.3869 (tpt) cc_final: 0.0041 (mpp) REVERT: P 89 MET cc_start: 0.0349 (tmm) cc_final: -0.0197 (ttt) outliers start: 44 outliers final: 42 residues processed: 188 average time/residue: 0.1664 time to fit residues: 55.0989 Evaluate side-chains 191 residues out of total 3381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 820 ASP Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 263 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 337 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 312 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.205781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128285 restraints weight = 49741.525| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 3.14 r_work: 0.3373 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31590 Z= 0.147 Angle : 0.549 15.843 43149 Z= 0.273 Chirality : 0.045 0.339 4980 Planarity : 0.004 0.047 5475 Dihedral : 5.154 56.966 5223 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.26 % Allowed : 13.19 % Favored : 85.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.13), residues: 3819 helix: 2.45 (0.20), residues: 643 sheet: -0.38 (0.17), residues: 929 loop : -0.87 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.020 0.001 TYR A 170 PHE 0.017 0.001 PHE A1121 TRP 0.029 0.001 TRP A 104 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00342 (31497) covalent geometry : angle 0.52450 (42912) SS BOND : bond 0.00317 ( 42) SS BOND : angle 0.76466 ( 84) hydrogen bonds : bond 0.03456 ( 1106) hydrogen bonds : angle 5.42348 ( 3057) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 1.07001 ( 9) link_NAG-ASN : bond 0.00462 ( 48) link_NAG-ASN : angle 2.83166 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14741.24 seconds wall clock time: 250 minutes 48.66 seconds (15048.66 seconds total)