Starting phenix.real_space_refine on Mon Jul 6 06:16:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcd_32421/07_2026/7wcd_32421.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21297 2.51 5 N 5514 2.21 5 O 6567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33525 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 7803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7803 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 50, 'TRANS': 949} Chain breaks: 10 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1575 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "H" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: J, C, G, A, I, B Time building chain proxies: 11.19, per 1000 atoms: 0.33 Number of scatterers: 33525 At special positions: 0 Unit cell: (147.44, 148.41, 231.83, 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 147 16.00 O 6567 8.00 N 5514 7.00 C 21297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS H 131 " - pdb=" SG CYS H 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 291 " - pdb=" SG CYS H 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 336 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 379 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 391 " - pdb=" SG CYS H 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 480 " - pdb=" SG CYS H 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 538 " - pdb=" SG CYS H 590 " distance=2.03 Simple disulfide: pdb=" SG CYS H 617 " - pdb=" SG CYS H 649 " distance=2.04 Simple disulfide: pdb=" SG CYS H 662 " - pdb=" SG CYS H 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 760 " distance=2.03 Simple disulfide: pdb=" SG CYS H 743 " - pdb=" SG CYS H 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H1032 " - pdb=" SG CYS H1043 " distance=2.03 Simple disulfide: pdb=" SG CYS H1082 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 379 " - pdb=" SG CYS J 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 391 " - pdb=" SG CYS J 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS J 538 " - pdb=" SG CYS J 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS J 617 " - pdb=" SG CYS J 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS J 743 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J1032 " - pdb=" SG CYS J1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS J1082 " - pdb=" SG CYS J1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 199 " 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 NAG-ASN " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C1134 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 165 " " NAG H1301 " - " ASN H1074 " " NAG H1302 " - " ASN H 234 " " NAG H1303 " - " ASN H 282 " " NAG H1304 " - " ASN H1134 " " NAG H1305 " - " ASN H1098 " " NAG H1306 " - " ASN H 801 " " NAG H1307 " - " ASN H 709 " " NAG H1308 " - " ASN H 657 " " NAG H1309 " - " ASN H 616 " " NAG H1310 " - " ASN H 603 " " NAG H1311 " - " ASN H 165 " " NAG J1301 " - " ASN J1074 " " NAG J1302 " - " ASN J 234 " " NAG J1303 " - " ASN J 282 " " NAG J1304 " - " ASN J1134 " " NAG J1305 " - " ASN J1098 " " NAG J1306 " - " ASN J 801 " " NAG J1307 " - " ASN J 709 " " NAG J1308 " - " ASN J 657 " " NAG J1309 " - " ASN J 616 " " NAG J1310 " - " ASN J 603 " " NAG J1311 " - " ASN J 165 " Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7962 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 75 sheets defined 19.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'H' and resid 294 through 304 Processing helix chain 'H' and resid 338 through 343 Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'H' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU H 387 " --> pdb=" O PRO H 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN H 388 " --> pdb=" O THR H 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 384 through 388' Processing helix chain 'H' and resid 405 through 410 removed outlier: 4.296A pdb=" N ARG H 408 " --> pdb=" O ASP H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 422 Processing helix chain 'H' and resid 737 through 743 Processing helix chain 'H' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN H 755 " --> pdb=" O ASN H 751 " (cutoff:3.500A) Processing helix chain 'H' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN H 762 " --> pdb=" O SER H 758 " (cutoff:3.500A) Processing helix chain 'H' and resid 816 through 826 removed outlier: 3.614A pdb=" N VAL H 826 " --> pdb=" O LEU H 822 " (cutoff:3.500A) Processing helix chain 'H' and resid 866 through 885 Processing helix chain 'H' and resid 886 through 890 Processing helix chain 'H' and resid 897 through 909 removed outlier: 3.518A pdb=" N ILE H 909 " --> pdb=" O ARG H 905 " (cutoff:3.500A) Processing helix chain 'H' and resid 912 through 919 removed outlier: 4.177A pdb=" N LEU H 916 " --> pdb=" O THR H 912 " (cutoff:3.500A) Processing helix chain 'H' and resid 919 through 941 Processing helix chain 'H' and resid 945 through 966 Processing helix chain 'H' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE H 980 " --> pdb=" O VAL H 976 " (cutoff:3.500A) Processing helix chain 'H' and resid 985 through 1033 removed outlier: 4.848A pdb=" N VAL H 991 " --> pdb=" O PRO H 987 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLN H 992 " --> pdb=" O GLU H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1140 through 1146 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 187 through 193 Processing helix chain 'J' and resid 294 through 304 Processing helix chain 'J' and resid 338 through 343 Processing helix chain 'J' and resid 365 through 371 Processing helix chain 'J' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU J 387 " --> pdb=" O PRO J 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN J 388 " --> pdb=" O THR J 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 384 through 388' Processing helix chain 'J' and resid 405 through 410 removed outlier: 4.296A pdb=" N ARG J 408 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 737 through 743 Processing helix chain 'J' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN J 755 " --> pdb=" O ASN J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN J 762 " --> pdb=" O SER J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 removed outlier: 3.614A pdb=" N VAL J 826 " --> pdb=" O LEU J 822 " (cutoff:3.500A) Processing helix chain 'J' and resid 866 through 885 Processing helix chain 'J' and resid 886 through 890 Processing helix chain 'J' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE J 909 " --> pdb=" O ARG J 905 " (cutoff:3.500A) Processing helix chain 'J' and resid 912 through 919 removed outlier: 4.178A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 919 through 941 Processing helix chain 'J' and resid 945 through 966 Processing helix chain 'J' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE J 980 " --> pdb=" O VAL J 976 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 1033 removed outlier: 4.849A pdb=" N VAL J 991 " --> pdb=" O PRO J 987 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN J 992 " --> pdb=" O GLU J 988 " (cutoff:3.500A) Processing helix chain 'J' and resid 1140 through 1146 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 133 Processing helix chain 'I' and resid 187 through 193 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.729A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.296A 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 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.844A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.630A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.614A 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 removed outlier: 3.518A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.178A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.594A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.848A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.846A pdb=" N GLU B 85 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 187 through 193 Processing sheet with id=AA1, first strand: chain 'H' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN H 61 " --> pdb=" O TYR H 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR H 269 " --> pdb=" O ASN H 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU H 191 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 203 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS H 207 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA H 222 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL H 36 " --> pdb=" O LEU H 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 42 through 43 removed outlier: 6.279A pdb=" N PHE H 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR H 274 " --> pdb=" O ASP H 290 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP H 290 " --> pdb=" O THR H 274 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 276 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA H 288 " --> pdb=" O LEU H 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 278 " --> pdb=" O THR H 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 169 through 172 Processing sheet with id=AA5, first strand: chain 'H' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE H 312 " --> pdb=" O THR H 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR H 599 " --> pdb=" O ILE H 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN H 314 " --> pdb=" O VAL H 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL H 597 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER H 316 " --> pdb=" O VAL H 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 324 through 325 removed outlier: 6.833A pdb=" N GLU H 324 " --> pdb=" O ASN H 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN H 542 " --> pdb=" O GLU H 324 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP H 574 " --> pdb=" O ILE H 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR H 572 " --> pdb=" O ASP H 568 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY H 566 " --> pdb=" O ASP H 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'H' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS H 361 " --> pdb=" O CYS H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'H' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU H 654 " --> pdb=" O ALA H 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR H 696 " --> pdb=" O GLU H 654 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA H 672 " --> pdb=" O PRO H 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR H1076 " --> pdb=" O SER H1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA H1078 " --> pdb=" O PHE H1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE H1095 " --> pdb=" O ALA H1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 717 through 718 Processing sheet with id=AB4, first strand: chain 'H' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY H1059 " --> pdb=" O ALA H1056 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR H1067 " --> pdb=" O HIS H1048 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS H1048 " --> pdb=" O TYR H1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS H 733 " --> pdb=" O LEU H 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 1120 through 1125 removed outlier: 4.836A pdb=" N ALA H1087 " --> pdb=" O SER H1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLU E 10 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP E 157 " --> pdb=" O TYR E 189 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR E 189 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP E 157 " --> pdb=" O TYR E 189 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR E 189 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR F 110 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN F 39 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU F 48 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR F 110 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 17 through 23 Processing sheet with id=AC6, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP F 144 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR F 178 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP F 144 " --> pdb=" O TYR F 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR F 178 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AC9, first strand: chain 'J' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 191 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS J 207 " --> pdb=" O ALA J 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA J 222 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL J 36 " --> pdb=" O LEU J 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR J 274 " --> pdb=" O ASP J 290 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP J 290 " --> pdb=" O THR J 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU J 276 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA J 288 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS J 278 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 169 through 172 Processing sheet with id=AD3, first strand: chain 'J' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE J 312 " --> pdb=" O THR J 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR J 599 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN J 314 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL J 597 " --> pdb=" O GLN J 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER J 316 " --> pdb=" O VAL J 595 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 324 through 325 removed outlier: 6.834A pdb=" N GLU J 324 " --> pdb=" O ASN J 540 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ASN J 542 " --> pdb=" O GLU J 324 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR J 572 " --> pdb=" O ASP J 568 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY J 566 " --> pdb=" O ASP J 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 356 through 358 Processing sheet with id=AD6, first strand: chain 'J' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS J 361 " --> pdb=" O CYS J 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.283A pdb=" N GLU J 654 " --> pdb=" O ALA J 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR J 696 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA J 672 " --> pdb=" O PRO J 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR J1076 " --> pdb=" O SER J1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA J1078 " --> pdb=" O PHE J1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE J1095 " --> pdb=" O ALA J1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 717 through 718 Processing sheet with id=AE2, first strand: chain 'J' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY J1059 " --> pdb=" O ALA J1056 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA J1087 " --> pdb=" O SER J1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU G 10 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 59 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP G 157 " --> pdb=" O TYR G 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR G 189 " --> pdb=" O ASP G 157 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP G 157 " --> pdb=" O TYR G 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR G 189 " --> pdb=" O ASP G 157 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR G 207 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR I 110 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR I 110 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AF4, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP I 144 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR I 178 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.562A pdb=" N ASP I 144 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR I 178 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AF7, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.941A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.393A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AG1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.667A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AG3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.540A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.284A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.583A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 717 through 718 Processing sheet with id=AG8, first strand: chain 'C' and resid 721 through 728 removed outlier: 3.602A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.837A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A 33 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 59 " --> pdb=" O TRP A 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP A 157 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.703A pdb=" N ASP A 157 " --> pdb=" O TYR A 189 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 189 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 164 through 167 removed outlier: 3.991A pdb=" N TYR A 207 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR B 110 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 12 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU B 48 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.721A pdb=" N THR B 110 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 12 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 17 through 23 Processing sheet with id=AI1, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.563A pdb=" N ASP B 144 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR B 178 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.563A pdb=" N ASP B 144 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TYR B 178 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'B' and resid 151 through 154 1378 hydrogen bonds defined for protein. 3630 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: 9.87 Time building geometry restraints manager: 3.85 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: 10635 1.34 - 1.46: 7842 1.46 - 1.58: 15639 1.58 - 1.70: 0 1.70 - 1.81: 186 Bond restraints: 34302 Sorted by residual: bond pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" N ASN A 52 " pdb=" CA ASN A 52 " ideal model delta sigma weight residual 1.457 1.512 -0.055 1.41e-02 5.03e+03 1.52e+01 bond pdb=" N ASN G 52 " pdb=" CA ASN G 52 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.41e-02 5.03e+03 1.48e+01 bond pdb=" N LEU J 650 " pdb=" CA LEU J 650 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.21e+00 bond pdb=" N LEU H 650 " pdb=" CA LEU H 650 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.21e+00 ... (remaining 34297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 46014 2.39 - 4.77: 637 4.77 - 7.16: 41 7.16 - 9.55: 6 9.55 - 11.93: 12 Bond angle restraints: 46710 Sorted by residual: angle pdb=" N ASN E 54 " pdb=" CA ASN E 54 " pdb=" C ASN E 54 " ideal model delta sigma weight residual 111.11 121.37 -10.26 1.20e+00 6.94e-01 7.31e+01 angle pdb=" N ASN A 54 " pdb=" CA ASN A 54 " pdb=" C ASN A 54 " ideal model delta sigma weight residual 111.11 121.37 -10.26 1.20e+00 6.94e-01 7.31e+01 angle pdb=" N ASN G 54 " pdb=" CA ASN G 54 " pdb=" C ASN G 54 " ideal model delta sigma weight residual 111.11 121.36 -10.25 1.20e+00 6.94e-01 7.29e+01 angle pdb=" N SER H 375 " pdb=" CA SER H 375 " pdb=" C SER H 375 " ideal model delta sigma weight residual 112.45 101.45 11.00 1.39e+00 5.18e-01 6.26e+01 angle pdb=" N SER C 375 " pdb=" CA SER C 375 " pdb=" C SER C 375 " ideal model delta sigma weight residual 112.45 101.47 10.98 1.39e+00 5.18e-01 6.24e+01 ... (remaining 46705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18350 17.89 - 35.78: 1429 35.78 - 53.66: 267 53.66 - 71.55: 42 71.55 - 89.44: 18 Dihedral angle restraints: 20106 sinusoidal: 7695 harmonic: 12411 Sorted by residual: dihedral pdb=" CB CYS J 336 " pdb=" SG CYS J 336 " pdb=" SG CYS J 361 " pdb=" CB CYS J 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.77 67.23 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS H 336 " pdb=" SG CYS H 336 " pdb=" SG CYS H 361 " pdb=" CB CYS H 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.78 67.22 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.79 67.21 1 1.00e+01 1.00e-02 5.88e+01 ... (remaining 20103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4947 0.094 - 0.189: 423 0.189 - 0.283: 9 0.283 - 0.378: 6 0.378 - 0.472: 9 Chirality restraints: 5394 Sorted by residual: chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CA PRO A 53 " pdb=" N PRO A 53 " pdb=" C PRO A 53 " pdb=" CB PRO A 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA PRO E 53 " pdb=" N PRO E 53 " pdb=" C PRO E 53 " pdb=" CB PRO E 53 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 5391 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER J 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER J 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER J 968 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER H 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER H 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER H 968 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 967 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER C 967 " -0.064 2.00e-02 2.50e+03 pdb=" O SER C 967 " 0.025 2.00e-02 2.50e+03 pdb=" N SER C 968 " 0.021 2.00e-02 2.50e+03 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1207 2.71 - 3.26: 32045 3.26 - 3.81: 51754 3.81 - 4.35: 64585 4.35 - 4.90: 113457 Nonbonded interactions: 263048 Sorted by model distance: nonbonded pdb=" O GLU H 484 " pdb=" CB CYS H 488 " model vdw 2.164 3.440 nonbonded pdb=" O GLU C 484 " pdb=" CB CYS C 488 " model vdw 2.165 3.440 nonbonded pdb=" O GLU J 484 " pdb=" CB CYS J 488 " model vdw 2.165 3.440 nonbonded pdb=" OE1 GLU J 484 " pdb=" OH TYR G 33 " model vdw 2.191 3.040 nonbonded pdb=" OE1 GLU H 484 " pdb=" OH TYR E 33 " model vdw 2.191 3.040 ... (remaining 263043 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: 0.09 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'A' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'B' } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.960 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34386 Z= 0.254 Angle : 0.653 11.933 46911 Z= 0.396 Chirality : 0.051 0.472 5394 Planarity : 0.004 0.044 5961 Dihedral : 13.005 89.441 11991 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.24 % Allowed : 0.84 % Favored : 98.92 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.32 % 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: 0.01 (0.14), residues: 4200 helix: 1.58 (0.20), residues: 780 sheet: 0.79 (0.15), residues: 1305 loop : -1.14 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 38 TYR 0.012 0.001 TYR C1067 PHE 0.017 0.001 PHE J 906 TRP 0.032 0.001 TRP E 36 HIS 0.003 0.001 HIS F 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.25 (34302) covalent geometry : angle 0.64728 / 0.39 (46710) SS BOND : bond 0.00229 / 0.13 ( 51) SS BOND : angle 1.01865 / 0.72 ( 102) hydrogen bonds : bond 0.19410 / 12.52 ( 1303) hydrogen bonds : angle 7.43335 / 5.13 ( 3630) link_NAG-ASN : bond 0.00294 / 0.17 ( 33) link_NAG-ASN : angle 1.78343 / 1.24 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 377 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6169 (mmt) cc_final: 0.5875 (mmt) outliers start: 9 outliers final: 3 residues processed: 383 average time/residue: 0.1916 time to fit residues: 123.3060 Evaluate side-chains 279 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 373 SER Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain C residue 373 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 0.1980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 52 GLN H 540 ASN H 675 GLN H 751 ASN E 52 ASN J 207 HIS J 675 GLN J 751 ASN G 52 ASN C 207 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.191626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.160309 restraints weight = 48724.360| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.20 r_work: 0.3597 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34386 Z= 0.201 Angle : 0.594 8.250 46911 Z= 0.308 Chirality : 0.047 0.286 5394 Planarity : 0.004 0.048 5961 Dihedral : 4.122 29.529 4575 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.19 % Allowed : 6.86 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.06 (0.13), residues: 4200 helix: 1.42 (0.19), residues: 768 sheet: 0.83 (0.15), residues: 1254 loop : -1.15 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.019 0.002 TYR I 51 PHE 0.023 0.002 PHE J 906 TRP 0.017 0.001 TRP A 50 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (34302) covalent geometry : angle 0.58856 / 0.31 (46710) SS BOND : bond 0.00420 / 0.25 ( 51) SS BOND : angle 1.04286 / 0.75 ( 102) hydrogen bonds : bond 0.05324 / 3.32 ( 1303) hydrogen bonds : angle 5.55521 / 3.79 ( 3630) link_NAG-ASN : bond 0.00289 / 0.16 ( 33) link_NAG-ASN : angle 1.55195 / 1.04 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 319 time to evaluate : 1.102 Fit side-chains REVERT: E 105 ASP cc_start: 0.8520 (t0) cc_final: 0.8312 (t0) REVERT: J 1041 ASP cc_start: 0.8208 (t0) cc_final: 0.7988 (t0) REVERT: J 1144 GLU cc_start: 0.7379 (tp30) cc_final: 0.7122 (tp30) REVERT: G 118 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7175 (mm-40) REVERT: C 1041 ASP cc_start: 0.8175 (t0) cc_final: 0.7860 (t0) REVERT: C 1144 GLU cc_start: 0.7286 (tp30) cc_final: 0.7069 (tp30) REVERT: A 81 MET cc_start: 0.6160 (tmm) cc_final: 0.5833 (tmm) REVERT: A 105 ASP cc_start: 0.8559 (t0) cc_final: 0.8268 (t0) outliers start: 44 outliers final: 32 residues processed: 351 average time/residue: 0.1934 time to fit residues: 114.8118 Evaluate side-chains 313 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 372 optimal weight: 0.6980 chunk 256 optimal weight: 30.0000 chunk 342 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 275 optimal weight: 50.0000 chunk 264 optimal weight: 10.0000 chunk 370 optimal weight: 0.7980 chunk 260 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 327 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 613 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.192086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.161357 restraints weight = 48572.778| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.16 r_work: 0.3607 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34386 Z= 0.161 Angle : 0.539 9.783 46911 Z= 0.280 Chirality : 0.046 0.289 5394 Planarity : 0.004 0.057 5961 Dihedral : 4.012 24.115 4573 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.43 % Allowed : 10.21 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.05 (0.13), residues: 4200 helix: 1.46 (0.19), residues: 774 sheet: 0.81 (0.15), residues: 1266 loop : -1.16 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 38 TYR 0.018 0.001 TYR C1067 PHE 0.024 0.001 PHE A 29 TRP 0.025 0.001 TRP G 36 HIS 0.010 0.001 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (34302) covalent geometry : angle 0.53415 / 0.28 (46710) SS BOND : bond 0.00303 / 0.18 ( 51) SS BOND : angle 0.83235 / 0.61 ( 102) hydrogen bonds : bond 0.04957 / 3.07 ( 1303) hydrogen bonds : angle 5.20558 / 3.54 ( 3630) link_NAG-ASN : bond 0.00278 / 0.15 ( 33) link_NAG-ASN : angle 1.48430 / 0.98 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 1.233 Fit side-chains REVERT: H 1144 GLU cc_start: 0.7263 (tp30) cc_final: 0.7027 (tp30) REVERT: G 81 MET cc_start: 0.6297 (tmm) cc_final: 0.6077 (tmm) REVERT: G 118 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7098 (mm-40) REVERT: A 81 MET cc_start: 0.6291 (tmm) cc_final: 0.5942 (tmm) REVERT: A 105 ASP cc_start: 0.8528 (t0) cc_final: 0.8250 (t0) outliers start: 53 outliers final: 41 residues processed: 342 average time/residue: 0.2071 time to fit residues: 119.1831 Evaluate side-chains 312 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 49 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 274 optimal weight: 40.0000 chunk 114 optimal weight: 40.0000 chunk 414 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 418 optimal weight: 40.0000 chunk 153 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.188772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.156309 restraints weight = 48399.928| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.25 r_work: 0.3508 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 34386 Z= 0.267 Angle : 0.623 10.246 46911 Z= 0.322 Chirality : 0.049 0.337 5394 Planarity : 0.005 0.069 5961 Dihedral : 4.421 26.764 4572 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.59 % Allowed : 11.48 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % 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: -0.29 (0.13), residues: 4200 helix: 1.14 (0.19), residues: 765 sheet: 0.66 (0.15), residues: 1290 loop : -1.26 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 646 TYR 0.022 0.002 TYR C1067 PHE 0.026 0.002 PHE H 86 TRP 0.033 0.002 TRP A 36 HIS 0.008 0.002 HIS I 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.27 (34302) covalent geometry : angle 0.61755 / 0.32 (46710) SS BOND : bond 0.00505 / 0.31 ( 51) SS BOND : angle 1.14914 / 0.83 ( 102) hydrogen bonds : bond 0.06024 / 3.75 ( 1303) hydrogen bonds : angle 5.22809 / 3.55 ( 3630) link_NAG-ASN : bond 0.00390 / 0.24 ( 33) link_NAG-ASN : angle 1.69200 / 1.14 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 286 time to evaluate : 1.576 Fit side-chains REVERT: H 1144 GLU cc_start: 0.7384 (tp30) cc_final: 0.7148 (tp30) REVERT: J 394 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8342 (m-40) REVERT: J 1144 GLU cc_start: 0.7479 (tp30) cc_final: 0.7196 (tp30) REVERT: G 81 MET cc_start: 0.6328 (tmm) cc_final: 0.6027 (tmm) REVERT: C 394 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8210 (m-40) REVERT: C 403 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8580 (ttp-170) REVERT: C 868 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7845 (tt0) REVERT: C 1144 GLU cc_start: 0.7432 (tp30) cc_final: 0.7160 (tp30) REVERT: A 81 MET cc_start: 0.6319 (tmm) cc_final: 0.5885 (tmm) outliers start: 96 outliers final: 79 residues processed: 358 average time/residue: 0.2104 time to fit residues: 127.1253 Evaluate side-chains 351 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 546 LEU Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 642 VAL Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 45 optimal weight: 0.9980 chunk 349 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 281 optimal weight: 50.0000 chunk 323 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 613 GLN J1002 GLN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN A 59 ASN A 168 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.191240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.159378 restraints weight = 48516.054| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.13 r_work: 0.3585 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34386 Z= 0.138 Angle : 0.530 9.702 46911 Z= 0.274 Chirality : 0.045 0.297 5394 Planarity : 0.004 0.045 5961 Dihedral : 4.138 32.442 4572 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.30 % Allowed : 12.86 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.13), residues: 4200 helix: 1.55 (0.20), residues: 750 sheet: 0.69 (0.15), residues: 1269 loop : -1.21 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 646 TYR 0.017 0.001 TYR C1067 PHE 0.013 0.001 PHE J 86 TRP 0.037 0.001 TRP A 36 HIS 0.008 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (34302) covalent geometry : angle 0.52452 / 0.27 (46710) SS BOND : bond 0.00298 / 0.19 ( 51) SS BOND : angle 1.04372 / 0.82 ( 102) hydrogen bonds : bond 0.04762 / 2.95 ( 1303) hydrogen bonds : angle 4.96638 / 3.38 ( 3630) link_NAG-ASN : bond 0.00296 / 0.17 ( 33) link_NAG-ASN : angle 1.51935 / 1.00 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 285 time to evaluate : 1.710 Fit side-chains REVERT: H 740 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8236 (ttt) REVERT: H 981 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8636 (mm) REVERT: E 81 MET cc_start: 0.6276 (tmm) cc_final: 0.5678 (tmm) REVERT: E 118 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7261 (mm-40) REVERT: J 394 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8242 (m-40) REVERT: J 981 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8754 (mm) REVERT: J 1144 GLU cc_start: 0.7418 (tp30) cc_final: 0.7164 (tp30) REVERT: G 81 MET cc_start: 0.6034 (tmm) cc_final: 0.5528 (tmm) REVERT: C 394 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8109 (m-40) REVERT: C 981 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8826 (mm) REVERT: C 1144 GLU cc_start: 0.7372 (tp30) cc_final: 0.7148 (tp30) REVERT: A 70 MET cc_start: 0.5735 (mmt) cc_final: 0.5385 (mmt) REVERT: A 81 MET cc_start: 0.6152 (tmm) cc_final: 0.5734 (tmm) REVERT: A 105 ASP cc_start: 0.8530 (t0) cc_final: 0.8328 (t0) outliers start: 85 outliers final: 59 residues processed: 356 average time/residue: 0.2087 time to fit residues: 126.0313 Evaluate side-chains 328 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 263 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 981 LEU Chi-restraints excluded: chain H residue 1050 MET Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 29 optimal weight: 3.9990 chunk 113 optimal weight: 50.0000 chunk 333 optimal weight: 0.7980 chunk 385 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 174 optimal weight: 0.0170 chunk 375 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 overall best weight: 1.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.158724 restraints weight = 48183.391| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.14 r_work: 0.3594 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34386 Z= 0.172 Angle : 0.552 9.480 46911 Z= 0.283 Chirality : 0.046 0.303 5394 Planarity : 0.004 0.046 5961 Dihedral : 4.217 32.718 4572 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.92 % Allowed : 12.88 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.15 (0.13), residues: 4200 helix: 1.54 (0.20), residues: 750 sheet: 0.70 (0.15), residues: 1290 loop : -1.24 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 646 TYR 0.017 0.001 TYR C1067 PHE 0.017 0.001 PHE H 86 TRP 0.035 0.001 TRP E 36 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (34302) covalent geometry : angle 0.54495 / 0.28 (46710) SS BOND : bond 0.00522 / 0.33 ( 51) SS BOND : angle 1.28698 / 0.89 ( 102) hydrogen bonds : bond 0.04970 / 3.08 ( 1303) hydrogen bonds : angle 4.90655 / 3.34 ( 3630) link_NAG-ASN : bond 0.00291 / 0.17 ( 33) link_NAG-ASN : angle 1.55654 / 1.03 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 271 time to evaluate : 1.681 Fit side-chains REVERT: H 740 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: H 981 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8624 (mm) REVERT: E 81 MET cc_start: 0.6341 (tmm) cc_final: 0.5732 (tmm) REVERT: E 118 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7194 (mm-40) REVERT: J 394 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (m-40) REVERT: J 981 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8767 (mm) REVERT: J 1144 GLU cc_start: 0.7410 (tp30) cc_final: 0.7168 (tp30) REVERT: G 81 MET cc_start: 0.6023 (tmm) cc_final: 0.5362 (tmm) REVERT: C 394 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8080 (m-40) REVERT: C 981 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8816 (mm) REVERT: A 81 MET cc_start: 0.6150 (tmm) cc_final: 0.5705 (tmm) outliers start: 108 outliers final: 80 residues processed: 358 average time/residue: 0.1998 time to fit residues: 121.0815 Evaluate side-chains 349 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 263 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 540 ASN Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 981 LEU Chi-restraints excluded: chain H residue 1050 MET Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1092 GLU Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 63 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 354 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 159 optimal weight: 0.0970 chunk 349 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157797 restraints weight = 48604.816| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.33 r_work: 0.3548 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34386 Z= 0.101 Angle : 0.503 9.601 46911 Z= 0.259 Chirality : 0.044 0.269 5394 Planarity : 0.004 0.041 5961 Dihedral : 3.956 33.056 4572 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.40 % Allowed : 13.59 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.02 (0.13), residues: 4200 helix: 1.74 (0.20), residues: 759 sheet: 0.74 (0.15), residues: 1272 loop : -1.16 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 72 TYR 0.014 0.001 TYR J1067 PHE 0.017 0.001 PHE G 113 TRP 0.022 0.001 TRP A 50 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (34302) covalent geometry : angle 0.49782 / 0.26 (46710) SS BOND : bond 0.00347 / 0.20 ( 51) SS BOND : angle 0.96444 / 0.66 ( 102) hydrogen bonds : bond 0.04074 / 2.51 ( 1303) hydrogen bonds : angle 4.70512 / 3.19 ( 3630) link_NAG-ASN : bond 0.00322 / 0.18 ( 33) link_NAG-ASN : angle 1.45522 / 0.95 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 282 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: H 740 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8308 (ttt) REVERT: E 81 MET cc_start: 0.6398 (tmm) cc_final: 0.5821 (tmm) REVERT: E 118 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7287 (mm-40) REVERT: J 394 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8283 (m-40) REVERT: J 1144 GLU cc_start: 0.7541 (tp30) cc_final: 0.7322 (tp30) REVERT: G 81 MET cc_start: 0.6089 (tmm) cc_final: 0.5409 (tmm) REVERT: G 85 ARG cc_start: 0.5606 (ppt170) cc_final: 0.5355 (ptt90) REVERT: C 394 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8111 (m-40) outliers start: 89 outliers final: 61 residues processed: 361 average time/residue: 0.1994 time to fit residues: 121.3275 Evaluate side-chains 327 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 263 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 389 ASP Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 364 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 396 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.189851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157994 restraints weight = 48423.576| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.14 r_work: 0.3578 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34386 Z= 0.231 Angle : 0.596 10.184 46911 Z= 0.305 Chirality : 0.048 0.312 5394 Planarity : 0.004 0.047 5961 Dihedral : 4.315 31.177 4572 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.73 % Allowed : 13.80 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 4200 helix: 1.35 (0.19), residues: 768 sheet: 0.70 (0.15), residues: 1308 loop : -1.27 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.018 0.002 TYR C1067 PHE 0.023 0.002 PHE H 86 TRP 0.045 0.002 TRP A 36 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 (34302) covalent geometry : angle 0.58924 / 0.30 (46710) SS BOND : bond 0.00508 / 0.33 ( 51) SS BOND : angle 1.38047 / 0.97 ( 102) hydrogen bonds : bond 0.05591 / 3.48 ( 1303) hydrogen bonds : angle 4.92017 / 3.34 ( 3630) link_NAG-ASN : bond 0.00323 / 0.20 ( 33) link_NAG-ASN : angle 1.61650 / 1.08 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 264 time to evaluate : 1.257 Fit side-chains REVERT: H 740 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8431 (ttt) REVERT: E 81 MET cc_start: 0.6293 (tmm) cc_final: 0.5782 (tmm) REVERT: E 118 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7221 (mm-40) REVERT: F 88 TYR cc_start: 0.7175 (m-10) cc_final: 0.6731 (m-10) REVERT: J 394 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: G 81 MET cc_start: 0.5967 (tmm) cc_final: 0.5466 (tmm) REVERT: C 1144 GLU cc_start: 0.7354 (tp30) cc_final: 0.7116 (tp30) outliers start: 101 outliers final: 81 residues processed: 352 average time/residue: 0.1955 time to fit residues: 116.3767 Evaluate side-chains 338 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 255 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 553 THR Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain H residue 1133 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 642 VAL Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 151 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 chunk 335 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 391 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 372 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN A 59 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.192471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159560 restraints weight = 48275.451| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.15 r_work: 0.3589 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34386 Z= 0.108 Angle : 0.524 11.330 46911 Z= 0.267 Chirality : 0.045 0.276 5394 Planarity : 0.004 0.043 5961 Dihedral : 4.015 32.381 4572 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.11 % Allowed : 14.37 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.01 (0.13), residues: 4200 helix: 1.71 (0.20), residues: 756 sheet: 0.76 (0.15), residues: 1278 loop : -1.15 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 646 TYR 0.015 0.001 TYR J1067 PHE 0.047 0.001 PHE C 541 TRP 0.050 0.001 TRP G 36 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (34302) covalent geometry : angle 0.51932 / 0.27 (46710) SS BOND : bond 0.00211 / 0.13 ( 51) SS BOND : angle 0.87431 / 0.61 ( 102) hydrogen bonds : bond 0.04243 / 2.62 ( 1303) hydrogen bonds : angle 4.71462 / 3.20 ( 3630) link_NAG-ASN : bond 0.00321 / 0.19 ( 33) link_NAG-ASN : angle 1.47021 / 0.96 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 276 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: H 574 ASP cc_start: 0.7774 (p0) cc_final: 0.7514 (t70) REVERT: H 740 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8179 (ttt) REVERT: E 81 MET cc_start: 0.6201 (tmm) cc_final: 0.5741 (tmm) REVERT: E 118 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7251 (mm-40) REVERT: F 88 TYR cc_start: 0.7076 (m-10) cc_final: 0.6636 (m-10) REVERT: J 394 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (m-40) REVERT: J 1144 GLU cc_start: 0.7484 (tp30) cc_final: 0.7215 (tp30) REVERT: C 1144 GLU cc_start: 0.7400 (tp30) cc_final: 0.7153 (tp30) REVERT: A 29 PHE cc_start: 0.8494 (t80) cc_final: 0.8222 (t80) REVERT: A 72 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.6182 (ptt-90) REVERT: B 55 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7698 (pttm) outliers start: 78 outliers final: 71 residues processed: 344 average time/residue: 0.2130 time to fit residues: 123.3447 Evaluate side-chains 344 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 270 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 564 GLN Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.3980 chunk 377 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 367 optimal weight: 0.8980 chunk 406 optimal weight: 20.0000 chunk 366 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 330 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 955 ASN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.159143 restraints weight = 48636.843| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.18 r_work: 0.3594 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34386 Z= 0.118 Angle : 0.525 11.402 46911 Z= 0.267 Chirality : 0.045 0.273 5394 Planarity : 0.004 0.045 5961 Dihedral : 3.971 30.969 4572 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.08 % Allowed : 14.67 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.01 (0.13), residues: 4200 helix: 1.75 (0.20), residues: 756 sheet: 0.73 (0.15), residues: 1293 loop : -1.15 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 646 TYR 0.014 0.001 TYR H1067 PHE 0.029 0.001 PHE A 113 TRP 0.064 0.002 TRP E 36 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (34302) covalent geometry : angle 0.52067 / 0.27 (46710) SS BOND : bond 0.00237 / 0.15 ( 51) SS BOND : angle 0.89021 / 0.62 ( 102) hydrogen bonds : bond 0.04271 / 2.64 ( 1303) hydrogen bonds : angle 4.66642 / 3.16 ( 3630) link_NAG-ASN : bond 0.00276 / 0.16 ( 33) link_NAG-ASN : angle 1.45475 / 0.96 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8400 Ramachandran restraints generated. 4200 Oldfield, 0 Emsley, 4200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: H 574 ASP cc_start: 0.7769 (p0) cc_final: 0.7524 (t70) REVERT: H 740 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8390 (ttt) REVERT: E 81 MET cc_start: 0.6138 (tmm) cc_final: 0.5733 (tmm) REVERT: E 118 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7219 (mm-40) REVERT: F 88 TYR cc_start: 0.7090 (m-10) cc_final: 0.6652 (m-10) REVERT: J 394 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8190 (m-40) REVERT: J 1144 GLU cc_start: 0.7476 (tp30) cc_final: 0.7209 (tp30) REVERT: C 1144 GLU cc_start: 0.7371 (tp30) cc_final: 0.7136 (tp30) REVERT: A 29 PHE cc_start: 0.8497 (t80) cc_final: 0.8250 (t80) REVERT: A 72 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.6187 (ptt-90) outliers start: 77 outliers final: 71 residues processed: 344 average time/residue: 0.1922 time to fit residues: 111.5845 Evaluate side-chains 339 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 265 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 227 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 588 THR Chi-restraints excluded: chain H residue 602 THR Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 740 MET Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 1061 VAL Chi-restraints excluded: chain H residue 1068 VAL Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 551 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 1061 VAL Chi-restraints excluded: chain J residue 1068 VAL Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1068 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain B residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 374 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 209 optimal weight: 0.0970 chunk 297 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN A 59 ASN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159268 restraints weight = 48356.500| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.16 r_work: 0.3587 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34386 Z= 0.124 Angle : 0.527 11.445 46911 Z= 0.267 Chirality : 0.045 0.271 5394 Planarity : 0.004 0.045 5961 Dihedral : 3.951 30.632 4572 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.24 % Allowed : 14.64 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.01 (0.13), residues: 4200 helix: 1.76 (0.20), residues: 756 sheet: 0.74 (0.15), residues: 1293 loop : -1.15 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 646 TYR 0.014 0.001 TYR H1067 PHE 0.012 0.001 PHE H1121 TRP 0.065 0.002 TRP A 36 HIS 0.008 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (34302) covalent geometry : angle 0.52223 / 0.27 (46710) SS BOND : bond 0.00243 / 0.16 ( 51) SS BOND : angle 0.88828 / 0.62 ( 102) hydrogen bonds : bond 0.04300 / 2.66 ( 1303) hydrogen bonds : angle 4.65147 / 3.15 ( 3630) link_NAG-ASN : bond 0.00268 / 0.15 ( 33) link_NAG-ASN : angle 1.43679 / 0.95 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8381.64 seconds wall clock time: 144 minutes 40.14 seconds (8680.14 seconds total)