Starting phenix.real_space_refine on Fri Mar 6 18:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcd_32421/03_2026/7wcd_32421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcd_32421/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcd_32421/03_2026/7wcd_32421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcd_32421/03_2026/7wcd_32421.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcd_32421/03_2026/7wcd_32421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcd_32421/03_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-5986/lib/python3.9/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 dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Restraints were copied for chains: J, C, G, A, I, B Time building chain proxies: 10.30, per 1000 atoms: 0.31 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: 3.09 Conformation dependent library (CDL) restraints added in 1.3 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: 1.51 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: 9.49 Time building geometry restraints manager: 3.99 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 - 21.43: 19387 21.43 - 42.87: 1142 42.87 - 64.30: 183 64.30 - 85.73: 36 85.73 - 107.16: 51 Dihedral angle restraints: 20799 sinusoidal: 8388 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 20796 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: 0.08 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 36.140 Find NCS groups from input model: 0.290 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 14.742 107.164 12684 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 covalent geometry : bond 0.00411 (34302) covalent geometry : angle 0.64728 (46710) SS BOND : bond 0.00229 ( 51) SS BOND : angle 1.01865 ( 102) hydrogen bonds : bond 0.19410 ( 1303) hydrogen bonds : angle 7.43335 ( 3630) link_NAG-ASN : bond 0.00294 ( 33) link_NAG-ASN : angle 1.78343 ( 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 : 1.239 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: 0.1929 time to fit residues: 123.9583 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 : 1.118 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: H 52 GLN H 540 ASN H 675 GLN H 751 ASN E 52 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4228 r_free = 0.4228 target = 0.191688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.160040 restraints weight = 48722.309| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.20 r_work: 0.3594 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34386 Z= 0.200 Angle : 0.604 8.301 46911 Z= 0.310 Chirality : 0.048 0.243 5394 Planarity : 0.004 0.048 5961 Dihedral : 9.813 82.317 5268 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.19 % Allowed : 6.97 % Favored : 91.84 % 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 0.018 0.002 TYR I 51 PHE 0.023 0.002 PHE J 906 TRP 0.016 0.001 TRP A 50 HIS 0.009 0.001 HIS B 100 Details of bonding type rmsd covalent geometry : bond 0.00481 (34302) covalent geometry : angle 0.59910 (46710) SS BOND : bond 0.00417 ( 51) SS BOND : angle 1.04541 ( 102) hydrogen bonds : bond 0.05346 ( 1303) hydrogen bonds : angle 5.55028 ( 3630) link_NAG-ASN : bond 0.00300 ( 33) link_NAG-ASN : angle 1.59668 ( 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 365 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 321 time to evaluate : 0.813 Fit side-chains REVERT: E 105 ASP cc_start: 0.8519 (t0) cc_final: 0.8317 (t0) REVERT: J 1041 ASP cc_start: 0.8209 (t0) cc_final: 0.7992 (t0) REVERT: J 1144 GLU cc_start: 0.7373 (tp30) cc_final: 0.7124 (tp30) REVERT: G 118 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7182 (mm-40) REVERT: C 1041 ASP cc_start: 0.8178 (t0) cc_final: 0.7863 (t0) REVERT: C 1144 GLU cc_start: 0.7313 (tp30) cc_final: 0.7109 (tp30) REVERT: A 81 MET cc_start: 0.6159 (tmm) cc_final: 0.5836 (tmm) REVERT: A 105 ASP cc_start: 0.8559 (t0) cc_final: 0.8277 (t0) outliers start: 44 outliers final: 31 residues processed: 354 average time/residue: 0.1835 time to fit residues: 110.3873 Evaluate side-chains 311 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 372 optimal weight: 0.9980 chunk 256 optimal weight: 30.0000 chunk 342 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 275 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 370 optimal weight: 0.6980 chunk 260 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 613 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 613 GLN G 39 GLN C 613 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.193432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.162628 restraints weight = 48580.599| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.15 r_work: 0.3567 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34386 Z= 0.121 Angle : 0.530 10.077 46911 Z= 0.270 Chirality : 0.045 0.259 5394 Planarity : 0.004 0.049 5961 Dihedral : 7.527 58.683 5266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.00 % Allowed : 10.21 % Favored : 88.79 % 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: -0.00 (0.13), residues: 4200 helix: 1.57 (0.19), residues: 777 sheet: 0.78 (0.15), residues: 1296 loop : -1.14 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 38 TYR 0.015 0.001 TYR C1067 PHE 0.023 0.001 PHE A 29 TRP 0.027 0.001 TRP G 36 HIS 0.010 0.001 HIS I 100 Details of bonding type rmsd covalent geometry : bond 0.00269 (34302) covalent geometry : angle 0.52586 (46710) SS BOND : bond 0.00219 ( 51) SS BOND : angle 0.67934 ( 102) hydrogen bonds : bond 0.04427 ( 1303) hydrogen bonds : angle 5.13711 ( 3630) link_NAG-ASN : bond 0.00326 ( 33) link_NAG-ASN : angle 1.54786 ( 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 344 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: H 1144 GLU cc_start: 0.7443 (tp30) cc_final: 0.7219 (tp30) REVERT: E 105 ASP cc_start: 0.8471 (t0) cc_final: 0.8253 (t0) REVERT: G 81 MET cc_start: 0.6420 (tmm) cc_final: 0.6214 (tmm) REVERT: G 118 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7228 (mm-40) REVERT: A 81 MET cc_start: 0.6406 (tmm) cc_final: 0.6081 (tmm) REVERT: A 105 ASP cc_start: 0.8518 (t0) cc_final: 0.8227 (t0) outliers start: 37 outliers final: 29 residues processed: 336 average time/residue: 0.1873 time to fit residues: 106.4767 Evaluate side-chains 297 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 602 THR 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 J residue 94 SER 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 723 THR Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 1128 VAL Chi-restraints excluded: chain G residue 107 LEU 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 602 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1128 VAL 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: 5.9990 chunk 285 optimal weight: 5.9990 chunk 274 optimal weight: 40.0000 chunk 114 optimal weight: 50.0000 chunk 414 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 390 optimal weight: 6.9990 chunk 418 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 540 ASN J1002 GLN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN C 613 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.187835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156934 restraints weight = 48412.660| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.10 r_work: 0.3520 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 34386 Z= 0.314 Angle : 0.675 9.392 46911 Z= 0.346 Chirality : 0.051 0.372 5394 Planarity : 0.005 0.068 5961 Dihedral : 6.524 48.548 5265 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.59 % Allowed : 11.43 % Favored : 85.98 % 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: -0.36 (0.13), residues: 4200 helix: 1.02 (0.19), residues: 765 sheet: 0.60 (0.15), residues: 1320 loop : -1.30 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 646 TYR 0.023 0.002 TYR C1067 PHE 0.031 0.002 PHE H 906 TRP 0.020 0.002 TRP A 36 HIS 0.009 0.002 HIS H1058 Details of bonding type rmsd covalent geometry : bond 0.00771 (34302) covalent geometry : angle 0.66777 (46710) SS BOND : bond 0.00597 ( 51) SS BOND : angle 1.29225 ( 102) hydrogen bonds : bond 0.06494 ( 1303) hydrogen bonds : angle 5.30285 ( 3630) link_NAG-ASN : bond 0.00582 ( 33) link_NAG-ASN : angle 1.91360 ( 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 385 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 289 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: J 394 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: J 1144 GLU cc_start: 0.7466 (tp30) cc_final: 0.7197 (tp30) REVERT: G 81 MET cc_start: 0.6325 (tmm) cc_final: 0.6021 (tmm) REVERT: C 394 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (m-40) REVERT: C 403 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8609 (ttp-170) REVERT: C 868 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7800 (tt0) REVERT: C 1144 GLU cc_start: 0.7442 (tp30) cc_final: 0.7181 (tp30) REVERT: A 81 MET cc_start: 0.6371 (tmm) cc_final: 0.5867 (tmm) outliers start: 96 outliers final: 75 residues processed: 362 average time/residue: 0.1897 time to fit residues: 115.3761 Evaluate side-chains 345 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 267 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 403 ARG Chi-restraints excluded: chain H residue 512 VAL 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 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 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 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 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 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 2 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 45 optimal weight: 0.9990 chunk 349 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 281 optimal weight: 50.0000 chunk 323 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 364 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 168 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN J1002 GLN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 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 = 0.4239 r_free = 0.4239 target = 0.192551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160767 restraints weight = 48518.783| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.12 r_work: 0.3607 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34386 Z= 0.111 Angle : 0.518 9.944 46911 Z= 0.267 Chirality : 0.045 0.331 5394 Planarity : 0.004 0.043 5961 Dihedral : 5.209 43.476 5265 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.16 % Allowed : 12.88 % Favored : 84.95 % 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: 1.67 (0.20), residues: 750 sheet: 0.72 (0.15), residues: 1269 loop : -1.16 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 646 TYR 0.015 0.001 TYR C1067 PHE 0.023 0.001 PHE H 541 TRP 0.035 0.001 TRP A 36 HIS 0.010 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00244 (34302) covalent geometry : angle 0.51219 (46710) SS BOND : bond 0.00212 ( 51) SS BOND : angle 0.84108 ( 102) hydrogen bonds : bond 0.04362 ( 1303) hydrogen bonds : angle 4.89544 ( 3630) link_NAG-ASN : bond 0.00379 ( 33) link_NAG-ASN : angle 1.67343 ( 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 371 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: E 81 MET cc_start: 0.6209 (tmm) cc_final: 0.5703 (tmm) REVERT: E 118 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7252 (mm-40) REVERT: J 394 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8188 (m-40) REVERT: J 981 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8724 (mm) REVERT: J 1144 GLU cc_start: 0.7426 (tp30) cc_final: 0.7192 (tp30) REVERT: G 81 MET cc_start: 0.6099 (tmm) cc_final: 0.5691 (tmm) REVERT: A 81 MET cc_start: 0.6119 (tmm) cc_final: 0.5698 (tmm) REVERT: A 105 ASP cc_start: 0.8520 (t0) cc_final: 0.8313 (t0) outliers start: 80 outliers final: 56 residues processed: 362 average time/residue: 0.1923 time to fit residues: 118.0431 Evaluate side-chains 325 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 340 GLU Chi-restraints excluded: chain H residue 512 VAL 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 856 ASN 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 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 501 ASN 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 981 LEU 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 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 720 ILE Chi-restraints excluded: chain C residue 856 ASN 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 2 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: 2.9990 chunk 113 optimal weight: 50.0000 chunk 333 optimal weight: 0.6980 chunk 385 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 375 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN J 540 ASN G 168 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.188186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155731 restraints weight = 48197.125| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.17 r_work: 0.3530 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 34386 Z= 0.253 Angle : 0.616 9.313 46911 Z= 0.315 Chirality : 0.048 0.344 5394 Planarity : 0.004 0.049 5961 Dihedral : 5.345 41.507 5265 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.03 % Allowed : 12.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4200 helix: 1.36 (0.19), residues: 747 sheet: 0.63 (0.15), residues: 1305 loop : -1.30 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 72 TYR 0.019 0.002 TYR C1067 PHE 0.024 0.002 PHE C 86 TRP 0.037 0.002 TRP A 36 HIS 0.009 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00620 (34302) covalent geometry : angle 0.60645 (46710) SS BOND : bond 0.00475 ( 51) SS BOND : angle 1.62744 ( 102) hydrogen bonds : bond 0.05771 ( 1303) hydrogen bonds : angle 5.05098 ( 3630) link_NAG-ASN : bond 0.00450 ( 33) link_NAG-ASN : angle 1.87355 ( 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 383 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 271 time to evaluate : 1.186 Fit side-chains REVERT: E 118 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7226 (mm-40) REVERT: F 55 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7752 (pttm) REVERT: J 394 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: J 981 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8743 (mm) REVERT: J 1144 GLU cc_start: 0.7476 (tp30) cc_final: 0.7252 (tp30) REVERT: G 81 MET cc_start: 0.6248 (tmm) cc_final: 0.5481 (tmm) REVERT: C 394 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8161 (m-40) REVERT: C 900 MET cc_start: 0.9150 (mtp) cc_final: 0.8908 (mtm) REVERT: A 81 MET cc_start: 0.6147 (tmm) cc_final: 0.5697 (tmm) outliers start: 112 outliers final: 85 residues processed: 364 average time/residue: 0.1948 time to fit residues: 119.0505 Evaluate side-chains 346 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 226 LEU 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 512 VAL 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 642 VAL Chi-restraints excluded: chain H residue 720 ILE Chi-restraints excluded: chain H residue 723 THR Chi-restraints excluded: chain H residue 791 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 1128 VAL Chi-restraints excluded: chain E residue 2 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 336 CYS Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 501 ASN Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 540 ASN 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 872 GLN Chi-restraints excluded: chain J residue 934 ILE Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU 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 35 VAL 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 389 ASP 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 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 1050 MET 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 2 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 63 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 354 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 349 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN A 59 ASN A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.191118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158304 restraints weight = 48463.406| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.17 r_work: 0.3576 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34386 Z= 0.112 Angle : 0.519 9.574 46911 Z= 0.266 Chirality : 0.044 0.305 5394 Planarity : 0.004 0.043 5961 Dihedral : 4.887 37.960 5265 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.46 % Allowed : 13.83 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.09 (0.13), residues: 4200 helix: 1.61 (0.20), residues: 753 sheet: 0.72 (0.15), residues: 1272 loop : -1.19 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 72 TYR 0.015 0.001 TYR C1067 PHE 0.022 0.001 PHE J 541 TRP 0.023 0.001 TRP A 36 HIS 0.010 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00252 (34302) covalent geometry : angle 0.51261 (46710) SS BOND : bond 0.00231 ( 51) SS BOND : angle 1.01094 ( 102) hydrogen bonds : bond 0.04417 ( 1303) hydrogen bonds : angle 4.80019 ( 3630) link_NAG-ASN : bond 0.00344 ( 33) link_NAG-ASN : angle 1.68404 ( 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 364 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 273 time to evaluate : 1.204 Fit side-chains REVERT: E 118 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7242 (mm-40) REVERT: J 394 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: J 981 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8732 (mm) REVERT: G 81 MET cc_start: 0.5995 (tmm) cc_final: 0.5335 (tmm) REVERT: G 85 ARG cc_start: 0.4999 (ppt170) cc_final: 0.4439 (mpt-90) REVERT: C 394 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.8066 (m-40) REVERT: C 1144 GLU cc_start: 0.7249 (tp30) cc_final: 0.6982 (tp30) REVERT: A 81 MET cc_start: 0.6142 (tmm) cc_final: 0.5758 (tmm) outliers start: 91 outliers final: 63 residues processed: 354 average time/residue: 0.1889 time to fit residues: 113.2929 Evaluate side-chains 330 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 226 LEU 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 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 2 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 130 VAL Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 327 VAL Chi-restraints excluded: chain J residue 336 CYS 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 501 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 588 THR Chi-restraints excluded: chain J residue 705 VAL Chi-restraints excluded: chain J residue 856 ASN Chi-restraints excluded: chain J residue 981 LEU 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 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 791 THR 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 2 VAL 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: 1.9990 chunk 273 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 chunk 396 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 382 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN J 540 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.157954 restraints weight = 48353.159| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.15 r_work: 0.3540 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34386 Z= 0.227 Angle : 0.588 8.685 46911 Z= 0.301 Chirality : 0.047 0.338 5394 Planarity : 0.004 0.049 5961 Dihedral : 5.079 40.214 5265 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.86 % Allowed : 13.56 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.22 (0.13), residues: 4200 helix: 1.32 (0.19), residues: 768 sheet: 0.70 (0.15), residues: 1308 loop : -1.30 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 646 TYR 0.023 0.002 TYR H 904 PHE 0.024 0.002 PHE G 113 TRP 0.021 0.001 TRP A 36 HIS 0.009 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00557 (34302) covalent geometry : angle 0.58043 (46710) SS BOND : bond 0.00460 ( 51) SS BOND : angle 1.35213 ( 102) hydrogen bonds : bond 0.05481 ( 1303) hydrogen bonds : angle 4.92427 ( 3630) link_NAG-ASN : bond 0.00375 ( 33) link_NAG-ASN : angle 1.80560 ( 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 373 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 267 time to evaluate : 1.007 Fit side-chains REVERT: E 118 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7226 (mm-40) REVERT: F 55 LYS cc_start: 0.7952 (ptpp) cc_final: 0.7739 (pttm) REVERT: J 394 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8251 (m-40) REVERT: J 981 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8774 (mm) REVERT: J 1144 GLU cc_start: 0.7509 (tp30) cc_final: 0.7283 (tp30) REVERT: G 81 MET cc_start: 0.6073 (tmm) cc_final: 0.5398 (tmm) REVERT: C 394 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: C 1144 GLU cc_start: 0.7222 (tp30) cc_final: 0.6995 (tp30) REVERT: A 81 MET cc_start: 0.6193 (tmm) cc_final: 0.5721 (tmm) outliers start: 106 outliers final: 85 residues processed: 359 average time/residue: 0.1877 time to fit residues: 113.7812 Evaluate side-chains 346 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 226 LEU 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 540 ASN Chi-restraints excluded: chain H residue 553 THR 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 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 1092 GLU Chi-restraints excluded: chain H residue 1128 VAL Chi-restraints excluded: chain E residue 2 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 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 336 CYS Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 501 ASN Chi-restraints excluded: chain J residue 512 VAL Chi-restraints excluded: chain J residue 540 ASN 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 720 ILE 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 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 G residue 111 SER 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 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 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 1050 MET 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 2 VAL Chi-restraints excluded: chain A residue 30 THR 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: 9.9990 chunk 117 optimal weight: 40.0000 chunk 335 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 391 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 372 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 540 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN J 540 ASN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN C 540 ASN A 59 ASN A 118 GLN ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158276 restraints weight = 48173.777| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.18 r_work: 0.3583 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34386 Z= 0.114 Angle : 0.529 11.778 46911 Z= 0.269 Chirality : 0.045 0.306 5394 Planarity : 0.004 0.043 5961 Dihedral : 4.757 37.745 5265 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.13 % Allowed : 14.40 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.65 (0.20), residues: 756 sheet: 0.75 (0.15), residues: 1278 loop : -1.18 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.019 0.001 TYR H 904 PHE 0.038 0.001 PHE H 541 TRP 0.056 0.002 TRP A 36 HIS 0.009 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00258 (34302) covalent geometry : angle 0.52233 (46710) SS BOND : bond 0.00226 ( 51) SS BOND : angle 0.92451 ( 102) hydrogen bonds : bond 0.04384 ( 1303) hydrogen bonds : angle 4.74866 ( 3630) link_NAG-ASN : bond 0.00328 ( 33) link_NAG-ASN : angle 1.66032 ( 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 359 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 280 time to evaluate : 1.026 Fit side-chains REVERT: H 574 ASP cc_start: 0.7754 (p0) cc_final: 0.7537 (t70) REVERT: E 72 ARG cc_start: 0.6772 (ptt-90) cc_final: 0.5798 (ttp80) REVERT: E 118 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7252 (mm-40) REVERT: J 394 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: J 981 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8753 (mm) REVERT: J 1144 GLU cc_start: 0.7541 (tp30) cc_final: 0.7279 (tp30) REVERT: G 81 MET cc_start: 0.5979 (tmm) cc_final: 0.5318 (tmm) REVERT: G 85 ARG cc_start: 0.5497 (ppt170) cc_final: 0.5241 (ptt90) REVERT: C 394 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: C 1144 GLU cc_start: 0.7230 (tp30) cc_final: 0.6981 (tp30) REVERT: A 81 MET cc_start: 0.6132 (tmm) cc_final: 0.5732 (tmm) REVERT: B 55 LYS cc_start: 0.7929 (ptpp) cc_final: 0.7714 (pttm) outliers start: 79 outliers final: 72 residues processed: 351 average time/residue: 0.1905 time to fit residues: 112.2159 Evaluate side-chains 345 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 270 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 226 LEU 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 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 723 THR 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 2 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 327 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 398 ASP 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 934 ILE Chi-restraints excluded: chain J residue 981 LEU 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 G residue 111 SER Chi-restraints excluded: chain C residue 105 ILE 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 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 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 2 VAL 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: 0.5980 chunk 377 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 367 optimal weight: 0.8980 chunk 406 optimal weight: 9.9990 chunk 366 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN 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 = 0.4239 r_free = 0.4239 target = 0.192762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.161432 restraints weight = 48609.643| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.11 r_work: 0.3623 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2114 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= 0.109 Angle : 0.517 9.598 46911 Z= 0.263 Chirality : 0.044 0.290 5394 Planarity : 0.004 0.046 5961 Dihedral : 4.555 36.053 5265 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.13 % Allowed : 14.72 % Favored : 83.14 % 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: -0.00 (0.13), residues: 4200 helix: 1.73 (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 0.020 0.001 TYR H 904 PHE 0.026 0.001 PHE A 29 TRP 0.057 0.002 TRP G 36 HIS 0.010 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00246 (34302) covalent geometry : angle 0.51106 (46710) SS BOND : bond 0.00214 ( 51) SS BOND : angle 0.86927 ( 102) hydrogen bonds : bond 0.04169 ( 1303) hydrogen bonds : angle 4.66671 ( 3630) link_NAG-ASN : bond 0.00307 ( 33) link_NAG-ASN : angle 1.61709 ( 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 360 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 1.001 Fit side-chains REVERT: E 118 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7263 (mm-40) REVERT: J 394 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8193 (m-40) REVERT: J 981 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8729 (mm) REVERT: J 1144 GLU cc_start: 0.7547 (tp30) cc_final: 0.7304 (tp30) REVERT: G 81 MET cc_start: 0.5865 (tmm) cc_final: 0.5219 (tmm) REVERT: G 85 ARG cc_start: 0.5432 (ppt170) cc_final: 0.5187 (ptt90) REVERT: C 394 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.8029 (m-40) REVERT: C 900 MET cc_start: 0.9050 (mtp) cc_final: 0.8759 (mtm) REVERT: C 1144 GLU cc_start: 0.7076 (tp30) cc_final: 0.6861 (tp30) REVERT: A 81 MET cc_start: 0.6097 (tmm) cc_final: 0.5638 (tmm) outliers start: 79 outliers final: 71 residues processed: 352 average time/residue: 0.1896 time to fit residues: 111.7629 Evaluate side-chains 345 residues out of total 3702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 271 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 226 LEU 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 791 THR Chi-restraints excluded: chain H residue 856 ASN Chi-restraints excluded: chain H residue 896 ILE Chi-restraints excluded: chain H residue 916 LEU 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 2 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 327 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 394 ASN Chi-restraints excluded: chain J residue 398 ASP Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 501 ASN Chi-restraints excluded: chain J residue 512 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 934 ILE Chi-restraints excluded: chain J residue 981 LEU 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 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 229 LEU 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 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 791 THR 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 2 VAL 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: 3.9990 chunk 285 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 250 optimal weight: 0.0170 chunk 209 optimal weight: 0.0370 chunk 297 optimal weight: 0.4980 chunk 266 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 501 ASN G 59 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN A 59 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 = 0.4248 r_free = 0.4248 target = 0.193556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160767 restraints weight = 48364.610| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.21 r_work: 0.3569 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34386 Z= 0.098 Angle : 0.511 12.471 46911 Z= 0.259 Chirality : 0.044 0.278 5394 Planarity : 0.004 0.046 5961 Dihedral : 4.382 34.432 5265 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.24 % Allowed : 14.67 % Favored : 83.09 % 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: 0.06 (0.13), residues: 4200 helix: 1.84 (0.20), residues: 756 sheet: 0.76 (0.15), residues: 1317 loop : -1.13 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 646 TYR 0.022 0.001 TYR H 904 PHE 0.025 0.001 PHE A 29 TRP 0.048 0.001 TRP G 36 HIS 0.010 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00217 (34302) covalent geometry : angle 0.50602 (46710) SS BOND : bond 0.00173 ( 51) SS BOND : angle 0.77581 ( 102) hydrogen bonds : bond 0.03893 ( 1303) hydrogen bonds : angle 4.57874 ( 3630) link_NAG-ASN : bond 0.00305 ( 33) link_NAG-ASN : angle 1.55667 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7991.76 seconds wall clock time: 137 minutes 45.45 seconds (8265.45 seconds total)