Starting phenix.real_space_refine on Thu Sep 18 01:30:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmq_38486/09_2025/8xmq_38486_neut.cif" } resolution = 3.21 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= 0.034 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: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 Fe 2 7.16 5 S 108 5.16 5 C 8074 2.51 5 N 2277 2.21 5 O 2477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12950 Number of models: 1 Model: "" Number of chains: 12 Chain: "2" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2117 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 13, 'TRANS': 256} Chain breaks: 2 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3367 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 4, 'TRANS': 435} Chain breaks: 2 Chain: "D" Number of atoms: 5066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5066 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 19, 'TRANS': 644} Chain breaks: 7 Chain: "C" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1057 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "G" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {' CA': 6, 'NAG': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 34 Unusual residues: {' CA': 6, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.14, per 1000 atoms: 0.24 Number of scatterers: 12950 At special positions: 0 Unit cell: (89.88, 127.33, 172.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 12 19.99 S 108 16.00 O 2477 8.00 N 2277 7.00 C 8074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 168 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 197 " - pdb=" SG CYS F 258 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 238 " distance=2.03 Simple disulfide: pdb=" SG CYS F 275 " - pdb=" SG CYS F 309 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 355 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 365 " distance=2.03 Simple disulfide: pdb=" SG CYS F 335 " - pdb=" SG CYS F 345 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 398 " - pdb=" SG CYS F 462 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 472 " distance=2.03 Simple disulfide: pdb=" SG CYS F 442 " - pdb=" SG CYS F 452 " distance=2.04 Simple disulfide: pdb=" SG CYS F 728 " - pdb=" SG CYS F 762 " distance=2.03 Simple disulfide: pdb=" SG CYS F 744 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 757 " - pdb=" SG CYS F 818 " distance=2.03 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.03 Simple disulfide: pdb=" SG CYS D 487 " - pdb=" SG CYS D 521 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.03 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 662 " distance=2.03 Simple disulfide: pdb=" SG CYS D 835 " - pdb=" SG CYS D 869 " distance=2.03 Simple disulfide: pdb=" SG CYS D 864 " - pdb=" SG CYS D 925 " distance=2.03 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.03 Simple disulfide: pdb=" SG CYS D 938 " - pdb=" SG CYS D 972 " distance=2.02 Simple disulfide: pdb=" SG CYS D 954 " - pdb=" SG CYS D1018 " distance=2.03 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " 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=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG A 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG D1102 " - " ASN D1027 " " NAG F1107 " - " ASN F 320 " " NAG F1108 " - " ASN F 445 " " NAG F1109 " - " ASN F 767 " " NAG Y 1 " - " ASN D 320 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 594.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 27 sheets defined 28.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 157 through 162 removed outlier: 3.923A pdb=" N THR 2 161 " --> pdb=" O ASP 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 333 through 344 removed outlier: 4.797A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.814A pdb=" N ASP F 253 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 403 through 415 removed outlier: 3.600A pdb=" N ALA F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 809 through 813 removed outlier: 3.604A pdb=" N ASP F 813 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.516A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.106A pdb=" N PHE D 507 " --> pdb=" O ASP D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 504 through 507' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 568 through 572 Processing helix chain 'D' and resid 613 through 620 Processing helix chain 'D' and resid 622 through 624 No H-bonds generated for 'chain 'D' and resid 622 through 624' Processing helix chain 'D' and resid 856 through 868 Processing helix chain 'D' and resid 901 through 905 removed outlier: 3.520A pdb=" N GLN D 904 " --> pdb=" O THR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 971 Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1019 through 1023 removed outlier: 3.641A pdb=" N ASP D1023 " --> pdb=" O HIS D1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.720A pdb=" N THR C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.670A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'G' and resid 4 through 17 removed outlier: 3.924A pdb=" N LYS G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 4.242A pdb=" N GLY G 24 " --> pdb=" O VAL G 20 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.593A pdb=" N PHE G 41 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU G 43 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 57 through 77 Processing helix chain 'G' and resid 80 through 85 removed outlier: 3.910A pdb=" N THR G 84 " --> pdb=" O ASN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 95 Processing helix chain 'G' and resid 99 through 119 removed outlier: 3.931A pdb=" N PHE G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG G 104 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 58 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.024A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.626A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.759A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.759A pdb=" N SER F 265 " --> pdb=" O ARG F 282 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 279 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE F 290 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N TRP F 287 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU F 330 " --> pdb=" O TRP F 287 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR F 289 " --> pdb=" O LEU F 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 371 through 377 removed outlier: 3.866A pdb=" N LYS F 421 " --> pdb=" O THR F 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 396 through 397 removed outlier: 6.932A pdb=" N LYS F 396 " --> pdb=" O LEU F 437 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU F 439 " --> pdb=" O LYS F 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 720 through 722 Processing sheet with id=AB2, first strand: chain 'F' and resid 720 through 722 removed outlier: 14.930A pdb=" N GLY F 730 " --> pdb=" O ASP F 745 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N ASP F 745 " --> pdb=" O GLY F 730 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL F 732 " --> pdb=" O ILE F 743 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE F 743 " --> pdb=" O VAL F 732 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU F 783 " --> pdb=" O THR F 742 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU F 785 " --> pdb=" O CYS F 744 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ASP F 746 " --> pdb=" O GLU F 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 823 through 824 Processing sheet with id=AB4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AB5, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.656A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.656A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS D 327 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 371 through 380 removed outlier: 3.511A pdb=" N GLY D 378 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR D 471 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 371 through 380 removed outlier: 3.511A pdb=" N GLY D 378 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.223A pdb=" N GLY D 574 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE D 527 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 576 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 476 through 481 removed outlier: 6.139A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TRP D 499 " --> pdb=" O GLN D 539 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AC4, first strand: chain 'D' and resid 597 through 600 Processing sheet with id=AC5, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AC6, first strand: chain 'D' and resid 836 through 838 removed outlier: 3.852A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 840 through 843 removed outlier: 6.352A pdb=" N TRP D 889 " --> pdb=" O TRP D 847 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D 849 " --> pdb=" O TRP D 889 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.311A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N TRP D 992 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR D 952 " --> pdb=" O TRP D 992 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 929 through 932 507 hydrogen bonds defined for protein. 1386 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: 2.72 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 5375 1.39 - 1.56: 7742 1.56 - 1.72: 0 1.72 - 1.89: 125 1.89 - 2.05: 8 Bond restraints: 13250 Sorted by residual: bond pdb=" N GLU D 920 " pdb=" CA GLU D 920 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.20e-02 6.94e+03 5.38e+00 bond pdb=" N VAL 2 271 " pdb=" CA VAL 2 271 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.58e+00 bond pdb=" N THR D 921 " pdb=" CA THR D 921 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.30e-02 5.92e+03 4.34e+00 bond pdb=" N ILE 2 344 " pdb=" CA ILE 2 344 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.25e-02 6.40e+03 3.74e+00 bond pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " ideal model delta sigma weight residual 1.331 1.302 0.028 1.46e-02 4.69e+03 3.68e+00 ... (remaining 13245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17429 1.38 - 2.76: 432 2.76 - 4.14: 93 4.14 - 5.52: 16 5.52 - 6.90: 7 Bond angle restraints: 17977 Sorted by residual: angle pdb=" C THR D 921 " pdb=" CA THR D 921 " pdb=" CB THR D 921 " ideal model delta sigma weight residual 111.83 104.93 6.90 1.60e+00 3.91e-01 1.86e+01 angle pdb=" N ALA 2 345 " pdb=" CA ALA 2 345 " pdb=" C ALA 2 345 " ideal model delta sigma weight residual 111.71 106.94 4.77 1.34e+00 5.57e-01 1.27e+01 angle pdb=" O VAL 2 269 " pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " ideal model delta sigma weight residual 122.69 118.75 3.94 1.14e+00 7.69e-01 1.20e+01 angle pdb=" CA THR D 921 " pdb=" C THR D 921 " pdb=" O THR D 921 " ideal model delta sigma weight residual 122.41 118.40 4.01 1.21e+00 6.83e-01 1.10e+01 angle pdb=" C VAL 2 269 " pdb=" N GLY 2 270 " pdb=" CA GLY 2 270 " ideal model delta sigma weight residual 121.41 114.93 6.48 1.96e+00 2.60e-01 1.09e+01 ... (remaining 17972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7115 17.93 - 35.86: 639 35.86 - 53.80: 115 53.80 - 71.73: 25 71.73 - 89.66: 11 Dihedral angle restraints: 7905 sinusoidal: 3272 harmonic: 4633 Sorted by residual: dihedral pdb=" CB CYS F 275 " pdb=" SG CYS F 275 " pdb=" SG CYS F 309 " pdb=" CB CYS F 309 " ideal model delta sinusoidal sigma weight residual 93.00 179.91 -86.91 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -144.09 58.09 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CB CYS 2 90 " pdb=" SG CYS 2 90 " pdb=" SG CYS 2 207 " pdb=" CB CYS 2 207 " ideal model delta sinusoidal sigma weight residual 93.00 35.31 57.69 1 1.00e+01 1.00e-02 4.47e+01 ... (remaining 7902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1262 0.036 - 0.072: 475 0.072 - 0.108: 158 0.108 - 0.144: 35 0.144 - 0.180: 3 Chirality restraints: 1933 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 320 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA ILE 2 344 " pdb=" N ILE 2 344 " pdb=" C ILE 2 344 " pdb=" CB ILE 2 344 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA PRO D 310 " pdb=" N PRO D 310 " pdb=" C PRO D 310 " pdb=" CB PRO D 310 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1930 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR 2 343 " -0.020 2.00e-02 2.50e+03 4.17e-02 1.74e+01 pdb=" C THR 2 343 " 0.072 2.00e-02 2.50e+03 pdb=" O THR 2 343 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE 2 344 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 2 269 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL 2 269 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL 2 269 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY 2 270 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO G 124 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO G 125 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 210 2.64 - 3.20: 11619 3.20 - 3.77: 20918 3.77 - 4.33: 29302 4.33 - 4.90: 48073 Nonbonded interactions: 110122 Sorted by model distance: nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.074 3.040 nonbonded pdb=" OG SER D 366 " pdb=" OD1 ASP D 370 " model vdw 2.184 3.040 nonbonded pdb=" NH1 ARG C 31 " pdb=" OE1 GLN G 127 " model vdw 2.186 3.120 nonbonded pdb=" O ILE D 328 " pdb=" NE2 HIS D 353 " model vdw 2.200 3.120 nonbonded pdb=" OE1 GLU D 359 " pdb="CA CA D1103 " model vdw 2.229 2.510 ... (remaining 110117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'Y' } 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=0.52 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 0.095 13307 Z= 0.165 Angle : 0.563 6.899 18098 Z= 0.305 Chirality : 0.043 0.180 1933 Planarity : 0.003 0.043 2309 Dihedral : 13.774 89.662 4813 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 0.15 % Allowed : 0.37 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.24 (0.21), residues: 1625 helix: 1.85 (0.28), residues: 377 sheet: -0.56 (0.41), residues: 180 loop : -0.86 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 252 TYR 0.008 0.001 TYR 2 221 PHE 0.010 0.001 PHE G 71 TRP 0.010 0.001 TRP D 992 HIS 0.010 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00357 (13250) covalent geometry : angle 0.55838 (17977) SS BOND : bond 0.00243 ( 44) SS BOND : angle 1.05328 ( 88) hydrogen bonds : bond 0.20196 ( 469) hydrogen bonds : angle 7.82158 ( 1386) Misc. bond : bond 0.06863 ( 2) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 0.95521 ( 6) link_NAG-ASN : bond 0.00210 ( 9) link_NAG-ASN : angle 1.03377 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8563 (m) cc_final: 0.8046 (t) REVERT: 2 202 ARG cc_start: 0.7619 (mtm-85) cc_final: 0.7015 (mtp85) REVERT: 2 232 LYS cc_start: 0.8534 (tptt) cc_final: 0.8319 (ttpp) REVERT: 2 286 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7813 (ttpp) REVERT: F 187 ASN cc_start: 0.7765 (t0) cc_final: 0.7507 (t0) REVERT: F 269 VAL cc_start: 0.7895 (p) cc_final: 0.7652 (m) REVERT: F 822 MET cc_start: 0.6572 (mtm) cc_final: 0.5961 (ttp) REVERT: D 840 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6283 (pt0) REVERT: D 874 LYS cc_start: 0.7965 (mttm) cc_final: 0.7657 (pttp) REVERT: D 919 GLU cc_start: 0.4229 (OUTLIER) cc_final: 0.3954 (pt0) REVERT: D 960 LEU cc_start: 0.7961 (tp) cc_final: 0.7572 (tt) REVERT: C 56 LYS cc_start: 0.7132 (tttt) cc_final: 0.6556 (mmmt) REVERT: C 90 LYS cc_start: 0.7988 (tttp) cc_final: 0.7515 (mtpt) REVERT: C 127 LYS cc_start: 0.8659 (mttp) cc_final: 0.8279 (mtmt) REVERT: G 95 LYS cc_start: 0.8384 (mppt) cc_final: 0.8160 (ttpt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.1363 time to fit residues: 61.8801 Evaluate side-chains 183 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 272 GLN Chi-restraints excluded: chain D residue 919 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 341 GLN F 189 ASN F 327 HIS F 759 GLN ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 801 HIS F 810 HIS D 431 GLN D 622 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.181438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.140303 restraints weight = 15414.053| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.92 r_work: 0.3167 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 13307 Z= 0.184 Angle : 0.597 9.085 18098 Z= 0.308 Chirality : 0.044 0.175 1933 Planarity : 0.004 0.051 2309 Dihedral : 6.618 79.279 1989 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.14 % Allowed : 9.29 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.38 (0.21), residues: 1625 helix: 1.81 (0.27), residues: 375 sheet: -1.05 (0.36), residues: 185 loop : -0.90 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 374 TYR 0.016 0.002 TYR C 140 PHE 0.021 0.001 PHE D 842 TRP 0.020 0.001 TRP F 847 HIS 0.010 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00438 (13250) covalent geometry : angle 0.59018 (17977) SS BOND : bond 0.00372 ( 44) SS BOND : angle 1.19228 ( 88) hydrogen bonds : bond 0.03778 ( 469) hydrogen bonds : angle 5.27583 ( 1386) Misc. bond : bond 0.07931 ( 2) link_BETA1-4 : bond 0.00711 ( 2) link_BETA1-4 : angle 0.90835 ( 6) link_NAG-ASN : bond 0.00339 ( 9) link_NAG-ASN : angle 1.54325 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8683 (m) cc_final: 0.8377 (t) REVERT: 2 202 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7350 (mtp85) REVERT: 2 232 LYS cc_start: 0.8885 (tptt) cc_final: 0.8677 (ttpp) REVERT: F 187 ASN cc_start: 0.7984 (t0) cc_final: 0.7312 (t0) REVERT: F 283 PHE cc_start: 0.7466 (t80) cc_final: 0.7183 (t80) REVERT: F 349 GLU cc_start: 0.7715 (mp0) cc_final: 0.7459 (mp0) REVERT: F 447 THR cc_start: 0.8600 (t) cc_final: 0.8304 (p) REVERT: F 822 MET cc_start: 0.7562 (mtm) cc_final: 0.6543 (ttp) REVERT: F 847 TRP cc_start: 0.7070 (m100) cc_final: 0.6810 (m100) REVERT: D 167 MET cc_start: 0.7977 (mtm) cc_final: 0.7771 (mtm) REVERT: D 286 GLU cc_start: 0.8020 (pt0) cc_final: 0.7482 (pt0) REVERT: D 327 HIS cc_start: 0.8550 (m90) cc_final: 0.7965 (m90) REVERT: D 874 LYS cc_start: 0.7970 (mttm) cc_final: 0.7405 (pttp) REVERT: D 930 ARG cc_start: 0.7833 (ptt180) cc_final: 0.7550 (ptt180) REVERT: D 960 LEU cc_start: 0.7877 (tp) cc_final: 0.7465 (tt) REVERT: D 994 ASN cc_start: 0.7368 (p0) cc_final: 0.6754 (p0) REVERT: D 1012 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8107 (mtp85) REVERT: C 50 HIS cc_start: 0.8732 (t70) cc_final: 0.8499 (t-90) REVERT: C 56 LYS cc_start: 0.7776 (tttt) cc_final: 0.7208 (mmmt) REVERT: C 90 LYS cc_start: 0.8299 (tttp) cc_final: 0.7909 (mtpt) REVERT: C 127 LYS cc_start: 0.9031 (mttp) cc_final: 0.8722 (mtmt) REVERT: G 95 LYS cc_start: 0.8662 (mppt) cc_final: 0.8171 (ttpt) outliers start: 29 outliers final: 17 residues processed: 216 average time/residue: 0.1275 time to fit residues: 38.9194 Evaluate side-chains 184 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 787 LYS Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 240 HIS F 327 HIS D 539 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142995 restraints weight = 15495.305| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.79 r_work: 0.3181 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 13307 Z= 0.167 Angle : 0.551 6.668 18098 Z= 0.283 Chirality : 0.043 0.157 1933 Planarity : 0.004 0.040 2309 Dihedral : 6.083 84.061 1983 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.99 % Allowed : 11.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.49 (0.20), residues: 1625 helix: 1.83 (0.27), residues: 377 sheet: -1.50 (0.34), residues: 189 loop : -0.94 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 647 TYR 0.015 0.002 TYR C 140 PHE 0.015 0.001 PHE D 842 TRP 0.032 0.001 TRP D1013 HIS 0.011 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00410 (13250) covalent geometry : angle 0.54498 (17977) SS BOND : bond 0.00327 ( 44) SS BOND : angle 1.02051 ( 88) hydrogen bonds : bond 0.03386 ( 469) hydrogen bonds : angle 5.00247 ( 1386) Misc. bond : bond 0.08023 ( 2) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 0.85022 ( 6) link_NAG-ASN : bond 0.00195 ( 9) link_NAG-ASN : angle 1.40040 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8634 (m) cc_final: 0.8401 (t) REVERT: 2 202 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7408 (mtp85) REVERT: 2 272 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8318 (tp40) REVERT: F 159 MET cc_start: 0.6196 (ptm) cc_final: 0.5456 (ptm) REVERT: F 187 ASN cc_start: 0.7911 (t0) cc_final: 0.7260 (t0) REVERT: F 283 PHE cc_start: 0.7666 (t80) cc_final: 0.7297 (t80) REVERT: F 447 THR cc_start: 0.8526 (t) cc_final: 0.8271 (p) REVERT: F 822 MET cc_start: 0.7431 (mtm) cc_final: 0.7207 (mtt) REVERT: D 400 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7841 (ttm110) REVERT: D 543 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8139 (mt-10) REVERT: D 874 LYS cc_start: 0.7982 (mttm) cc_final: 0.7488 (pttp) REVERT: D 932 GLN cc_start: 0.8302 (mt0) cc_final: 0.7954 (mt0) REVERT: D 960 LEU cc_start: 0.7943 (tp) cc_final: 0.7440 (tt) REVERT: C 50 HIS cc_start: 0.8747 (t70) cc_final: 0.8540 (t-90) REVERT: C 56 LYS cc_start: 0.7874 (tttt) cc_final: 0.7358 (mmmt) REVERT: C 127 LYS cc_start: 0.9050 (mttp) cc_final: 0.8764 (mtmt) REVERT: G 95 LYS cc_start: 0.8649 (mppt) cc_final: 0.8257 (ttpt) outliers start: 27 outliers final: 20 residues processed: 189 average time/residue: 0.1127 time to fit residues: 31.3686 Evaluate side-chains 179 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 272 GLN Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 787 LYS Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 132 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 150 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 327 HIS F 797 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143344 restraints weight = 15453.504| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.57 r_work: 0.3171 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 13307 Z= 0.151 Angle : 0.534 6.775 18098 Z= 0.274 Chirality : 0.043 0.156 1933 Planarity : 0.003 0.041 2309 Dihedral : 5.849 87.038 1983 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 2.36 % Allowed : 13.56 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.48 (0.20), residues: 1625 helix: 1.90 (0.27), residues: 377 sheet: -1.57 (0.33), residues: 189 loop : -0.94 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1012 TYR 0.012 0.001 TYR 2 239 PHE 0.017 0.001 PHE D 842 TRP 0.039 0.001 TRP D1013 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00370 (13250) covalent geometry : angle 0.52884 (17977) SS BOND : bond 0.00277 ( 44) SS BOND : angle 1.00422 ( 88) hydrogen bonds : bond 0.03094 ( 469) hydrogen bonds : angle 4.82089 ( 1386) Misc. bond : bond 0.07267 ( 2) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 0.87285 ( 6) link_NAG-ASN : bond 0.00167 ( 9) link_NAG-ASN : angle 1.26458 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8640 (m) cc_final: 0.8421 (t) REVERT: 2 202 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7435 (mtp85) REVERT: F 187 ASN cc_start: 0.7935 (t0) cc_final: 0.7242 (t0) REVERT: F 283 PHE cc_start: 0.7645 (t80) cc_final: 0.7192 (t80) REVERT: F 447 THR cc_start: 0.8494 (t) cc_final: 0.8235 (p) REVERT: F 822 MET cc_start: 0.7464 (mtm) cc_final: 0.7165 (mtt) REVERT: D 874 LYS cc_start: 0.8028 (mttm) cc_final: 0.7547 (pttp) REVERT: D 932 GLN cc_start: 0.8334 (mt0) cc_final: 0.7936 (mt0) REVERT: D 960 LEU cc_start: 0.7949 (tp) cc_final: 0.7403 (tt) REVERT: C 56 LYS cc_start: 0.7911 (tttt) cc_final: 0.7401 (mmmt) REVERT: C 127 LYS cc_start: 0.9056 (mttp) cc_final: 0.8788 (mtmt) REVERT: G 95 LYS cc_start: 0.8645 (mppt) cc_final: 0.8272 (ttpt) outliers start: 32 outliers final: 19 residues processed: 182 average time/residue: 0.1190 time to fit residues: 31.4234 Evaluate side-chains 169 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 104 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 240 HIS F 327 HIS F 338 HIS D 456 GLN D 651 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.175200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136458 restraints weight = 15477.326| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.90 r_work: 0.3065 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 13307 Z= 0.235 Angle : 0.603 8.688 18098 Z= 0.307 Chirality : 0.045 0.171 1933 Planarity : 0.004 0.050 2309 Dihedral : 6.021 89.237 1983 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.65 % Allowed : 14.66 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.67 (0.20), residues: 1625 helix: 1.59 (0.27), residues: 379 sheet: -1.79 (0.35), residues: 189 loop : -0.97 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1011 TYR 0.016 0.002 TYR 2 239 PHE 0.016 0.002 PHE D 842 TRP 0.029 0.001 TRP D1013 HIS 0.011 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00572 (13250) covalent geometry : angle 0.59637 (17977) SS BOND : bond 0.00495 ( 44) SS BOND : angle 1.24942 ( 88) hydrogen bonds : bond 0.03395 ( 469) hydrogen bonds : angle 4.99297 ( 1386) Misc. bond : bond 0.10488 ( 2) link_BETA1-4 : bond 0.00426 ( 2) link_BETA1-4 : angle 0.83865 ( 6) link_NAG-ASN : bond 0.00167 ( 9) link_NAG-ASN : angle 1.38840 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.497 Fit side-chains REVERT: 2 198 SER cc_start: 0.8733 (m) cc_final: 0.8489 (t) REVERT: 2 202 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7383 (mtp85) REVERT: F 187 ASN cc_start: 0.7962 (t0) cc_final: 0.7157 (t0) REVERT: F 447 THR cc_start: 0.8533 (t) cc_final: 0.8264 (p) REVERT: F 847 TRP cc_start: 0.7414 (m100) cc_final: 0.7129 (m100) REVERT: D 344 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: D 874 LYS cc_start: 0.8101 (mttm) cc_final: 0.7514 (pttp) REVERT: D 932 GLN cc_start: 0.8461 (mt0) cc_final: 0.8123 (mt0) REVERT: D 1013 TRP cc_start: 0.6396 (m-10) cc_final: 0.6179 (m-90) REVERT: C 56 LYS cc_start: 0.7905 (tttt) cc_final: 0.7337 (mmmt) REVERT: C 90 LYS cc_start: 0.8424 (tttp) cc_final: 0.8017 (mtpt) REVERT: G 95 LYS cc_start: 0.8649 (mppt) cc_final: 0.8227 (ttpt) outliers start: 36 outliers final: 26 residues processed: 180 average time/residue: 0.1203 time to fit residues: 31.6864 Evaluate side-chains 168 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.0670 chunk 80 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 272 GLN F 327 HIS D 651 HIS ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123680 restraints weight = 15632.418| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.23 r_work: 0.3272 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 13307 Z= 0.134 Angle : 0.531 8.152 18098 Z= 0.274 Chirality : 0.042 0.155 1933 Planarity : 0.004 0.046 2309 Dihedral : 5.648 83.785 1983 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.58 % Allowed : 16.80 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.45 (0.21), residues: 1625 helix: 1.98 (0.27), residues: 378 sheet: -1.72 (0.34), residues: 186 loop : -0.91 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1012 TYR 0.018 0.001 TYR 2 183 PHE 0.022 0.001 PHE F 283 TRP 0.020 0.001 TRP D1013 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00328 (13250) covalent geometry : angle 0.52539 (17977) SS BOND : bond 0.00250 ( 44) SS BOND : angle 1.07204 ( 88) hydrogen bonds : bond 0.02918 ( 469) hydrogen bonds : angle 4.69437 ( 1386) Misc. bond : bond 0.07106 ( 2) link_BETA1-4 : bond 0.00280 ( 2) link_BETA1-4 : angle 0.85621 ( 6) link_NAG-ASN : bond 0.00147 ( 9) link_NAG-ASN : angle 1.18040 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.497 Fit side-chains REVERT: 2 198 SER cc_start: 0.8760 (m) cc_final: 0.8508 (t) REVERT: 2 202 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7207 (mtp85) REVERT: F 187 ASN cc_start: 0.7754 (t0) cc_final: 0.7399 (t0) REVERT: F 200 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5565 (mp) REVERT: F 447 THR cc_start: 0.8472 (t) cc_final: 0.8192 (p) REVERT: F 847 TRP cc_start: 0.7230 (m100) cc_final: 0.6862 (m100) REVERT: D 344 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7062 (mp10) REVERT: D 435 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.7427 (m) REVERT: D 874 LYS cc_start: 0.8064 (mttm) cc_final: 0.7363 (pttp) REVERT: D 932 GLN cc_start: 0.8373 (mt0) cc_final: 0.8059 (mt0) REVERT: C 56 LYS cc_start: 0.7607 (tttt) cc_final: 0.7012 (mmmt) REVERT: C 90 LYS cc_start: 0.8537 (tttp) cc_final: 0.8050 (mtpt) REVERT: G 95 LYS cc_start: 0.8648 (mppt) cc_final: 0.8099 (ttpt) outliers start: 35 outliers final: 24 residues processed: 174 average time/residue: 0.1104 time to fit residues: 28.7170 Evaluate side-chains 171 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 155 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 338 HIS D 651 HIS ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120498 restraints weight = 15713.807| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.23 r_work: 0.3228 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 13307 Z= 0.201 Angle : 0.574 7.827 18098 Z= 0.294 Chirality : 0.044 0.166 1933 Planarity : 0.004 0.045 2309 Dihedral : 5.793 84.245 1983 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.26 % Rotamer: Outliers : 2.73 % Allowed : 17.46 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.56 (0.20), residues: 1625 helix: 1.80 (0.27), residues: 378 sheet: -1.86 (0.36), residues: 176 loop : -0.95 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 930 TYR 0.019 0.002 TYR 2 183 PHE 0.022 0.002 PHE F 283 TRP 0.019 0.001 TRP D1013 HIS 0.009 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00490 (13250) covalent geometry : angle 0.56642 (17977) SS BOND : bond 0.00376 ( 44) SS BOND : angle 1.24441 ( 88) hydrogen bonds : bond 0.03133 ( 469) hydrogen bonds : angle 4.83091 ( 1386) Misc. bond : bond 0.09589 ( 2) link_BETA1-4 : bond 0.00368 ( 2) link_BETA1-4 : angle 0.74406 ( 6) link_NAG-ASN : bond 0.00142 ( 9) link_NAG-ASN : angle 1.30061 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.507 Fit side-chains REVERT: 2 198 SER cc_start: 0.8798 (m) cc_final: 0.8559 (t) REVERT: 2 202 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7275 (mtp85) REVERT: F 187 ASN cc_start: 0.7830 (t0) cc_final: 0.7198 (t0) REVERT: F 200 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5685 (mp) REVERT: F 283 PHE cc_start: 0.6749 (t80) cc_final: 0.6192 (t80) REVERT: F 447 THR cc_start: 0.8463 (t) cc_final: 0.8196 (p) REVERT: F 450 TRP cc_start: 0.8898 (OUTLIER) cc_final: 0.8372 (m100) REVERT: F 842 PHE cc_start: 0.6235 (t80) cc_final: 0.5728 (t80) REVERT: D 344 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: D 435 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7979 (t) REVERT: D 874 LYS cc_start: 0.8060 (mttm) cc_final: 0.7337 (pttp) REVERT: D 932 GLN cc_start: 0.8425 (mt0) cc_final: 0.8183 (mt0) REVERT: C 56 LYS cc_start: 0.7637 (tttt) cc_final: 0.7042 (mmmt) REVERT: C 90 LYS cc_start: 0.8522 (tttp) cc_final: 0.7944 (mtpt) REVERT: G 95 LYS cc_start: 0.8662 (mppt) cc_final: 0.8111 (ttpt) outliers start: 37 outliers final: 30 residues processed: 179 average time/residue: 0.1027 time to fit residues: 27.3257 Evaluate side-chains 181 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 450 TRP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.178362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122743 restraints weight = 15646.947| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.21 r_work: 0.3284 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 13307 Z= 0.153 Angle : 0.544 8.796 18098 Z= 0.281 Chirality : 0.043 0.164 1933 Planarity : 0.004 0.046 2309 Dihedral : 5.655 82.392 1983 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 2.65 % Allowed : 17.61 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.46 (0.21), residues: 1625 helix: 2.01 (0.27), residues: 376 sheet: -1.80 (0.35), residues: 186 loop : -0.91 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1011 TYR 0.017 0.001 TYR 2 183 PHE 0.020 0.001 PHE F 283 TRP 0.060 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00376 (13250) covalent geometry : angle 0.53769 (17977) SS BOND : bond 0.00279 ( 44) SS BOND : angle 1.16195 ( 88) hydrogen bonds : bond 0.02943 ( 469) hydrogen bonds : angle 4.70716 ( 1386) Misc. bond : bond 0.07821 ( 2) link_BETA1-4 : bond 0.00291 ( 2) link_BETA1-4 : angle 0.77697 ( 6) link_NAG-ASN : bond 0.00141 ( 9) link_NAG-ASN : angle 1.20147 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.499 Fit side-chains REVERT: 2 198 SER cc_start: 0.8754 (m) cc_final: 0.8512 (t) REVERT: 2 202 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7300 (mtp85) REVERT: F 187 ASN cc_start: 0.7833 (t0) cc_final: 0.7191 (t0) REVERT: F 283 PHE cc_start: 0.6680 (t80) cc_final: 0.6053 (t80) REVERT: F 447 THR cc_start: 0.8436 (t) cc_final: 0.8204 (p) REVERT: F 450 TRP cc_start: 0.8908 (OUTLIER) cc_final: 0.8250 (m100) REVERT: F 842 PHE cc_start: 0.6289 (t80) cc_final: 0.5954 (t80) REVERT: D 344 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: D 435 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.7418 (p) REVERT: D 874 LYS cc_start: 0.8076 (mttm) cc_final: 0.7413 (pttp) REVERT: D 932 GLN cc_start: 0.8387 (mt0) cc_final: 0.8147 (mt0) REVERT: C 56 LYS cc_start: 0.7618 (tttt) cc_final: 0.7062 (mmmt) REVERT: C 90 LYS cc_start: 0.8496 (tttp) cc_final: 0.7994 (mtpt) REVERT: G 95 LYS cc_start: 0.8649 (mppt) cc_final: 0.8118 (ttpt) outliers start: 36 outliers final: 30 residues processed: 171 average time/residue: 0.1075 time to fit residues: 27.2867 Evaluate side-chains 177 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 284 MET Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 334 SER Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 450 TRP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 849 THR Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 54 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 797 GLN ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130235 restraints weight = 15646.239| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.20 r_work: 0.3277 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 13307 Z= 0.130 Angle : 0.533 7.171 18098 Z= 0.277 Chirality : 0.043 0.175 1933 Planarity : 0.004 0.044 2309 Dihedral : 5.591 81.976 1983 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.43 % Allowed : 17.76 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.40 (0.21), residues: 1625 helix: 2.10 (0.27), residues: 377 sheet: -1.80 (0.35), residues: 186 loop : -0.88 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1011 TYR 0.016 0.001 TYR 2 183 PHE 0.018 0.001 PHE F 283 TRP 0.109 0.002 TRP D1013 HIS 0.012 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00320 (13250) covalent geometry : angle 0.52812 (17977) SS BOND : bond 0.00249 ( 44) SS BOND : angle 1.04235 ( 88) hydrogen bonds : bond 0.02859 ( 469) hydrogen bonds : angle 4.63652 ( 1386) Misc. bond : bond 0.06937 ( 2) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 0.80565 ( 6) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 1.11777 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8757 (m) cc_final: 0.8514 (t) REVERT: 2 202 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7219 (mtp85) REVERT: F 187 ASN cc_start: 0.7796 (t0) cc_final: 0.7395 (t0) REVERT: F 447 THR cc_start: 0.8441 (t) cc_final: 0.8217 (p) REVERT: F 450 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.8233 (m100) REVERT: D 200 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7781 (mp) REVERT: D 344 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: D 435 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.7329 (p) REVERT: D 874 LYS cc_start: 0.8069 (mttm) cc_final: 0.7387 (pttp) REVERT: D 932 GLN cc_start: 0.8393 (mt0) cc_final: 0.8165 (mt0) REVERT: D 1012 ARG cc_start: 0.8357 (ptm160) cc_final: 0.8094 (ttm-80) REVERT: C 56 LYS cc_start: 0.7549 (tttt) cc_final: 0.6984 (mmmt) REVERT: C 90 LYS cc_start: 0.8510 (tttp) cc_final: 0.7981 (mtpt) REVERT: G 95 LYS cc_start: 0.8636 (mppt) cc_final: 0.8071 (ttpt) outliers start: 33 outliers final: 27 residues processed: 173 average time/residue: 0.1091 time to fit residues: 28.1504 Evaluate side-chains 179 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 450 TRP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 31 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128049 restraints weight = 15663.020| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.43 r_work: 0.3276 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 13307 Z= 0.143 Angle : 0.550 11.469 18098 Z= 0.281 Chirality : 0.043 0.206 1933 Planarity : 0.004 0.045 2309 Dihedral : 5.629 82.179 1983 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 2.36 % Allowed : 17.83 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.21), residues: 1625 helix: 2.09 (0.27), residues: 378 sheet: -1.78 (0.35), residues: 186 loop : -0.90 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1012 TYR 0.017 0.001 TYR 2 183 PHE 0.016 0.001 PHE D 842 TRP 0.120 0.002 TRP D1013 HIS 0.012 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00352 (13250) covalent geometry : angle 0.54593 (17977) SS BOND : bond 0.00266 ( 44) SS BOND : angle 0.99962 ( 88) hydrogen bonds : bond 0.02902 ( 469) hydrogen bonds : angle 4.64130 ( 1386) Misc. bond : bond 0.07362 ( 2) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 0.83213 ( 6) link_NAG-ASN : bond 0.00164 ( 9) link_NAG-ASN : angle 1.08296 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8779 (m) cc_final: 0.8536 (t) REVERT: 2 202 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7228 (mtp85) REVERT: F 159 MET cc_start: 0.5052 (ppp) cc_final: 0.4081 (ppp) REVERT: F 187 ASN cc_start: 0.7734 (t0) cc_final: 0.7043 (t0) REVERT: D 200 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7793 (mp) REVERT: D 344 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: D 435 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7949 (t) REVERT: D 874 LYS cc_start: 0.8104 (mttm) cc_final: 0.7356 (pttp) REVERT: D 932 GLN cc_start: 0.8405 (mt0) cc_final: 0.8161 (mt0) REVERT: C 56 LYS cc_start: 0.7516 (tttt) cc_final: 0.6961 (mmmt) REVERT: C 90 LYS cc_start: 0.8522 (tttp) cc_final: 0.7991 (mtpt) REVERT: G 95 LYS cc_start: 0.8646 (mppt) cc_final: 0.8068 (ttpt) outliers start: 32 outliers final: 28 residues processed: 174 average time/residue: 0.1171 time to fit residues: 30.1506 Evaluate side-chains 178 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 128 THR Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 211 LYS Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 248 CYS Chi-restraints excluded: chain F residue 343 TRP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 SER Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 527 ILE Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 127 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.124269 restraints weight = 15607.165| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.50 r_work: 0.3248 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 13307 Z= 0.141 Angle : 0.541 9.231 18098 Z= 0.278 Chirality : 0.043 0.177 1933 Planarity : 0.004 0.049 2309 Dihedral : 5.611 81.803 1983 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 2.43 % Allowed : 17.54 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1625 helix: 2.13 (0.27), residues: 378 sheet: -1.74 (0.35), residues: 184 loop : -0.92 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1012 TYR 0.016 0.001 TYR 2 183 PHE 0.016 0.001 PHE D 842 TRP 0.127 0.002 TRP D1013 HIS 0.010 0.001 HIS F 240 Details of bonding type rmsd covalent geometry : bond 0.00347 (13250) covalent geometry : angle 0.53706 (17977) SS BOND : bond 0.00253 ( 44) SS BOND : angle 0.98471 ( 88) hydrogen bonds : bond 0.02858 ( 469) hydrogen bonds : angle 4.61685 ( 1386) Misc. bond : bond 0.07046 ( 2) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 0.81094 ( 6) link_NAG-ASN : bond 0.00166 ( 9) link_NAG-ASN : angle 1.06204 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4167.56 seconds wall clock time: 71 minutes 57.17 seconds (4317.17 seconds total)