Starting phenix.real_space_refine on Thu Jul 31 01:19:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmq_38486/07_2025/8xmq_38486_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmq_38486/07_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_38486/07_2025/8xmq_38486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2025/8xmq_38486.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2025/8xmq_38486_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmq_38486/07_2025/8xmq_38486_neut.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.80, per 1000 atoms: 0.68 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: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.07 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: 5.74 Time building geometry restraints manager: 4.27 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP D 992 HIS 0.010 0.001 HIS C 122 PHE 0.010 0.001 PHE G 71 TYR 0.008 0.001 TYR 2 221 ARG 0.002 0.000 ARG 2 252 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 9) link_NAG-ASN : angle 1.03377 ( 27) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 0.95521 ( 6) hydrogen bonds : bond 0.20196 ( 469) hydrogen bonds : angle 7.82158 ( 1386) SS BOND : bond 0.00243 ( 44) SS BOND : angle 1.05328 ( 88) covalent geometry : bond 0.00357 (13250) covalent geometry : angle 0.55838 (17977) Misc. bond : bond 0.06863 ( 2) *********************** 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 : 1.418 Fit side-chains 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: 0.7016 (mtp85) REVERT: 2 232 LYS cc_start: 0.8534 (tptt) cc_final: 0.8320 (ttpp) REVERT: 2 286 LYS cc_start: 0.8028 (ptmm) cc_final: 0.7814 (ttpp) REVERT: F 187 ASN cc_start: 0.7765 (t0) cc_final: 0.7506 (t0) REVERT: F 269 VAL cc_start: 0.7895 (p) cc_final: 0.7653 (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: 0.6282 (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: 0.7571 (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: 0.8280 (mtmt) REVERT: G 95 LYS cc_start: 0.8384 (mppt) cc_final: 0.8161 (ttpt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.2911 time to fit residues: 132.3858 Evaluate side-chains 185 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 139 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 539 GLN D 622 GLN D 651 HIS G 2 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141477 restraints weight = 15321.369| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.70 r_work: 0.3139 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 13307 Z= 0.232 Angle : 0.631 8.686 18098 Z= 0.323 Chirality : 0.046 0.183 1933 Planarity : 0.004 0.058 2309 Dihedral : 6.769 79.659 1989 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 2.36 % Allowed : 10.10 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1625 helix: 1.62 (0.27), residues: 376 sheet: -1.25 (0.35), residues: 194 loop : -0.97 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 847 HIS 0.011 0.001 HIS C 122 PHE 0.019 0.002 PHE D 842 TYR 0.018 0.002 TYR C 140 ARG 0.008 0.001 ARG D 562 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 9) link_NAG-ASN : angle 1.58875 ( 27) link_BETA1-4 : bond 0.00546 ( 2) link_BETA1-4 : angle 0.92169 ( 6) hydrogen bonds : bond 0.04036 ( 469) hydrogen bonds : angle 5.40092 ( 1386) SS BOND : bond 0.00387 ( 44) SS BOND : angle 1.30099 ( 88) covalent geometry : bond 0.00562 (13250) covalent geometry : angle 0.62304 (17977) Misc. bond : bond 0.09461 ( 2) *********************** 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 227 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.359 Fit side-chains REVERT: 2 198 SER cc_start: 0.8667 (m) cc_final: 0.8379 (t) REVERT: 2 202 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7425 (mtp85) REVERT: F 187 ASN cc_start: 0.8000 (t0) cc_final: 0.7391 (t0) REVERT: F 283 PHE cc_start: 0.7452 (t80) cc_final: 0.7157 (t80) REVERT: F 447 THR cc_start: 0.8575 (t) cc_final: 0.8297 (p) REVERT: F 847 TRP cc_start: 0.7072 (m100) cc_final: 0.6796 (m100) REVERT: D 399 ASP cc_start: 0.9002 (p0) cc_final: 0.8760 (p0) REVERT: D 874 LYS cc_start: 0.7940 (mttm) cc_final: 0.7432 (pttp) REVERT: D 960 LEU cc_start: 0.7948 (tp) cc_final: 0.7536 (tt) REVERT: D 994 ASN cc_start: 0.7460 (p0) cc_final: 0.6888 (p0) REVERT: D 1012 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8142 (mtp85) REVERT: C 50 HIS cc_start: 0.8747 (t70) cc_final: 0.8517 (t-90) REVERT: C 56 LYS cc_start: 0.7937 (tttt) cc_final: 0.7404 (mmmt) REVERT: C 90 LYS cc_start: 0.8240 (tttp) cc_final: 0.7944 (mtpt) REVERT: G 95 LYS cc_start: 0.8671 (mppt) cc_final: 0.8228 (ttpt) outliers start: 32 outliers final: 18 residues processed: 213 average time/residue: 0.2841 time to fit residues: 85.4138 Evaluate side-chains 183 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 204 MET 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 471 THR 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 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 115 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 272 GLN F 240 HIS F 327 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 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 = 0.3985 r_free = 0.3985 target = 0.175969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138745 restraints weight = 15488.653| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.89 r_work: 0.3098 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 13307 Z= 0.239 Angle : 0.610 8.258 18098 Z= 0.312 Chirality : 0.045 0.166 1933 Planarity : 0.004 0.041 2309 Dihedral : 6.288 84.924 1983 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 3.02 % Allowed : 12.60 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1625 helix: 1.47 (0.27), residues: 378 sheet: -1.78 (0.35), residues: 182 loop : -1.07 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1013 HIS 0.011 0.002 HIS F 240 PHE 0.020 0.002 PHE D 842 TYR 0.016 0.002 TYR D 465 ARG 0.004 0.001 ARG F 160 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 9) link_NAG-ASN : angle 1.59340 ( 27) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 0.78577 ( 6) hydrogen bonds : bond 0.03679 ( 469) hydrogen bonds : angle 5.17916 ( 1386) SS BOND : bond 0.00434 ( 44) SS BOND : angle 1.23850 ( 88) covalent geometry : bond 0.00582 (13250) covalent geometry : angle 0.60222 (17977) Misc. bond : bond 0.09989 ( 2) *********************** 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 209 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8726 (m) cc_final: 0.8515 (t) REVERT: 2 202 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7415 (mtp85) REVERT: F 159 MET cc_start: 0.5966 (ptm) cc_final: 0.5253 (ptm) REVERT: F 187 ASN cc_start: 0.7976 (t0) cc_final: 0.7258 (t0) REVERT: F 245 LYS cc_start: 0.8159 (tttt) cc_final: 0.7648 (ttpt) REVERT: F 283 PHE cc_start: 0.7674 (t80) cc_final: 0.7263 (t80) REVERT: F 400 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7483 (ttt180) REVERT: F 822 MET cc_start: 0.7460 (mtt) cc_final: 0.5739 (ttp) REVERT: F 847 TRP cc_start: 0.7393 (m100) cc_final: 0.7125 (m100) REVERT: D 543 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 874 LYS cc_start: 0.8014 (mttm) cc_final: 0.7376 (pttp) REVERT: D 960 LEU cc_start: 0.7924 (tp) cc_final: 0.7418 (tt) REVERT: D 1012 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8194 (mtp85) REVERT: C 56 LYS cc_start: 0.7890 (tttt) cc_final: 0.7387 (mmmt) REVERT: C 90 LYS cc_start: 0.8391 (tttp) cc_final: 0.8034 (mtpt) REVERT: G 95 LYS cc_start: 0.8656 (mppt) cc_final: 0.8242 (ttpt) outliers start: 41 outliers final: 26 residues processed: 196 average time/residue: 0.2557 time to fit residues: 72.3561 Evaluate side-chains 170 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 369 SER 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 162 THR Chi-restraints excluded: chain D residue 218 SER 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 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 F 338 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141188 restraints weight = 15252.041| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.68 r_work: 0.3124 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2961 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= 0.141 Angle : 0.540 7.026 18098 Z= 0.277 Chirality : 0.043 0.158 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.941 89.742 1983 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.21 % Allowed : 15.48 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1625 helix: 1.75 (0.27), residues: 378 sheet: -1.59 (0.33), residues: 189 loop : -1.01 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 PHE 0.017 0.001 PHE D 842 TYR 0.019 0.001 TYR 2 183 ARG 0.002 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 9) link_NAG-ASN : angle 1.26954 ( 27) link_BETA1-4 : bond 0.00358 ( 2) link_BETA1-4 : angle 0.88847 ( 6) hydrogen bonds : bond 0.03071 ( 469) hydrogen bonds : angle 4.84170 ( 1386) SS BOND : bond 0.00485 ( 44) SS BOND : angle 0.96910 ( 88) covalent geometry : bond 0.00343 (13250) covalent geometry : angle 0.53537 (17977) Misc. bond : bond 0.07775 ( 2) *********************** 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 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.493 Fit side-chains REVERT: 2 198 SER cc_start: 0.8683 (m) cc_final: 0.8473 (t) REVERT: 2 202 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7431 (mtp85) REVERT: F 187 ASN cc_start: 0.7905 (t0) cc_final: 0.7167 (t0) REVERT: F 283 PHE cc_start: 0.7664 (t80) cc_final: 0.7136 (t80) REVERT: F 389 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7498 (mm-30) REVERT: F 822 MET cc_start: 0.7471 (mtt) cc_final: 0.5756 (ttp) REVERT: F 847 TRP cc_start: 0.7323 (m100) cc_final: 0.7092 (m100) REVERT: D 344 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: D 874 LYS cc_start: 0.7951 (mttm) cc_final: 0.7488 (pttp) REVERT: D 960 LEU cc_start: 0.7968 (tp) cc_final: 0.7415 (tt) REVERT: C 56 LYS cc_start: 0.7778 (tttt) cc_final: 0.7244 (mmmt) REVERT: G 95 LYS cc_start: 0.8640 (mppt) cc_final: 0.8242 (ttpt) outliers start: 30 outliers final: 23 residues processed: 180 average time/residue: 0.2534 time to fit residues: 67.5791 Evaluate side-chains 171 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 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 470 ILE Chi-restraints excluded: chain F residue 793 SER 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 456 GLN 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 D residue 893 VAL Chi-restraints excluded: chain G residue 50 THR 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 16 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 ** 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 = 0.4043 r_free = 0.4043 target = 0.178608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127221 restraints weight = 15715.000| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.17 r_work: 0.3268 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 13307 Z= 0.154 Angle : 0.548 10.004 18098 Z= 0.279 Chirality : 0.043 0.156 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.812 88.285 1983 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 2.65 % Allowed : 16.58 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1625 helix: 1.84 (0.27), residues: 377 sheet: -1.67 (0.35), residues: 179 loop : -0.98 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D1013 HIS 0.006 0.001 HIS C 122 PHE 0.017 0.001 PHE D 842 TYR 0.016 0.001 TYR 2 183 ARG 0.003 0.000 ARG D1011 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 9) link_NAG-ASN : angle 1.26378 ( 27) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 0.92044 ( 6) hydrogen bonds : bond 0.03027 ( 469) hydrogen bonds : angle 4.76640 ( 1386) SS BOND : bond 0.00313 ( 44) SS BOND : angle 1.01260 ( 88) covalent geometry : bond 0.00378 (13250) covalent geometry : angle 0.54306 (17977) Misc. bond : bond 0.07924 ( 2) *********************** 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 186 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.449 Fit side-chains REVERT: 2 198 SER cc_start: 0.8744 (m) cc_final: 0.8499 (t) REVERT: 2 202 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7178 (mtp85) REVERT: F 187 ASN cc_start: 0.7703 (t0) cc_final: 0.7368 (t0) REVERT: F 389 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7497 (mm-30) REVERT: F 822 MET cc_start: 0.7324 (mtt) cc_final: 0.5621 (ttp) REVERT: F 847 TRP cc_start: 0.7226 (m100) cc_final: 0.6844 (m100) REVERT: D 344 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: D 400 ARG cc_start: 0.7903 (ttm110) cc_final: 0.7550 (ttm110) REVERT: D 435 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7388 (m) REVERT: D 874 LYS cc_start: 0.8060 (mttm) cc_final: 0.7349 (pttp) REVERT: C 56 LYS cc_start: 0.7562 (tttt) cc_final: 0.6990 (mmmt) REVERT: G 95 LYS cc_start: 0.8636 (mppt) cc_final: 0.8086 (ttpt) outliers start: 36 outliers final: 26 residues processed: 170 average time/residue: 0.2450 time to fit residues: 61.4386 Evaluate side-chains 164 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 266 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 190 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 793 SER 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 537 ASN Chi-restraints excluded: chain D residue 664 VAL Chi-restraints excluded: chain D residue 893 VAL Chi-restraints excluded: chain G residue 50 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 152 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 99 optimal weight: 0.0270 chunk 154 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 272 GLN F 240 HIS F 338 HIS ** F 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124898 restraints weight = 15973.060| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.20 r_work: 0.3228 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 13307 Z= 0.198 Angle : 0.566 7.764 18098 Z= 0.291 Chirality : 0.044 0.169 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.832 84.073 1983 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 16.73 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.20), residues: 1625 helix: 1.68 (0.27), residues: 384 sheet: -1.78 (0.34), residues: 193 loop : -0.98 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D1013 HIS 0.010 0.001 HIS F 240 PHE 0.021 0.001 PHE F 283 TYR 0.015 0.002 TYR 2 183 ARG 0.004 0.000 ARG D1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 9) link_NAG-ASN : angle 1.28795 ( 27) link_BETA1-4 : bond 0.00364 ( 2) link_BETA1-4 : angle 0.76462 ( 6) hydrogen bonds : bond 0.03213 ( 469) hydrogen bonds : angle 4.83529 ( 1386) SS BOND : bond 0.00340 ( 44) SS BOND : angle 1.10790 ( 88) covalent geometry : bond 0.00482 (13250) covalent geometry : angle 0.56025 (17977) Misc. bond : bond 0.09377 ( 2) *********************** 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 197 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.598 Fit side-chains REVERT: 2 198 SER cc_start: 0.8795 (m) cc_final: 0.8540 (t) REVERT: 2 202 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7205 (mtp85) REVERT: F 187 ASN cc_start: 0.7797 (t0) cc_final: 0.7183 (t0) REVERT: F 245 LYS cc_start: 0.8136 (tttt) cc_final: 0.7758 (tmtt) REVERT: F 389 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7504 (mm-30) REVERT: F 822 MET cc_start: 0.7310 (mtt) cc_final: 0.5687 (ttp) REVERT: F 842 PHE cc_start: 0.6242 (t80) cc_final: 0.5742 (t80) REVERT: D 344 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: D 435 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.7966 (t) REVERT: D 874 LYS cc_start: 0.8048 (mttm) cc_final: 0.7273 (pttp) REVERT: D 1012 ARG cc_start: 0.8794 (ptm160) cc_final: 0.7419 (ptm160) REVERT: C 56 LYS cc_start: 0.7628 (tttt) cc_final: 0.7019 (mmmt) REVERT: C 90 LYS cc_start: 0.8554 (tttp) cc_final: 0.7954 (mtpt) REVERT: G 95 LYS cc_start: 0.8646 (mppt) cc_final: 0.8091 (ttpt) outliers start: 40 outliers final: 33 residues processed: 179 average time/residue: 0.2552 time to fit residues: 66.9223 Evaluate side-chains 182 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 240 HIS Chi-restraints excluded: chain F residue 248 CYS 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 471 THR 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 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 4 THR Chi-restraints excluded: chain G residue 50 THR 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 48 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 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** F 797 GLN D 932 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127244 restraints weight = 15794.529| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.21 r_work: 0.3258 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 13307 Z= 0.166 Angle : 0.560 10.104 18098 Z= 0.288 Chirality : 0.044 0.180 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.784 82.949 1983 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.95 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1625 helix: 1.87 (0.27), residues: 378 sheet: -1.74 (0.35), residues: 186 loop : -0.99 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP D1013 HIS 0.025 0.001 HIS F 240 PHE 0.016 0.001 PHE D 842 TYR 0.013 0.001 TYR 2 183 ARG 0.005 0.000 ARG D1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 9) link_NAG-ASN : angle 1.25997 ( 27) link_BETA1-4 : bond 0.00295 ( 2) link_BETA1-4 : angle 0.76125 ( 6) hydrogen bonds : bond 0.03037 ( 469) hydrogen bonds : angle 4.76176 ( 1386) SS BOND : bond 0.00353 ( 44) SS BOND : angle 1.41814 ( 88) covalent geometry : bond 0.00407 (13250) covalent geometry : angle 0.55106 (17977) Misc. bond : bond 0.08580 ( 2) *********************** 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 186 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8762 (m) cc_final: 0.8503 (t) REVERT: 2 202 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7200 (mtp85) REVERT: F 187 ASN cc_start: 0.7737 (t0) cc_final: 0.7093 (t0) REVERT: F 245 LYS cc_start: 0.8162 (tttt) cc_final: 0.7752 (tmtt) REVERT: F 796 TRP cc_start: 0.6274 (p90) cc_final: 0.5938 (p-90) REVERT: F 822 MET cc_start: 0.7279 (mtt) cc_final: 0.5681 (ttp) REVERT: F 842 PHE cc_start: 0.6104 (t80) cc_final: 0.5844 (t80) REVERT: D 200 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7805 (mp) REVERT: D 344 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: D 435 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.7385 (p) REVERT: D 874 LYS cc_start: 0.8057 (mttm) cc_final: 0.7303 (pttp) REVERT: C 56 LYS cc_start: 0.7533 (tttt) cc_final: 0.6942 (mmmt) REVERT: C 90 LYS cc_start: 0.8534 (tttp) cc_final: 0.7912 (mtpt) REVERT: G 95 LYS cc_start: 0.8626 (mppt) cc_final: 0.8058 (ttpt) outliers start: 40 outliers final: 31 residues processed: 170 average time/residue: 0.2594 time to fit residues: 65.1069 Evaluate side-chains 174 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 324 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 226 LEU Chi-restraints excluded: chain F residue 248 CYS 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 471 THR 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 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 50 THR 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 137 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 157 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.0570 chunk 136 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.178974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127963 restraints weight = 15764.288| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.20 r_work: 0.3284 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 13307 Z= 0.129 Angle : 0.524 6.927 18098 Z= 0.270 Chirality : 0.043 0.153 1933 Planarity : 0.004 0.043 2309 Dihedral : 5.591 81.741 1983 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 2.80 % Allowed : 17.98 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1625 helix: 2.11 (0.27), residues: 377 sheet: -1.71 (0.35), residues: 186 loop : -0.92 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP D1013 HIS 0.013 0.001 HIS F 240 PHE 0.015 0.001 PHE D 842 TYR 0.013 0.001 TYR 2 183 ARG 0.005 0.000 ARG D 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 9) link_NAG-ASN : angle 1.11645 ( 27) link_BETA1-4 : bond 0.00338 ( 2) link_BETA1-4 : angle 0.85970 ( 6) hydrogen bonds : bond 0.02890 ( 469) hydrogen bonds : angle 4.64073 ( 1386) SS BOND : bond 0.00246 ( 44) SS BOND : angle 1.01074 ( 88) covalent geometry : bond 0.00318 (13250) covalent geometry : angle 0.51882 (17977) Misc. bond : bond 0.06828 ( 2) *********************** 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 192 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: 2 198 SER cc_start: 0.8760 (m) cc_final: 0.8525 (t) REVERT: 2 202 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7254 (mtp85) REVERT: F 245 LYS cc_start: 0.8161 (tttt) cc_final: 0.7771 (tmtt) REVERT: F 450 TRP cc_start: 0.8807 (OUTLIER) cc_final: 0.7936 (m100) REVERT: F 796 TRP cc_start: 0.6322 (p90) cc_final: 0.5928 (p-90) REVERT: F 822 MET cc_start: 0.7213 (mtt) cc_final: 0.5682 (ttp) REVERT: D 200 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7875 (mp) REVERT: D 344 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: D 874 LYS cc_start: 0.8076 (mttm) cc_final: 0.7396 (pttp) REVERT: C 56 LYS cc_start: 0.7411 (tttt) cc_final: 0.6791 (mmmt) REVERT: C 90 LYS cc_start: 0.8548 (tttp) cc_final: 0.7993 (mtpt) REVERT: G 95 LYS cc_start: 0.8633 (mppt) cc_final: 0.8082 (ttpt) outliers start: 38 outliers final: 31 residues processed: 177 average time/residue: 0.2630 time to fit residues: 68.8174 Evaluate side-chains 176 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain 2 residue 163 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 324 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 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 450 TRP Chi-restraints excluded: chain F residue 470 ILE Chi-restraints excluded: chain F residue 471 THR Chi-restraints excluded: chain F residue 793 SER 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 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 1020 HIS Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 50 THR 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 144 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 160 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130159 restraints weight = 15681.724| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.18 r_work: 0.3290 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 13307 Z= 0.120 Angle : 0.524 11.181 18098 Z= 0.266 Chirality : 0.042 0.165 1933 Planarity : 0.003 0.043 2309 Dihedral : 5.525 81.886 1983 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.95 % Allowed : 17.46 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1625 helix: 2.21 (0.27), residues: 378 sheet: -1.67 (0.35), residues: 186 loop : -0.87 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D1013 HIS 0.012 0.001 HIS F 240 PHE 0.015 0.001 PHE D 842 TYR 0.012 0.001 TYR 2 183 ARG 0.005 0.000 ARG D 400 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 9) link_NAG-ASN : angle 1.06297 ( 27) link_BETA1-4 : bond 0.00386 ( 2) link_BETA1-4 : angle 0.91233 ( 6) hydrogen bonds : bond 0.02798 ( 469) hydrogen bonds : angle 4.56921 ( 1386) SS BOND : bond 0.00260 ( 44) SS BOND : angle 0.95835 ( 88) covalent geometry : bond 0.00296 (13250) covalent geometry : angle 0.51930 (17977) Misc. bond : bond 0.06452 ( 2) *********************** 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 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.528 Fit side-chains REVERT: 2 198 SER cc_start: 0.8743 (m) cc_final: 0.8496 (t) REVERT: 2 202 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7194 (mtp85) REVERT: F 179 ARG cc_start: 0.6105 (tpt170) cc_final: 0.5855 (tpt90) REVERT: F 187 ASN cc_start: 0.7686 (t0) cc_final: 0.7274 (t0) REVERT: F 245 LYS cc_start: 0.8145 (tttt) cc_final: 0.7755 (tmtt) REVERT: F 796 TRP cc_start: 0.6323 (p90) cc_final: 0.5906 (p-90) REVERT: F 822 MET cc_start: 0.7255 (mtt) cc_final: 0.5732 (ttp) REVERT: D 200 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7870 (mp) REVERT: D 298 TYR cc_start: 0.8788 (m-80) cc_final: 0.8269 (m-80) REVERT: D 344 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: D 435 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7293 (p) REVERT: D 874 LYS cc_start: 0.8089 (mttm) cc_final: 0.7453 (pttp) REVERT: D 1012 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.7933 (ptm-80) REVERT: C 56 LYS cc_start: 0.7371 (tttt) cc_final: 0.6798 (mmmt) REVERT: C 90 LYS cc_start: 0.8575 (tttp) cc_final: 0.8009 (mtpt) REVERT: G 95 LYS cc_start: 0.8634 (mppt) cc_final: 0.8057 (ttpt) outliers start: 40 outliers final: 33 residues processed: 176 average time/residue: 0.2694 time to fit residues: 69.5253 Evaluate side-chains 182 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 113 SER 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 324 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 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 F residue 471 THR Chi-restraints excluded: chain F residue 808 CYS 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 D residue 1020 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.0570 chunk 16 optimal weight: 0.0870 chunk 112 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.179373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127481 restraints weight = 15692.083| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.25 r_work: 0.3258 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 13307 Z= 0.154 Angle : 0.553 11.652 18098 Z= 0.280 Chirality : 0.043 0.171 1933 Planarity : 0.004 0.042 2309 Dihedral : 5.607 82.421 1983 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 2.87 % Allowed : 18.13 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1625 helix: 2.14 (0.27), residues: 378 sheet: -1.66 (0.35), residues: 184 loop : -0.92 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.002 TRP D1013 HIS 0.013 0.001 HIS F 240 PHE 0.015 0.001 PHE D 842 TYR 0.013 0.001 TYR 2 183 ARG 0.005 0.000 ARG D1012 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 9) link_NAG-ASN : angle 1.08204 ( 27) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 0.77277 ( 6) hydrogen bonds : bond 0.02953 ( 469) hydrogen bonds : angle 4.65553 ( 1386) SS BOND : bond 0.00270 ( 44) SS BOND : angle 1.00645 ( 88) covalent geometry : bond 0.00379 (13250) covalent geometry : angle 0.54856 (17977) Misc. bond : bond 0.07923 ( 2) ********************** 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 185 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.523 Fit side-chains REVERT: 2 198 SER cc_start: 0.8746 (m) cc_final: 0.8512 (t) REVERT: 2 202 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7270 (mtp85) REVERT: F 187 ASN cc_start: 0.7767 (t0) cc_final: 0.7356 (t0) REVERT: F 450 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.8183 (m100) REVERT: F 796 TRP cc_start: 0.6500 (p90) cc_final: 0.6062 (p-90) REVERT: F 822 MET cc_start: 0.7347 (mtt) cc_final: 0.5866 (ttp) REVERT: D 200 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7882 (mp) REVERT: D 344 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: D 435 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.7937 (t) REVERT: D 874 LYS cc_start: 0.8133 (mttm) cc_final: 0.7542 (pttp) REVERT: D 932 GLN cc_start: 0.8297 (mt0) cc_final: 0.7900 (mt0) REVERT: C 56 LYS cc_start: 0.7555 (tttt) cc_final: 0.7014 (mmmt) REVERT: C 90 LYS cc_start: 0.8559 (tttp) cc_final: 0.8027 (mtpt) REVERT: G 95 LYS cc_start: 0.8644 (mppt) cc_final: 0.8081 (ttpt) outliers start: 39 outliers final: 34 residues processed: 169 average time/residue: 0.2917 time to fit residues: 72.1424 Evaluate side-chains 176 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 113 SER 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 324 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 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 F residue 471 THR Chi-restraints excluded: chain F residue 808 CYS 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 D residue 1020 HIS Chi-restraints excluded: chain C residue 55 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 Chi-restraints excluded: chain G residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 35 optimal weight: 7.9990 overall best weight: 0.4122 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.179789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130276 restraints weight = 15779.523| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.18 r_work: 0.3306 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 13307 Z= 0.120 Angle : 0.523 10.607 18098 Z= 0.266 Chirality : 0.042 0.164 1933 Planarity : 0.003 0.043 2309 Dihedral : 5.498 81.249 1983 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 3.02 % Allowed : 17.76 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.21), residues: 1625 helix: 2.32 (0.27), residues: 377 sheet: -1.57 (0.36), residues: 172 loop : -0.87 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.002 TRP D1013 HIS 0.012 0.001 HIS F 240 PHE 0.015 0.001 PHE D 842 TYR 0.012 0.001 TYR 2 183 ARG 0.004 0.000 ARG D1011 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.00621 ( 27) link_BETA1-4 : bond 0.00315 ( 2) link_BETA1-4 : angle 0.86484 ( 6) hydrogen bonds : bond 0.02750 ( 469) hydrogen bonds : angle 4.53918 ( 1386) SS BOND : bond 0.00217 ( 44) SS BOND : angle 0.88583 ( 88) covalent geometry : bond 0.00296 (13250) covalent geometry : angle 0.51933 (17977) Misc. bond : bond 0.05877 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8950.98 seconds wall clock time: 155 minutes 16.43 seconds (9316.43 seconds total)