Starting phenix.real_space_refine on Fri Jul 3 16:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/07_2026/9fmu_50570.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.088 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 3 9.91 5 Fe 2 7.16 5 S 131 5.16 5 C 9192 2.51 5 N 2618 2.21 5 O 2817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14763 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1982 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 5585 Classifications: {'peptide': 738} Link IDs: {'PTRANS': 23, 'TRANS': 714} Chain breaks: 1 Chain: "E" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 4845 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 19, 'TRANS': 620} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" 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: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.67, per 1000 atoms: 0.18 Number of scatterers: 14763 At special positions: 0 Unit cell: (92.22, 137.8, 161.12, 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 3 19.99 S 131 16.00 O 2817 8.00 N 2618 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 266 " distance=2.05 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 351 " - pdb=" SG CYS C 381 " distance=2.05 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=2.04 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=2.04 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=2.04 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=2.05 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS D 516 " - pdb=" SG CYS D 577 " distance=2.04 Simple disulfide: pdb=" SG CYS D 547 " - pdb=" SG CYS D 557 " distance=2.06 Simple disulfide: pdb=" SG CYS D 592 " - pdb=" SG CYS D 626 " distance=2.02 Simple disulfide: pdb=" SG CYS D 608 " - pdb=" SG CYS D 672 " distance=2.03 Simple disulfide: pdb=" SG CYS D 621 " - pdb=" SG CYS D 682 " 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=2.02 Simple disulfide: pdb=" SG CYS D 895 " - pdb=" SG CYS D 905 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS D 967 " - pdb=" SG CYS D1028 " distance=2.04 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1008 " distance=2.03 Simple disulfide: pdb=" SG CYS E 275 " - pdb=" SG CYS E 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 355 " distance=2.04 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 365 " distance=2.03 Simple disulfide: pdb=" SG CYS E 335 " - pdb=" SG CYS E 345 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS E 398 " - pdb=" SG CYS E 462 " distance=2.02 Simple disulfide: pdb=" SG CYS E 411 " - pdb=" SG CYS E 472 " distance=2.03 Simple disulfide: pdb=" SG CYS E 442 " - pdb=" SG CYS E 452 " distance=2.04 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 567 " distance=2.03 Simple disulfide: pdb=" SG CYS E 516 " - pdb=" SG CYS E 577 " distance=2.02 Simple disulfide: pdb=" SG CYS E 547 " - pdb=" SG CYS E 557 " distance=2.05 Simple disulfide: pdb=" SG CYS E 592 " - pdb=" SG CYS E 626 " distance=2.03 Simple disulfide: pdb=" SG CYS E 608 " - pdb=" SG CYS E 672 " distance=2.03 Simple disulfide: pdb=" SG CYS E 621 " - pdb=" SG CYS E 682 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 662 " distance=2.03 Simple disulfide: pdb=" SG CYS E 728 " - pdb=" SG CYS E 762 " distance=2.03 Simple disulfide: pdb=" SG CYS E 744 " - pdb=" SG CYS E 808 " distance=2.03 Simple disulfide: pdb=" SG CYS E 757 " - pdb=" SG CYS E 818 " distance=2.04 Simple disulfide: pdb=" SG CYS E 788 " - pdb=" SG CYS E 798 " distance=2.03 Simple disulfide: pdb=" SG CYS E 835 " - pdb=" SG CYS E 869 " distance=2.03 Simple disulfide: pdb=" SG CYS E 864 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E 895 " - pdb=" SG CYS E 905 " distance=2.05 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=5, symmetry=0 Links applied NAG-ASN " NAG C1001 " - " ASN C 184 " " NAG C1002 " - " ASN C 241 " " NAG D2003 " - " ASN D 320 " " NAG D2004 " - " ASN D1027 " " NAG E1102 " - " ASN E 767 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 548.7 milliseconds 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3428 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 33 sheets defined 29.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.517A pdb=" N LYS A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.180A pdb=" N ALA A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.955A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.739A pdb=" N PHE B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.800A pdb=" N LYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 removed outlier: 4.188A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.829A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 305 through 314 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 210 through 215 removed outlier: 4.370A pdb=" N PHE D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.521A pdb=" N ASP D 253 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 504 through 507 removed outlier: 4.120A 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 624 Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'D' and resid 856 through 867 Processing helix chain 'D' and resid 901 through 905 Processing helix chain 'D' and resid 959 through 970 Processing helix chain 'D' and resid 1004 through 1008 Processing helix chain 'D' and resid 1019 through 1023 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 341 through 345 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.884A pdb=" N ASP E 360 " --> pdb=" O HIS E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.917A pdb=" N PHE E 507 " --> pdb=" O ASP E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 519 Processing helix chain 'E' and resid 553 through 557 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 613 through 624 Processing helix chain 'E' and resid 658 through 662 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 794 through 798 Processing helix chain 'E' and resid 809 through 813 Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 901 through 905 Processing helix chain 'E' and resid 916 through 920 Processing sheet with id=AA1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AA2, first strand: chain 'C' and resid 297 through 302 removed outlier: 8.320A pdb=" N VAL C 278 " --> pdb=" O HIS C 362 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS C 362 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C 282 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA C 358 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 373 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 361 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA C 371 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP C 363 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP C 369 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL C 388 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 157 through 166 removed outlier: 4.701A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 157 through 166 removed outlier: 4.701A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 269 Processing sheet with id=AA6, first strand: chain 'D' and resid 264 through 269 removed outlier: 6.755A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TRP D 329 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N THR D 289 " --> pdb=" O TRP D 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.922A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.922A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 476 through 482 Processing sheet with id=AB1, first strand: chain 'D' and resid 476 through 482 removed outlier: 6.793A pdb=" N VAL D 491 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE D 502 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 498 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TRP D 541 " --> pdb=" O TRP D 499 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N SER D 501 " --> pdb=" O TRP D 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AB3, first strand: chain 'D' and resid 583 through 586 Processing sheet with id=AB4, first strand: chain 'D' and resid 583 through 586 removed outlier: 6.108A pdb=" N VAL D 596 " --> pdb=" O LEU D 607 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP D 646 " --> pdb=" O TRP D 604 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N SER D 606 " --> pdb=" O TRP D 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AB6, first strand: chain 'D' and resid 823 through 827 Processing sheet with id=AB7, first strand: chain 'D' and resid 823 through 827 removed outlier: 4.501A pdb=" N TRP D 922 " --> pdb=" O ASN D 876 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 887 through 888 Processing sheet with id=AB9, first strand: chain 'D' and resid 929 through 932 Processing sheet with id=AC1, first strand: chain 'D' and resid 929 through 932 removed outlier: 6.664A pdb=" N VAL D 942 " --> pdb=" O VAL D 953 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 953 " --> pdb=" O VAL D 942 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N TRP D 950 " --> pdb=" O ILE D 991 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N LEU D 993 " --> pdb=" O TRP D 950 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 952 " --> pdb=" O LEU D 993 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 264 through 269 Processing sheet with id=AC3, first strand: chain 'E' and resid 264 through 269 Processing sheet with id=AC4, first strand: chain 'E' and resid 372 through 380 removed outlier: 5.065A pdb=" N ALA E 383 " --> pdb=" O GLY E 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 372 through 380 removed outlier: 5.065A pdb=" N ALA E 383 " --> pdb=" O GLY E 378 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL E 386 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LEU E 437 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS E 396 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 476 through 482 removed outlier: 6.673A pdb=" N GLY E 574 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE E 527 " --> pdb=" O GLY E 574 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 576 " --> pdb=" O VAL E 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 476 through 482 removed outlier: 3.624A pdb=" N THR E 498 " --> pdb=" O HIS E 495 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN E 539 " --> pdb=" O TRP E 499 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 543 through 545 Processing sheet with id=AC9, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.655A pdb=" N ILE E 681 " --> pdb=" O LEU E 630 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 583 through 586 removed outlier: 6.388A pdb=" N VAL E 596 " --> pdb=" O LEU E 607 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TRP E 646 " --> pdb=" O TRP E 604 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER E 606 " --> pdb=" O TRP E 646 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 649 through 650 Processing sheet with id=AD3, first strand: chain 'E' and resid 719 through 726 removed outlier: 4.829A pdb=" N ALA E 729 " --> pdb=" O GLY E 724 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 719 through 726 removed outlier: 4.829A pdb=" N ALA E 729 " --> pdb=" O GLY E 724 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL E 732 " --> pdb=" O ILE E 743 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE E 743 " --> pdb=" O VAL E 732 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N TRP E 782 " --> pdb=" O TRP E 740 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR E 742 " --> pdb=" O TRP E 782 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 823 through 827 removed outlier: 4.591A pdb=" N TRP E 922 " --> pdb=" O ASN E 876 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 823 through 827 removed outlier: 6.227A pdb=" N LEU E 839 " --> pdb=" O VAL E 850 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6026 1.39 - 1.56: 8929 1.56 - 1.73: 7 1.73 - 1.90: 148 1.90 - 2.07: 8 Bond restraints: 15118 Sorted by residual: bond pdb=" CB CYS D 577 " pdb=" SG CYS D 577 " ideal model delta sigma weight residual 1.808 1.701 0.107 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " ideal model delta sigma weight residual 1.808 1.714 0.094 3.30e-02 9.18e+02 8.07e+00 bond pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.81e+00 bond pdb=" CB CYS D 895 " pdb=" SG CYS D 895 " ideal model delta sigma weight residual 1.808 1.723 0.085 3.30e-02 9.18e+02 6.65e+00 bond pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.15e+00 ... (remaining 15113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 20295 4.22 - 8.45: 196 8.45 - 12.67: 27 12.67 - 16.89: 7 16.89 - 21.11: 3 Bond angle restraints: 20528 Sorted by residual: angle pdb=" CA CYS D 557 " pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " ideal model delta sigma weight residual 114.40 135.51 -21.11 2.30e+00 1.89e-01 8.43e+01 angle pdb=" CA CYS E 547 " pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 114.40 132.19 -17.79 2.30e+00 1.89e-01 5.98e+01 angle pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " pdb=" SG CYS D 547 " ideal model delta sigma weight residual 114.40 131.94 -17.54 2.30e+00 1.89e-01 5.81e+01 angle pdb=" CA CYS D 516 " pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 114.40 129.79 -15.39 2.30e+00 1.89e-01 4.48e+01 angle pdb=" C CYS D 547 " pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " ideal model delta sigma weight residual 109.54 120.92 -11.38 1.84e+00 2.95e-01 3.83e+01 ... (remaining 20523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8260 17.77 - 35.54: 581 35.54 - 53.30: 112 53.30 - 71.07: 32 71.07 - 88.84: 17 Dihedral angle restraints: 9002 sinusoidal: 3631 harmonic: 5371 Sorted by residual: dihedral pdb=" CB CYS D 835 " pdb=" SG CYS D 835 " pdb=" SG CYS D 869 " pdb=" CB CYS D 869 " ideal model delta sinusoidal sigma weight residual 93.00 169.99 -76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS D 335 " pdb=" SG CYS D 335 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 248 " pdb=" CB CYS D 248 " ideal model delta sinusoidal sigma weight residual 93.00 25.60 67.40 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 8999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2000 0.103 - 0.207: 177 0.207 - 0.310: 19 0.310 - 0.413: 7 0.413 - 0.516: 2 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA CYS D 547 " pdb=" N CYS D 547 " pdb=" C CYS D 547 " pdb=" CB CYS D 547 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA CYS E 547 " pdb=" N CYS E 547 " pdb=" C CYS E 547 " pdb=" CB CYS E 547 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2202 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 102 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ASN B 102 " 0.094 2.00e-02 2.50e+03 pdb=" O ASN B 102 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE B 103 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 40 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C ARG B 40 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG B 40 " 0.035 2.00e-02 2.50e+03 pdb=" N PHE B 41 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 25 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLY A 25 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY A 25 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 26 " 0.026 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 160 2.55 - 3.14: 12275 3.14 - 3.72: 23995 3.72 - 4.31: 32449 4.31 - 4.90: 51821 Nonbonded interactions: 120700 Sorted by model distance: nonbonded pdb=" OD2 ASP D 225 " pdb="CA CA D2001 " model vdw 1.959 3.250 nonbonded pdb=" OH TYR D 424 " pdb=" O GLU D 467 " model vdw 1.979 3.040 nonbonded pdb=" OG SER E 879 " pdb=" OD1 ASP E 881 " model vdw 1.993 3.040 nonbonded pdb=" O GLY D 294 " pdb="CA CA D2002 " model vdw 2.104 3.250 nonbonded pdb=" OD1 ASP C 349 " pdb=" N THR C 350 " model vdw 2.124 3.120 ... (remaining 120695 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.007 0.569 15181 Z= 0.240 Angle : 1.222 21.112 20649 Z= 0.670 Chirality : 0.065 0.516 2205 Planarity : 0.009 0.100 2656 Dihedral : 13.083 88.839 5415 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.31 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 1903 helix: -1.81 (0.20), residues: 415 sheet: -0.55 (0.32), residues: 237 loop : -0.47 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG D 198 TYR 0.038 0.003 TYR D 465 PHE 0.037 0.002 PHE E 438 TRP 0.039 0.003 TRP E 796 HIS 0.011 0.001 HIS C 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (15118) covalent geometry : angle 1.18243 / 0.65 (20528) SS BOND : bond 0.00922 / 0.60 ( 53) SS BOND : angle 4.29482 / 2.96 ( 106) hydrogen bonds : bond 0.13502 / 9.75 ( 577) hydrogen bonds : angle 8.99672 / 6.37 ( 1704) Misc. bond : bond 0.25616 / 18.23 ( 5) link_NAG-ASN : bond 0.05169 / 2.76 ( 5) link_NAG-ASN : angle 3.55535 / 1.82 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8523 (pt0) cc_final: 0.8121 (tm-30) REVERT: A 104 CYS cc_start: 0.9389 (m) cc_final: 0.8699 (p) REVERT: B 19 ASN cc_start: 0.8830 (m-40) cc_final: 0.8446 (t0) REVERT: B 47 ASP cc_start: 0.8030 (p0) cc_final: 0.7752 (m-30) REVERT: B 65 LYS cc_start: 0.9749 (pptt) cc_final: 0.9103 (mmpt) REVERT: C 175 TRP cc_start: 0.8692 (p90) cc_final: 0.7995 (p90) REVERT: C 191 LEU cc_start: 0.8436 (tp) cc_final: 0.8112 (mm) REVERT: C 230 LEU cc_start: 0.9394 (tp) cc_final: 0.9074 (tt) REVERT: C 263 MET cc_start: 0.8262 (tmm) cc_final: 0.8025 (tmm) REVERT: C 343 MET cc_start: 0.7348 (ppp) cc_final: 0.6937 (ppp) REVERT: C 378 ASP cc_start: 0.8509 (p0) cc_final: 0.8203 (p0) REVERT: D 330 LEU cc_start: 0.8635 (mm) cc_final: 0.8398 (mt) REVERT: D 339 GLU cc_start: 0.6642 (mp0) cc_final: 0.6414 (mp0) REVERT: D 884 MET cc_start: 0.0288 (ppp) cc_final: -0.0854 (tmm) REVERT: D 903 TRP cc_start: 0.8887 (m-90) cc_final: 0.8656 (m-90) REVERT: D 931 LEU cc_start: 0.7079 (mm) cc_final: 0.6843 (mm) REVERT: D 992 TRP cc_start: 0.8761 (m100) cc_final: 0.8539 (m100) REVERT: E 298 TYR cc_start: 0.8847 (m-10) cc_final: 0.8623 (m-80) REVERT: E 466 GLU cc_start: 0.4802 (mt-10) cc_final: 0.4411 (mm-30) REVERT: E 507 PHE cc_start: 0.8839 (t80) cc_final: 0.8562 (t80) REVERT: E 659 MET cc_start: 0.7215 (mpp) cc_final: 0.6927 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1106 time to fit residues: 33.7403 Evaluate side-chains 103 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 HIS ** D 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN D 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.068887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051003 restraints weight = 91978.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.052969 restraints weight = 50828.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.054299 restraints weight = 32990.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.055208 restraints weight = 23940.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.055829 restraints weight = 18896.258| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 15181 Z= 0.220 Angle : 0.753 10.659 20649 Z= 0.393 Chirality : 0.048 0.207 2205 Planarity : 0.005 0.064 2656 Dihedral : 6.748 82.662 2143 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.19 % Allowed : 5.60 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.19), residues: 1903 helix: 0.39 (0.25), residues: 415 sheet: -0.05 (0.31), residues: 263 loop : -0.32 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 865 TYR 0.017 0.002 TYR C 386 PHE 0.017 0.002 PHE E 821 TRP 0.031 0.002 TRP D 450 HIS 0.010 0.002 HIS E 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (15118) covalent geometry : angle 0.74487 / 0.39 (20528) SS BOND : bond 0.00637 / 0.39 ( 53) SS BOND : angle 1.57344 / 1.08 ( 106) hydrogen bonds : bond 0.04433 / 3.12 ( 577) hydrogen bonds : angle 6.10716 / 4.40 ( 1704) Misc. bond : bond 0.13917 / 7.70 ( 5) link_NAG-ASN : bond 0.00560 / 0.27 ( 5) link_NAG-ASN : angle 1.89224 / 1.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8526 (pt0) cc_final: 0.7731 (tm-30) REVERT: A 104 CYS cc_start: 0.9064 (m) cc_final: 0.8124 (t) REVERT: B 19 ASN cc_start: 0.9085 (m-40) cc_final: 0.8826 (t0) REVERT: B 39 GLN cc_start: 0.8223 (pp30) cc_final: 0.7985 (pp30) REVERT: B 65 LYS cc_start: 0.9749 (pptt) cc_final: 0.9039 (mmpt) REVERT: B 103 PHE cc_start: 0.9211 (m-10) cc_final: 0.8987 (m-80) REVERT: C 175 TRP cc_start: 0.8947 (p90) cc_final: 0.8525 (p90) REVERT: C 230 LEU cc_start: 0.9202 (tp) cc_final: 0.8805 (tt) REVERT: C 349 ASP cc_start: 0.8163 (t0) cc_final: 0.7860 (t0) REVERT: C 378 ASP cc_start: 0.8297 (p0) cc_final: 0.7890 (p0) REVERT: D 449 LEU cc_start: 0.9145 (pp) cc_final: 0.8656 (tp) REVERT: D 450 TRP cc_start: 0.8433 (m-90) cc_final: 0.8170 (m-10) REVERT: D 644 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: D 884 MET cc_start: 0.1668 (ppp) cc_final: -0.0192 (tmm) REVERT: D 931 LEU cc_start: 0.7619 (mm) cc_final: 0.7376 (mm) REVERT: E 507 PHE cc_start: 0.8684 (t80) cc_final: 0.8220 (t80) REVERT: E 556 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8475 (pp) REVERT: E 640 LYS cc_start: 0.8699 (pttt) cc_final: 0.8375 (tptp) REVERT: E 884 MET cc_start: 0.4445 (tmm) cc_final: 0.4195 (tmm) outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.1056 time to fit residues: 21.5752 Evaluate side-chains 89 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 97 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN A 103 HIS ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 HIS C 362 HIS ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 ASN D 213 ASN D 250 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN D 932 GLN E 648 HIS E 754 HIS ** E 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.065153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047210 restraints weight = 95299.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048977 restraints weight = 54396.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050171 restraints weight = 36128.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050997 restraints weight = 26642.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.051519 restraints weight = 21462.171| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.397 15181 Z= 0.312 Angle : 0.833 15.234 20649 Z= 0.435 Chirality : 0.050 0.219 2205 Planarity : 0.006 0.058 2656 Dihedral : 7.551 85.016 2143 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 1903 helix: 0.24 (0.25), residues: 398 sheet: -0.40 (0.32), residues: 234 loop : -0.68 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 171 TYR 0.028 0.003 TYR D 427 PHE 0.019 0.003 PHE E 821 TRP 0.024 0.003 TRP D 450 HIS 0.011 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.31 (15118) covalent geometry : angle 0.82286 / 0.43 (20528) SS BOND : bond 0.00730 / 0.46 ( 53) SS BOND : angle 1.58772 / 1.07 ( 106) hydrogen bonds : bond 0.04733 / 3.27 ( 577) hydrogen bonds : angle 6.38491 / 4.57 ( 1704) Misc. bond : bond 0.18159 / 8.87 ( 5) link_NAG-ASN : bond 0.01076 / 0.41 ( 5) link_NAG-ASN : angle 3.23884 / 1.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8344 (pt0) cc_final: 0.7485 (tm-30) REVERT: A 104 CYS cc_start: 0.9053 (m) cc_final: 0.8174 (t) REVERT: B 19 ASN cc_start: 0.9246 (m-40) cc_final: 0.8839 (t0) REVERT: C 349 ASP cc_start: 0.7794 (t0) cc_final: 0.7353 (t0) REVERT: D 659 MET cc_start: 0.8611 (tpp) cc_final: 0.8313 (tpt) REVERT: D 884 MET cc_start: 0.1986 (ppp) cc_final: 0.0047 (tmm) REVERT: E 507 PHE cc_start: 0.8439 (t80) cc_final: 0.8072 (t80) REVERT: E 640 LYS cc_start: 0.8683 (pttt) cc_final: 0.8356 (tptp) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0993 time to fit residues: 15.8402 Evaluate side-chains 65 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 179 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** E 539 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 = 0.3626 r_free = 0.3626 target = 0.067828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049987 restraints weight = 90388.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051937 restraints weight = 49801.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053250 restraints weight = 32389.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054143 restraints weight = 23618.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054732 restraints weight = 18722.258| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 15181 Z= 0.132 Angle : 0.635 10.530 20649 Z= 0.328 Chirality : 0.045 0.182 2205 Planarity : 0.006 0.186 2656 Dihedral : 6.644 79.919 2143 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1903 helix: 0.81 (0.25), residues: 411 sheet: -0.29 (0.32), residues: 232 loop : -0.54 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 865 TYR 0.008 0.001 TYR D 427 PHE 0.017 0.001 PHE A 36 TRP 0.028 0.001 TRP D 992 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15118) covalent geometry : angle 0.62987 / 0.33 (20528) SS BOND : bond 0.00319 / 0.21 ( 53) SS BOND : angle 1.12092 / 0.80 ( 106) hydrogen bonds : bond 0.03658 / 2.61 ( 577) hydrogen bonds : angle 5.61040 / 4.01 ( 1704) Misc. bond : bond 0.08671 / 4.27 ( 5) link_NAG-ASN : bond 0.00408 / 0.17 ( 5) link_NAG-ASN : angle 1.57313 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8460 (pt0) cc_final: 0.7936 (tm-30) REVERT: A 104 CYS cc_start: 0.9112 (m) cc_final: 0.8095 (t) REVERT: B 19 ASN cc_start: 0.9280 (m-40) cc_final: 0.8904 (t0) REVERT: B 141 LEU cc_start: 0.9174 (tp) cc_final: 0.8935 (tp) REVERT: C 179 MET cc_start: 0.8933 (ttm) cc_final: 0.8395 (tmm) REVERT: C 349 ASP cc_start: 0.7728 (t0) cc_final: 0.7300 (t0) REVERT: C 370 TYR cc_start: 0.7198 (m-80) cc_final: 0.6991 (m-10) REVERT: D 659 MET cc_start: 0.8644 (tpp) cc_final: 0.8352 (tpt) REVERT: D 884 MET cc_start: 0.2221 (ppp) cc_final: 0.1684 (tmm) REVERT: E 507 PHE cc_start: 0.8404 (t80) cc_final: 0.8061 (t80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1130 time to fit residues: 20.3843 Evaluate side-chains 77 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 94 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 187 optimal weight: 0.0020 chunk 138 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.067996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.050129 restraints weight = 90779.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.052121 restraints weight = 50142.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053478 restraints weight = 32609.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054395 restraints weight = 23652.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.055050 restraints weight = 18626.148| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.167 15181 Z= 0.117 Angle : 0.605 9.049 20649 Z= 0.311 Chirality : 0.044 0.200 2205 Planarity : 0.005 0.118 2656 Dihedral : 6.362 79.575 2143 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1903 helix: 1.15 (0.26), residues: 412 sheet: -0.36 (0.31), residues: 237 loop : -0.51 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 865 TYR 0.013 0.001 TYR D 465 PHE 0.013 0.001 PHE A 36 TRP 0.035 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15118) covalent geometry : angle 0.60132 / 0.31 (20528) SS BOND : bond 0.00302 / 0.19 ( 53) SS BOND : angle 0.98657 / 0.69 ( 106) hydrogen bonds : bond 0.03371 / 2.41 ( 577) hydrogen bonds : angle 5.33833 / 3.82 ( 1704) Misc. bond : bond 0.07538 / 3.62 ( 5) link_NAG-ASN : bond 0.00397 / 0.18 ( 5) link_NAG-ASN : angle 1.51298 / 0.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8452 (pt0) cc_final: 0.7965 (tm-30) REVERT: A 104 CYS cc_start: 0.9110 (m) cc_final: 0.8044 (t) REVERT: B 7 GLU cc_start: 0.8773 (mp0) cc_final: 0.8353 (mp0) REVERT: B 19 ASN cc_start: 0.9238 (m-40) cc_final: 0.8896 (t0) REVERT: B 141 LEU cc_start: 0.9132 (tp) cc_final: 0.8859 (tp) REVERT: C 179 MET cc_start: 0.8892 (ttm) cc_final: 0.8456 (tmm) REVERT: C 203 ASN cc_start: 0.7693 (m110) cc_final: 0.7397 (m-40) REVERT: C 343 MET cc_start: 0.8056 (ppp) cc_final: 0.7766 (ppp) REVERT: C 349 ASP cc_start: 0.7871 (t0) cc_final: 0.7371 (t0) REVERT: C 370 TYR cc_start: 0.6937 (m-80) cc_final: 0.6668 (m-80) REVERT: D 659 MET cc_start: 0.8557 (tpp) cc_final: 0.8263 (tpt) REVERT: D 884 MET cc_start: 0.2161 (ppp) cc_final: 0.1566 (tmm) REVERT: E 507 PHE cc_start: 0.8404 (t80) cc_final: 0.7841 (t80) REVERT: E 786 MET cc_start: 0.8341 (pmm) cc_final: 0.7849 (pmm) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.0982 time to fit residues: 18.2153 Evaluate side-chains 76 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 40.0000 chunk 145 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 54 optimal weight: 0.0010 chunk 151 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 187 optimal weight: 0.0970 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.068594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050621 restraints weight = 89199.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.052646 restraints weight = 49351.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.054041 restraints weight = 32099.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054978 restraints weight = 23199.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055627 restraints weight = 18225.691| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 15181 Z= 0.112 Angle : 0.594 8.444 20649 Z= 0.303 Chirality : 0.043 0.187 2205 Planarity : 0.004 0.091 2656 Dihedral : 6.146 81.307 2143 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1903 helix: 1.35 (0.26), residues: 413 sheet: -0.43 (0.30), residues: 251 loop : -0.40 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 865 TYR 0.008 0.001 TYR D 354 PHE 0.010 0.001 PHE A 36 TRP 0.022 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (15118) covalent geometry : angle 0.59006 / 0.30 (20528) SS BOND : bond 0.00420 / 0.24 ( 53) SS BOND : angle 1.01199 / 0.68 ( 106) hydrogen bonds : bond 0.03187 / 2.27 ( 577) hydrogen bonds : angle 5.22468 / 3.71 ( 1704) Misc. bond : bond 0.06627 / 3.17 ( 5) link_NAG-ASN : bond 0.00342 / 0.16 ( 5) link_NAG-ASN : angle 1.38626 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8404 (pt0) cc_final: 0.7897 (tm-30) REVERT: A 104 CYS cc_start: 0.9096 (m) cc_final: 0.8036 (t) REVERT: B 19 ASN cc_start: 0.9247 (m-40) cc_final: 0.8917 (t0) REVERT: B 52 ASP cc_start: 0.8869 (m-30) cc_final: 0.8433 (p0) REVERT: B 106 LEU cc_start: 0.9279 (tt) cc_final: 0.8988 (pp) REVERT: B 141 LEU cc_start: 0.9092 (tp) cc_final: 0.8797 (tp) REVERT: C 175 TRP cc_start: 0.8535 (p90) cc_final: 0.8194 (p90) REVERT: C 179 MET cc_start: 0.8802 (ttm) cc_final: 0.8396 (tmm) REVERT: C 349 ASP cc_start: 0.7879 (t0) cc_final: 0.7426 (t0) REVERT: D 659 MET cc_start: 0.8632 (tpp) cc_final: 0.8291 (tpt) REVERT: D 884 MET cc_start: 0.2494 (ppp) cc_final: 0.2068 (tmm) REVERT: D 888 MET cc_start: 0.3394 (tpt) cc_final: 0.2666 (tpt) REVERT: E 507 PHE cc_start: 0.8476 (t80) cc_final: 0.8260 (t80) REVERT: E 786 MET cc_start: 0.8572 (pmm) cc_final: 0.8014 (pmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0902 time to fit residues: 17.1170 Evaluate side-chains 81 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 149 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.068559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050658 restraints weight = 90298.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.052631 restraints weight = 50042.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.054009 restraints weight = 32699.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054936 restraints weight = 23666.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.055570 restraints weight = 18620.189| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 15181 Z= 0.111 Angle : 0.586 8.254 20649 Z= 0.300 Chirality : 0.043 0.188 2205 Planarity : 0.005 0.189 2656 Dihedral : 6.074 82.658 2143 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1903 helix: 1.41 (0.26), residues: 412 sheet: -0.41 (0.30), residues: 239 loop : -0.40 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 865 TYR 0.012 0.001 TYR D 465 PHE 0.009 0.001 PHE A 36 TRP 0.017 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (15118) covalent geometry : angle 0.58172 / 0.30 (20528) SS BOND : bond 0.00250 / 0.16 ( 53) SS BOND : angle 1.05726 / 0.73 ( 106) hydrogen bonds : bond 0.03155 / 2.24 ( 577) hydrogen bonds : angle 5.12235 / 3.64 ( 1704) Misc. bond : bond 0.06607 / 3.16 ( 5) link_NAG-ASN : bond 0.00374 / 0.16 ( 5) link_NAG-ASN : angle 1.31712 / 0.74 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8424 (pt0) cc_final: 0.7892 (tm-30) REVERT: A 104 CYS cc_start: 0.9098 (m) cc_final: 0.8043 (t) REVERT: B 52 ASP cc_start: 0.8922 (m-30) cc_final: 0.8416 (p0) REVERT: B 141 LEU cc_start: 0.9113 (tp) cc_final: 0.8817 (tp) REVERT: C 175 TRP cc_start: 0.8555 (p90) cc_final: 0.8342 (p90) REVERT: C 179 MET cc_start: 0.8808 (ttm) cc_final: 0.8392 (tmm) REVERT: C 203 ASN cc_start: 0.7631 (m110) cc_final: 0.7243 (m-40) REVERT: C 349 ASP cc_start: 0.7905 (t0) cc_final: 0.7434 (t0) REVERT: D 659 MET cc_start: 0.8572 (tpp) cc_final: 0.8258 (tpt) REVERT: D 884 MET cc_start: 0.2192 (ppp) cc_final: 0.1531 (tmm) REVERT: E 786 MET cc_start: 0.8482 (pmm) cc_final: 0.7913 (pmm) REVERT: E 884 MET cc_start: 0.3782 (ppp) cc_final: 0.3503 (ppp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0875 time to fit residues: 16.6391 Evaluate side-chains 76 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 117 HIS ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN E 876 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.069404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051531 restraints weight = 89976.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.053534 restraints weight = 49841.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054915 restraints weight = 32441.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055794 restraints weight = 23466.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.056479 restraints weight = 18579.676| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 15181 Z= 0.101 Angle : 0.576 7.523 20649 Z= 0.294 Chirality : 0.043 0.176 2205 Planarity : 0.005 0.146 2656 Dihedral : 5.920 84.664 2143 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.19), residues: 1903 helix: 1.42 (0.26), residues: 412 sheet: -0.52 (0.30), residues: 231 loop : -0.37 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 865 TYR 0.009 0.001 TYR E 424 PHE 0.010 0.001 PHE D 507 TRP 0.016 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15118) covalent geometry : angle 0.57319 / 0.29 (20528) SS BOND : bond 0.00224 / 0.14 ( 53) SS BOND : angle 0.94143 / 0.66 ( 106) hydrogen bonds : bond 0.03069 / 2.18 ( 577) hydrogen bonds : angle 4.99519 / 3.54 ( 1704) Misc. bond : bond 0.04366 / 2.08 ( 5) link_NAG-ASN : bond 0.00374 / 0.17 ( 5) link_NAG-ASN : angle 1.16856 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8384 (pt0) cc_final: 0.7821 (tm-30) REVERT: A 104 CYS cc_start: 0.9099 (m) cc_final: 0.8029 (t) REVERT: B 52 ASP cc_start: 0.8931 (m-30) cc_final: 0.8424 (p0) REVERT: B 99 ASP cc_start: 0.8635 (t0) cc_final: 0.8236 (t0) REVERT: C 179 MET cc_start: 0.8812 (ttm) cc_final: 0.8499 (tmm) REVERT: C 203 ASN cc_start: 0.7598 (m110) cc_final: 0.7229 (m-40) REVERT: C 349 ASP cc_start: 0.7920 (t0) cc_final: 0.7482 (t0) REVERT: C 370 TYR cc_start: 0.7273 (m-10) cc_final: 0.7043 (m-80) REVERT: D 659 MET cc_start: 0.8670 (tpp) cc_final: 0.8319 (tpt) REVERT: D 822 MET cc_start: 0.7017 (tmm) cc_final: 0.6523 (tmm) REVERT: E 640 LYS cc_start: 0.8488 (pttt) cc_final: 0.8082 (tmtt) REVERT: E 786 MET cc_start: 0.8435 (pmm) cc_final: 0.7846 (pmm) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1064 time to fit residues: 21.0739 Evaluate side-chains 90 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 83 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 162 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 ASN ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS E 454 ASN E 539 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.069397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.051535 restraints weight = 90133.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.053499 restraints weight = 50027.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054851 restraints weight = 32646.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055774 restraints weight = 23730.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.056371 restraints weight = 18702.584| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 15181 Z= 0.102 Angle : 0.578 7.349 20649 Z= 0.294 Chirality : 0.043 0.169 2205 Planarity : 0.005 0.131 2656 Dihedral : 5.861 84.362 2143 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1903 helix: 1.41 (0.26), residues: 414 sheet: -0.57 (0.29), residues: 247 loop : -0.32 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 865 TYR 0.019 0.001 TYR B 145 PHE 0.010 0.001 PHE E 507 TRP 0.017 0.001 TRP D 450 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (15118) covalent geometry : angle 0.57413 / 0.29 (20528) SS BOND : bond 0.00228 / 0.14 ( 53) SS BOND : angle 0.98996 / 0.69 ( 106) hydrogen bonds : bond 0.02997 / 2.13 ( 577) hydrogen bonds : angle 4.93406 / 3.50 ( 1704) Misc. bond : bond 0.04563 / 2.18 ( 5) link_NAG-ASN : bond 0.00352 / 0.16 ( 5) link_NAG-ASN : angle 1.16303 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8388 (pt0) cc_final: 0.7886 (tm-30) REVERT: A 104 CYS cc_start: 0.9130 (m) cc_final: 0.8471 (p) REVERT: B 52 ASP cc_start: 0.8927 (m-30) cc_final: 0.8419 (p0) REVERT: B 99 ASP cc_start: 0.8712 (t0) cc_final: 0.8311 (t0) REVERT: B 103 PHE cc_start: 0.8696 (m-80) cc_final: 0.8364 (m-80) REVERT: B 106 LEU cc_start: 0.9245 (tt) cc_final: 0.8870 (pp) REVERT: C 179 MET cc_start: 0.8765 (ttm) cc_final: 0.8479 (tmm) REVERT: C 203 ASN cc_start: 0.7576 (m110) cc_final: 0.7234 (m-40) REVERT: C 349 ASP cc_start: 0.8059 (t0) cc_final: 0.6352 (t0) REVERT: C 370 TYR cc_start: 0.7233 (m-10) cc_final: 0.6992 (m-10) REVERT: D 659 MET cc_start: 0.8637 (tpp) cc_final: 0.8353 (tpt) REVERT: D 998 CYS cc_start: 0.5067 (m) cc_final: 0.4842 (m) REVERT: E 640 LYS cc_start: 0.8518 (pttt) cc_final: 0.8083 (tmtt) REVERT: E 786 MET cc_start: 0.8419 (pmm) cc_final: 0.7889 (pmm) REVERT: E 884 MET cc_start: 0.3659 (ppp) cc_final: 0.3300 (ppp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1006 time to fit residues: 20.2906 Evaluate side-chains 94 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 146 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 8 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN E 357 HIS E 391 GLN E 539 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.068048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050137 restraints weight = 90669.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052061 restraints weight = 50383.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.053390 restraints weight = 33022.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054297 restraints weight = 24137.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054929 restraints weight = 19101.883| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 15181 Z= 0.135 Angle : 0.602 9.737 20649 Z= 0.308 Chirality : 0.043 0.167 2205 Planarity : 0.005 0.135 2656 Dihedral : 6.043 84.218 2143 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.06 % Allowed : 0.51 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.19), residues: 1903 helix: 1.38 (0.26), residues: 412 sheet: -0.70 (0.29), residues: 252 loop : -0.39 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 865 TYR 0.011 0.001 TYR B 145 PHE 0.011 0.001 PHE E 821 TRP 0.022 0.001 TRP D 450 HIS 0.011 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (15118) covalent geometry : angle 0.59763 / 0.31 (20528) SS BOND : bond 0.00245 / 0.16 ( 53) SS BOND : angle 1.06107 / 0.72 ( 106) hydrogen bonds : bond 0.03097 / 2.18 ( 577) hydrogen bonds : angle 5.06220 / 3.60 ( 1704) Misc. bond : bond 0.08604 / 4.13 ( 5) link_NAG-ASN : bond 0.00279 / 0.12 ( 5) link_NAG-ASN : angle 1.41384 / 0.79 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8397 (pt0) cc_final: 0.7838 (tm-30) REVERT: A 104 CYS cc_start: 0.9098 (m) cc_final: 0.8088 (t) REVERT: B 52 ASP cc_start: 0.8914 (m-30) cc_final: 0.8423 (p0) REVERT: B 99 ASP cc_start: 0.8871 (t0) cc_final: 0.8506 (t0) REVERT: B 103 PHE cc_start: 0.8725 (m-80) cc_final: 0.8473 (m-80) REVERT: B 106 LEU cc_start: 0.9267 (tt) cc_final: 0.8914 (pp) REVERT: C 179 MET cc_start: 0.8730 (ttm) cc_final: 0.8273 (tmm) REVERT: C 187 THR cc_start: 0.8584 (m) cc_final: 0.8384 (p) REVERT: C 349 ASP cc_start: 0.8391 (t0) cc_final: 0.7876 (t70) REVERT: C 370 TYR cc_start: 0.7134 (m-10) cc_final: 0.6929 (m-80) REVERT: D 620 LEU cc_start: 0.9688 (tp) cc_final: 0.9449 (tt) REVERT: D 644 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7544 (pp30) REVERT: D 659 MET cc_start: 0.8603 (tpp) cc_final: 0.8304 (tpt) REVERT: D 888 MET cc_start: 0.4770 (tpt) cc_final: 0.4226 (tpt) REVERT: E 640 LYS cc_start: 0.8470 (pttt) cc_final: 0.8074 (tmtt) REVERT: E 786 MET cc_start: 0.8542 (pmm) cc_final: 0.8237 (pmm) REVERT: E 884 MET cc_start: 0.3510 (ppp) cc_final: 0.3187 (ppp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0976 time to fit residues: 17.8639 Evaluate side-chains 87 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 189 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.068586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050730 restraints weight = 89216.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052685 restraints weight = 49534.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.054020 restraints weight = 32400.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054938 restraints weight = 23664.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.055534 restraints weight = 18684.578| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 15181 Z= 0.112 Angle : 0.583 8.224 20649 Z= 0.296 Chirality : 0.043 0.164 2205 Planarity : 0.005 0.129 2656 Dihedral : 5.946 83.402 2143 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1903 helix: 1.44 (0.26), residues: 411 sheet: -0.71 (0.29), residues: 252 loop : -0.35 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 865 TYR 0.009 0.001 TYR B 145 PHE 0.008 0.001 PHE E 438 TRP 0.017 0.001 TRP D 903 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (15118) covalent geometry : angle 0.57995 / 0.30 (20528) SS BOND : bond 0.00216 / 0.13 ( 53) SS BOND : angle 0.96967 / 0.67 ( 106) hydrogen bonds : bond 0.03026 / 2.14 ( 577) hydrogen bonds : angle 4.96891 / 3.52 ( 1704) Misc. bond : bond 0.06585 / 3.15 ( 5) link_NAG-ASN : bond 0.00312 / 0.14 ( 5) link_NAG-ASN : angle 1.31494 / 0.73 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.82 seconds wall clock time: 43 minutes 18.66 seconds (2598.66 seconds total)