Starting phenix.real_space_refine on Sat Aug 23 22:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_50570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_50570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_50570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_50570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/08_2025/9fmu_50570.map" } 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-2.0-5787/lib/python3.9/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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.50, per 1000 atoms: 0.24 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: 1.02 Conformation dependent library (CDL) restraints added in 695.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 2.72 Time building geometry restraints manager: 1.50 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 2.510 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 2.510 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: 2.280 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.000 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 aren 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 covalent geometry : bond 0.00541 (15118) covalent geometry : angle 1.18243 (20528) SS BOND : bond 0.00922 ( 53) SS BOND : angle 4.29482 ( 106) hydrogen bonds : bond 0.13502 ( 577) hydrogen bonds : angle 8.99672 ( 1704) Misc. bond : bond 0.25616 ( 5) link_NAG-ASN : bond 0.05169 ( 5) link_NAG-ASN : angle 3.55535 ( 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 : 0.591 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: 0.7753 (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: 0.7997 (p90) REVERT: C 191 LEU cc_start: 0.8435 (tp) cc_final: 0.8111 (mm) REVERT: C 230 LEU cc_start: 0.9394 (tp) cc_final: 0.9075 (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: 0.6941 (ppp) REVERT: C 378 ASP cc_start: 0.8510 (p0) cc_final: 0.8204 (p0) REVERT: D 330 LEU cc_start: 0.8635 (mm) cc_final: 0.8399 (mt) REVERT: D 339 GLU cc_start: 0.6642 (mp0) cc_final: 0.6413 (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: 0.8840 (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: 0.1170 time to fit residues: 35.5006 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 : 0.544 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 986 GLN ** E 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.068981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051108 restraints weight = 92429.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053066 restraints weight = 51152.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054395 restraints weight = 33251.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055278 restraints weight = 24142.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055912 restraints weight = 19065.146| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 15181 Z= 0.228 Angle : 0.756 10.782 20649 Z= 0.395 Chirality : 0.048 0.205 2205 Planarity : 0.005 0.066 2656 Dihedral : 6.753 82.648 2143 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % 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 aren not related in a simple way. whole: -0.23 (0.19), residues: 1903 helix: 0.39 (0.25), residues: 415 sheet: -0.02 (0.31), residues: 268 loop : -0.32 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 865 TYR 0.018 0.002 TYR C 386 PHE 0.017 0.002 PHE E 821 TRP 0.031 0.002 TRP D 450 HIS 0.014 0.002 HIS E 611 Details of bonding type rmsd covalent geometry : bond 0.00491 (15118) covalent geometry : angle 0.74791 (20528) SS BOND : bond 0.00471 ( 53) SS BOND : angle 1.61818 ( 106) hydrogen bonds : bond 0.04451 ( 577) hydrogen bonds : angle 6.12579 ( 1704) Misc. bond : bond 0.13573 ( 5) link_NAG-ASN : bond 0.00405 ( 5) link_NAG-ASN : angle 1.88716 ( 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 127 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8533 (pt0) cc_final: 0.7734 (tm-30) REVERT: A 104 CYS cc_start: 0.9061 (m) cc_final: 0.8125 (t) REVERT: B 19 ASN cc_start: 0.9083 (m-40) cc_final: 0.8828 (t0) REVERT: B 39 GLN cc_start: 0.8263 (pp30) cc_final: 0.8033 (pp30) REVERT: B 65 LYS cc_start: 0.9745 (pptt) cc_final: 0.9033 (mmpt) REVERT: B 103 PHE cc_start: 0.9208 (m-10) cc_final: 0.8989 (m-80) REVERT: C 175 TRP cc_start: 0.8944 (p90) cc_final: 0.8523 (p90) REVERT: C 230 LEU cc_start: 0.9202 (tp) cc_final: 0.8807 (tt) REVERT: C 349 ASP cc_start: 0.8079 (t0) cc_final: 0.7778 (t0) REVERT: C 378 ASP cc_start: 0.8283 (p0) cc_final: 0.7858 (p0) REVERT: D 449 LEU cc_start: 0.9146 (pp) cc_final: 0.8650 (tp) REVERT: D 450 TRP cc_start: 0.8430 (m-90) cc_final: 0.8161 (m-10) REVERT: D 884 MET cc_start: 0.1661 (ppp) cc_final: -0.0183 (tmm) REVERT: D 931 LEU cc_start: 0.7602 (mm) cc_final: 0.7357 (mm) REVERT: E 507 PHE cc_start: 0.8689 (t80) cc_final: 0.8227 (t80) REVERT: E 556 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8461 (pp) REVERT: E 640 LYS cc_start: 0.8742 (pttt) cc_final: 0.8410 (tptp) REVERT: E 884 MET cc_start: 0.4431 (tmm) cc_final: 0.4178 (tmm) outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.0932 time to fit residues: 18.7656 Evaluate side-chains 87 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 6.9990 chunk 142 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 213 ASN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047154 restraints weight = 94741.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048961 restraints weight = 52901.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050186 restraints weight = 34757.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051023 restraints weight = 25553.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051592 restraints weight = 20371.133| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.398 15181 Z= 0.320 Angle : 0.846 15.212 20649 Z= 0.442 Chirality : 0.050 0.220 2205 Planarity : 0.006 0.058 2656 Dihedral : 7.618 86.477 2143 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.19 % Allowed : 7.32 % Favored : 92.49 % 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 aren not related in a simple way. whole: -0.67 (0.18), residues: 1903 helix: 0.17 (0.24), residues: 398 sheet: -0.19 (0.33), residues: 230 loop : -0.69 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 392 TYR 0.028 0.003 TYR D 427 PHE 0.018 0.003 PHE C 339 TRP 0.038 0.003 TRP E 295 HIS 0.009 0.002 HIS E 648 Details of bonding type rmsd covalent geometry : bond 0.00696 (15118) covalent geometry : angle 0.83651 (20528) SS BOND : bond 0.00530 ( 53) SS BOND : angle 1.58173 ( 106) hydrogen bonds : bond 0.04803 ( 577) hydrogen bonds : angle 6.43033 ( 1704) Misc. bond : bond 0.18454 ( 5) link_NAG-ASN : bond 0.00385 ( 5) link_NAG-ASN : angle 3.00715 ( 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 98 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8357 (pt0) cc_final: 0.7496 (tm-30) REVERT: A 104 CYS cc_start: 0.9046 (m) cc_final: 0.8198 (t) REVERT: B 19 ASN cc_start: 0.9248 (m-40) cc_final: 0.8836 (t0) REVERT: C 349 ASP cc_start: 0.7949 (t0) cc_final: 0.7539 (t0) REVERT: C 370 TYR cc_start: 0.7426 (m-80) cc_final: 0.7001 (m-80) REVERT: D 659 MET cc_start: 0.8663 (tpp) cc_final: 0.8376 (tpt) REVERT: D 884 MET cc_start: 0.2252 (ppp) cc_final: 0.0156 (tmm) REVERT: E 640 LYS cc_start: 0.8676 (pttt) cc_final: 0.8350 (tptp) outliers start: 3 outliers final: 0 residues processed: 98 average time/residue: 0.0954 time to fit residues: 15.3601 Evaluate side-chains 63 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.066937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049045 restraints weight = 91424.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050935 restraints weight = 50761.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.052218 restraints weight = 33263.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053078 restraints weight = 24350.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053681 restraints weight = 19429.309| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 15181 Z= 0.161 Angle : 0.656 12.136 20649 Z= 0.340 Chirality : 0.045 0.195 2205 Planarity : 0.004 0.066 2656 Dihedral : 6.852 80.586 2143 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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 aren not related in a simple way. whole: -0.47 (0.19), residues: 1903 helix: 0.65 (0.25), residues: 409 sheet: -0.46 (0.31), residues: 243 loop : -0.59 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 913 TYR 0.011 0.002 TYR D 427 PHE 0.013 0.002 PHE A 36 TRP 0.026 0.002 TRP D 992 HIS 0.007 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00368 (15118) covalent geometry : angle 0.65081 (20528) SS BOND : bond 0.00344 ( 53) SS BOND : angle 1.13834 ( 106) hydrogen bonds : bond 0.03778 ( 577) hydrogen bonds : angle 5.77180 ( 1704) Misc. bond : bond 0.11134 ( 5) link_NAG-ASN : bond 0.00350 ( 5) link_NAG-ASN : angle 1.73376 ( 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 108 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8415 (pt0) cc_final: 0.7884 (tm-30) REVERT: A 104 CYS cc_start: 0.9088 (m) cc_final: 0.8098 (t) REVERT: B 19 ASN cc_start: 0.9247 (m-40) cc_final: 0.8862 (t0) REVERT: B 141 LEU cc_start: 0.9197 (tp) cc_final: 0.8960 (tp) REVERT: C 191 LEU cc_start: 0.8515 (tp) cc_final: 0.7892 (mm) REVERT: C 349 ASP cc_start: 0.7691 (t0) cc_final: 0.7239 (t0) REVERT: D 342 ILE cc_start: 0.8946 (mp) cc_final: 0.8737 (tp) REVERT: D 659 MET cc_start: 0.8552 (tpp) cc_final: 0.8299 (tpt) REVERT: D 884 MET cc_start: 0.2189 (ppp) cc_final: 0.1579 (tmm) REVERT: D 995 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9237 (mm-30) REVERT: E 507 PHE cc_start: 0.8473 (t80) cc_final: 0.8240 (t80) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0984 time to fit residues: 17.1486 Evaluate side-chains 72 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 9.9990 chunk 176 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 187 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS B 39 GLN ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.067715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049833 restraints weight = 91017.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051790 restraints weight = 50447.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053123 restraints weight = 32900.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054050 restraints weight = 23882.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054603 restraints weight = 18855.548| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.189 15181 Z= 0.125 Angle : 0.614 9.844 20649 Z= 0.317 Chirality : 0.044 0.210 2205 Planarity : 0.005 0.175 2656 Dihedral : 6.523 80.830 2143 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 1903 helix: 0.99 (0.26), residues: 412 sheet: -0.42 (0.30), residues: 252 loop : -0.50 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 865 TYR 0.016 0.001 TYR D 465 PHE 0.012 0.001 PHE C 377 TRP 0.031 0.001 TRP D 958 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00289 (15118) covalent geometry : angle 0.60921 (20528) SS BOND : bond 0.00314 ( 53) SS BOND : angle 1.06353 ( 106) hydrogen bonds : bond 0.03443 ( 577) hydrogen bonds : angle 5.45630 ( 1704) Misc. bond : bond 0.08524 ( 5) link_NAG-ASN : bond 0.00348 ( 5) link_NAG-ASN : angle 1.56845 ( 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 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8460 (pt0) cc_final: 0.7898 (tm-30) REVERT: A 104 CYS cc_start: 0.9116 (m) cc_final: 0.8094 (t) REVERT: B 19 ASN cc_start: 0.9221 (m-40) cc_final: 0.8859 (t0) REVERT: B 52 ASP cc_start: 0.8865 (m-30) cc_final: 0.8439 (p0) REVERT: B 106 LEU cc_start: 0.9302 (tt) cc_final: 0.8907 (pp) REVERT: B 141 LEU cc_start: 0.9092 (tp) cc_final: 0.8828 (tp) REVERT: C 179 MET cc_start: 0.8906 (ttm) cc_final: 0.8393 (tmm) REVERT: C 191 LEU cc_start: 0.8437 (tp) cc_final: 0.7860 (mm) REVERT: C 203 ASN cc_start: 0.7703 (m110) cc_final: 0.7373 (m-40) REVERT: C 263 MET cc_start: 0.8860 (tmm) cc_final: 0.8634 (tmm) REVERT: C 343 MET cc_start: 0.8002 (ppp) cc_final: 0.7764 (ppp) REVERT: C 349 ASP cc_start: 0.7781 (t0) cc_final: 0.7297 (t0) REVERT: D 342 ILE cc_start: 0.8960 (mp) cc_final: 0.8746 (tp) REVERT: D 659 MET cc_start: 0.8683 (tpp) cc_final: 0.8403 (tpt) REVERT: D 884 MET cc_start: 0.2364 (ppp) cc_final: 0.1999 (tmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.0927 time to fit residues: 16.6139 Evaluate side-chains 75 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 30.0000 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 164 optimal weight: 0.1980 chunk 174 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 876 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.067573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049621 restraints weight = 90242.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051563 restraints weight = 50176.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052894 restraints weight = 32738.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.053801 restraints weight = 23827.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054436 restraints weight = 18861.067| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.205 15181 Z= 0.131 Angle : 0.608 10.292 20649 Z= 0.314 Chirality : 0.043 0.182 2205 Planarity : 0.005 0.137 2656 Dihedral : 6.383 80.387 2143 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.19), residues: 1903 helix: 1.17 (0.26), residues: 412 sheet: -0.50 (0.30), residues: 250 loop : -0.50 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 865 TYR 0.011 0.001 TYR C 389 PHE 0.010 0.001 PHE B 118 TRP 0.019 0.001 TRP D 958 HIS 0.007 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00305 (15118) covalent geometry : angle 0.60345 (20528) SS BOND : bond 0.00270 ( 53) SS BOND : angle 1.04721 ( 106) hydrogen bonds : bond 0.03325 ( 577) hydrogen bonds : angle 5.36290 ( 1704) Misc. bond : bond 0.09277 ( 5) link_NAG-ASN : bond 0.00381 ( 5) link_NAG-ASN : angle 1.65254 ( 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 100 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8474 (pt0) cc_final: 0.7906 (tm-30) REVERT: A 104 CYS cc_start: 0.9061 (m) cc_final: 0.8004 (t) REVERT: B 19 ASN cc_start: 0.9235 (m-40) cc_final: 0.8877 (t0) REVERT: B 52 ASP cc_start: 0.8936 (m-30) cc_final: 0.8457 (p0) REVERT: B 106 LEU cc_start: 0.9316 (tt) cc_final: 0.8938 (pp) REVERT: B 141 LEU cc_start: 0.9091 (tp) cc_final: 0.8790 (tp) REVERT: C 179 MET cc_start: 0.8864 (ttm) cc_final: 0.8383 (tmm) REVERT: C 203 ASN cc_start: 0.7548 (m110) cc_final: 0.7261 (m-40) REVERT: C 349 ASP cc_start: 0.7792 (t0) cc_final: 0.7404 (t0) REVERT: C 370 TYR cc_start: 0.7331 (m-80) cc_final: 0.6880 (m-10) REVERT: D 644 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: D 659 MET cc_start: 0.8517 (tpp) cc_final: 0.8240 (tpt) REVERT: D 884 MET cc_start: 0.2383 (ppp) cc_final: 0.2022 (tmm) REVERT: D 888 MET cc_start: 0.3990 (tpt) cc_final: 0.3279 (tpt) REVERT: E 786 MET cc_start: 0.8489 (pmm) cc_final: 0.7943 (pmm) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.0943 time to fit residues: 16.0783 Evaluate side-chains 75 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 124 optimal weight: 0.0000 chunk 163 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 72 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 HIS D 618 HIS ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3649 r_free = 0.3649 target = 0.068682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050841 restraints weight = 89099.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052829 restraints weight = 49518.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.054181 restraints weight = 32228.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.055069 restraints weight = 23434.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.055735 restraints weight = 18471.493| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 15181 Z= 0.106 Angle : 0.591 7.928 20649 Z= 0.302 Chirality : 0.043 0.185 2205 Planarity : 0.005 0.117 2656 Dihedral : 6.153 84.425 2143 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.06 % Allowed : 1.21 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.19), residues: 1903 helix: 1.37 (0.27), residues: 412 sheet: -0.57 (0.29), residues: 262 loop : -0.39 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 865 TYR 0.010 0.001 TYR D 465 PHE 0.009 0.001 PHE E 438 TRP 0.017 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00248 (15118) covalent geometry : angle 0.58697 (20528) SS BOND : bond 0.00277 ( 53) SS BOND : angle 1.08105 ( 106) hydrogen bonds : bond 0.03199 ( 577) hydrogen bonds : angle 5.14934 ( 1704) Misc. bond : bond 0.05679 ( 5) link_NAG-ASN : bond 0.00373 ( 5) link_NAG-ASN : angle 1.23635 ( 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 116 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8418 (pt0) cc_final: 0.7894 (tm-30) REVERT: A 104 CYS cc_start: 0.9085 (m) cc_final: 0.8048 (t) REVERT: B 52 ASP cc_start: 0.8904 (m-30) cc_final: 0.8423 (p0) REVERT: B 99 ASP cc_start: 0.8740 (t0) cc_final: 0.8409 (t0) REVERT: B 106 LEU cc_start: 0.9249 (tt) cc_final: 0.8950 (pp) REVERT: B 141 LEU cc_start: 0.9038 (tp) cc_final: 0.8738 (tp) REVERT: C 179 MET cc_start: 0.8873 (ttm) cc_final: 0.8508 (tmm) REVERT: C 203 ASN cc_start: 0.7522 (m110) cc_final: 0.7209 (m-40) REVERT: C 343 MET cc_start: 0.7758 (ptt) cc_final: 0.7508 (ptt) REVERT: C 349 ASP cc_start: 0.7885 (t0) cc_final: 0.7429 (t0) REVERT: D 659 MET cc_start: 0.8631 (tpp) cc_final: 0.8293 (tpt) REVERT: D 884 MET cc_start: 0.2649 (ppp) cc_final: 0.2155 (tmm) REVERT: E 786 MET cc_start: 0.8508 (pmm) cc_final: 0.7965 (pmm) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.0845 time to fit residues: 16.6719 Evaluate side-chains 74 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 0.0870 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 464 HIS ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN E 539 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.069431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051675 restraints weight = 89597.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053679 restraints weight = 49602.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055050 restraints weight = 32313.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055985 restraints weight = 23432.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.056614 restraints weight = 18404.580| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15181 Z= 0.104 Angle : 0.586 7.540 20649 Z= 0.299 Chirality : 0.043 0.174 2205 Planarity : 0.004 0.092 2656 Dihedral : 5.989 84.203 2143 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1903 helix: 1.43 (0.26), residues: 414 sheet: -0.49 (0.29), residues: 262 loop : -0.36 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 865 TYR 0.009 0.001 TYR E 424 PHE 0.009 0.001 PHE D 507 TRP 0.017 0.001 TRP D 958 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00241 (15118) covalent geometry : angle 0.58087 (20528) SS BOND : bond 0.00372 ( 53) SS BOND : angle 1.19747 ( 106) hydrogen bonds : bond 0.03096 ( 577) hydrogen bonds : angle 5.00370 ( 1704) Misc. bond : bond 0.04334 ( 5) link_NAG-ASN : bond 0.00359 ( 5) link_NAG-ASN : angle 1.21298 ( 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 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8373 (pt0) cc_final: 0.7834 (tm-30) REVERT: A 104 CYS cc_start: 0.9109 (m) cc_final: 0.8028 (t) REVERT: B 52 ASP cc_start: 0.8916 (m-30) cc_final: 0.8399 (p0) REVERT: B 99 ASP cc_start: 0.8648 (t0) cc_final: 0.8235 (t0) REVERT: C 179 MET cc_start: 0.8815 (ttm) cc_final: 0.8507 (tmm) REVERT: C 191 LEU cc_start: 0.8134 (tp) cc_final: 0.7891 (mm) REVERT: C 203 ASN cc_start: 0.7503 (m110) cc_final: 0.7110 (m-40) REVERT: C 343 MET cc_start: 0.7472 (ptt) cc_final: 0.7166 (ptt) REVERT: C 349 ASP cc_start: 0.7795 (t0) cc_final: 0.7378 (t0) REVERT: D 659 MET cc_start: 0.8638 (tpp) cc_final: 0.8319 (tpt) REVERT: D 822 MET cc_start: 0.6938 (tmm) cc_final: 0.6489 (tmm) REVERT: D 884 MET cc_start: 0.2497 (ppp) cc_final: 0.2217 (tmm) REVERT: D 888 MET cc_start: 0.4105 (tpt) cc_final: 0.3831 (tpt) REVERT: E 786 MET cc_start: 0.8397 (pmm) cc_final: 0.7842 (pmm) REVERT: E 884 MET cc_start: 0.3824 (ppp) cc_final: 0.3484 (ppp) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0902 time to fit residues: 16.7378 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 : 0.510 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 115 optimal weight: 0.2980 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS B 117 HIS D 618 HIS ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 HIS E 353 HIS E 357 HIS E 539 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.067839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050041 restraints weight = 90857.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052009 restraints weight = 50448.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.053332 restraints weight = 32830.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.054226 restraints weight = 23873.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054857 restraints weight = 18828.310| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 15181 Z= 0.143 Angle : 0.609 9.626 20649 Z= 0.313 Chirality : 0.043 0.189 2205 Planarity : 0.005 0.092 2656 Dihedral : 6.111 83.195 2143 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.19), residues: 1903 helix: 1.33 (0.26), residues: 414 sheet: -0.65 (0.28), residues: 269 loop : -0.44 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 865 TYR 0.010 0.001 TYR E 424 PHE 0.016 0.001 PHE B 103 TRP 0.038 0.001 TRP D 992 HIS 0.008 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00335 (15118) covalent geometry : angle 0.60332 (20528) SS BOND : bond 0.00253 ( 53) SS BOND : angle 1.16958 ( 106) hydrogen bonds : bond 0.03195 ( 577) hydrogen bonds : angle 5.11665 ( 1704) Misc. bond : bond 0.08683 ( 5) link_NAG-ASN : bond 0.00257 ( 5) link_NAG-ASN : angle 1.47150 ( 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 101 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8426 (pt0) cc_final: 0.7891 (tm-30) REVERT: A 104 CYS cc_start: 0.9146 (m) cc_final: 0.8102 (t) REVERT: B 52 ASP cc_start: 0.8911 (m-30) cc_final: 0.8387 (p0) REVERT: B 99 ASP cc_start: 0.8822 (t0) cc_final: 0.8375 (t0) REVERT: B 103 PHE cc_start: 0.8950 (m-10) cc_final: 0.8668 (m-80) REVERT: B 106 LEU cc_start: 0.9248 (tt) cc_final: 0.8969 (pp) REVERT: C 175 TRP cc_start: 0.8654 (p90) cc_final: 0.8349 (p90) REVERT: C 179 MET cc_start: 0.8832 (ttm) cc_final: 0.8484 (tmm) REVERT: C 203 ASN cc_start: 0.7252 (m110) cc_final: 0.7028 (m-40) REVERT: C 343 MET cc_start: 0.7500 (ptt) cc_final: 0.7223 (ptt) REVERT: C 349 ASP cc_start: 0.7955 (t0) cc_final: 0.7471 (t0) REVERT: D 659 MET cc_start: 0.8555 (tpp) cc_final: 0.8271 (tpt) REVERT: D 888 MET cc_start: 0.4323 (tpt) cc_final: 0.3921 (tpt) REVERT: E 786 MET cc_start: 0.8575 (pmm) cc_final: 0.8024 (pmm) REVERT: E 884 MET cc_start: 0.3565 (ppp) cc_final: 0.3284 (ppp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0933 time to fit residues: 15.7056 Evaluate side-chains 75 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 0.3980 chunk 68 optimal weight: 0.0270 chunk 146 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.069477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051714 restraints weight = 89641.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053718 restraints weight = 49569.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055087 restraints weight = 32233.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.056003 restraints weight = 23314.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056648 restraints weight = 18374.179| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.092 15181 Z= 0.102 Angle : 0.588 8.386 20649 Z= 0.298 Chirality : 0.043 0.174 2205 Planarity : 0.006 0.194 2656 Dihedral : 5.929 82.518 2143 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 1903 helix: 1.44 (0.27), residues: 411 sheet: -0.71 (0.30), residues: 226 loop : -0.41 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 400 TYR 0.010 0.001 TYR E 580 PHE 0.023 0.001 PHE B 103 TRP 0.025 0.001 TRP D 992 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00236 (15118) covalent geometry : angle 0.58494 (20528) SS BOND : bond 0.00226 ( 53) SS BOND : angle 0.97303 ( 106) hydrogen bonds : bond 0.03046 ( 577) hydrogen bonds : angle 4.93891 ( 1704) Misc. bond : bond 0.04255 ( 5) link_NAG-ASN : bond 0.00365 ( 5) link_NAG-ASN : angle 1.23768 ( 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 117 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8393 (pt0) cc_final: 0.7833 (tm-30) REVERT: A 104 CYS cc_start: 0.9105 (m) cc_final: 0.8108 (t) REVERT: A 136 LEU cc_start: 0.9631 (mm) cc_final: 0.9161 (tp) REVERT: B 52 ASP cc_start: 0.8916 (m-30) cc_final: 0.8426 (p0) REVERT: B 99 ASP cc_start: 0.8921 (t0) cc_final: 0.8228 (t0) REVERT: B 103 PHE cc_start: 0.9140 (m-10) cc_final: 0.8594 (m-80) REVERT: B 106 LEU cc_start: 0.9207 (tt) cc_final: 0.8935 (pp) REVERT: C 175 TRP cc_start: 0.8446 (p90) cc_final: 0.8201 (p90) REVERT: C 179 MET cc_start: 0.8814 (ttm) cc_final: 0.8497 (tmm) REVERT: C 203 ASN cc_start: 0.7023 (m110) cc_final: 0.6755 (m-40) REVERT: C 343 MET cc_start: 0.7474 (ptt) cc_final: 0.7252 (ptt) REVERT: C 349 ASP cc_start: 0.7925 (t0) cc_final: 0.7553 (t0) REVERT: D 659 MET cc_start: 0.8638 (tpp) cc_final: 0.8320 (tpt) REVERT: D 888 MET cc_start: 0.4406 (tpt) cc_final: 0.4190 (tpt) REVERT: E 786 MET cc_start: 0.8441 (pmm) cc_final: 0.7914 (pmm) REVERT: E 884 MET cc_start: 0.3496 (ppp) cc_final: 0.3210 (ppp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1138 time to fit residues: 21.4747 Evaluate side-chains 85 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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: 9.9990 chunk 159 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 137 optimal weight: 0.6980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 337 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS D 539 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 = 0.3599 r_free = 0.3599 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.048903 restraints weight = 92212.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.050749 restraints weight = 52053.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052016 restraints weight = 34377.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052862 restraints weight = 25337.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053480 restraints weight = 20215.679| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 15181 Z= 0.191 Angle : 0.660 12.933 20649 Z= 0.339 Chirality : 0.045 0.293 2205 Planarity : 0.006 0.192 2656 Dihedral : 6.467 87.146 2143 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.19), residues: 1903 helix: 1.13 (0.26), residues: 408 sheet: -0.77 (0.29), residues: 241 loop : -0.61 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 479 TYR 0.015 0.002 TYR E 424 PHE 0.027 0.002 PHE B 103 TRP 0.023 0.002 TRP D 450 HIS 0.014 0.001 HIS D 495 Details of bonding type rmsd covalent geometry : bond 0.00437 (15118) covalent geometry : angle 0.65495 (20528) SS BOND : bond 0.00312 ( 53) SS BOND : angle 1.17765 ( 106) hydrogen bonds : bond 0.03487 ( 577) hydrogen bonds : angle 5.33614 ( 1704) Misc. bond : bond 0.12458 ( 5) link_NAG-ASN : bond 0.00243 ( 5) link_NAG-ASN : angle 1.85684 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.49 seconds wall clock time: 42 minutes 27.82 seconds (2547.82 seconds total)