Starting phenix.real_space_refine on Fri Jun 13 11:47:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/06_2025/9fmu_50570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9fmu_50570/06_2025/9fmu_50570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/06_2025/9fmu_50570.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/06_2025/9fmu_50570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/06_2025/9fmu_50570.cif" } resolution = 4.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.29, per 1000 atoms: 0.63 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.28 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: 6.03 Time building geometry restraints manager: 5.09 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: 1.970 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- 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 : 20.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.003 TRP E 796 HIS 0.011 0.001 HIS C 337 PHE 0.037 0.002 PHE E 438 TYR 0.038 0.003 TYR D 465 ARG 0.022 0.003 ARG D 198 Details of bonding type rmsd link_NAG-ASN : bond 0.05169 ( 5) link_NAG-ASN : angle 3.55535 ( 15) hydrogen bonds : bond 0.13502 ( 577) hydrogen bonds : angle 8.99672 ( 1704) SS BOND : bond 0.00922 ( 53) SS BOND : angle 4.29482 ( 106) covalent geometry : bond 0.00541 (15118) covalent geometry : angle 1.18243 (20528) Misc. bond : bond 0.25616 ( 5) *********************** 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 : 1.733 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: 0.8450 (t0) REVERT: B 47 ASP cc_start: 0.8030 (p0) cc_final: 0.7752 (m-30) REVERT: B 65 LYS cc_start: 0.9749 (pptt) cc_final: 0.9102 (mmpt) REVERT: C 175 TRP cc_start: 0.8692 (p90) cc_final: 0.7991 (p90) REVERT: C 191 LEU cc_start: 0.8435 (tp) cc_final: 0.8116 (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: 0.8026 (tmm) REVERT: C 343 MET cc_start: 0.7348 (ppp) cc_final: 0.6937 (ppp) REVERT: C 378 ASP cc_start: 0.8510 (p0) cc_final: 0.8203 (p0) REVERT: D 330 LEU cc_start: 0.8635 (mm) cc_final: 0.8394 (mt) REVERT: D 339 GLU cc_start: 0.6642 (mp0) cc_final: 0.6415 (mp0) REVERT: D 884 MET cc_start: 0.0288 (ppp) cc_final: -0.0857 (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: 0.6845 (mm) 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: 0.4413 (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: 0.6928 (mmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2603 time to fit residues: 78.5213 Evaluate side-chains 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 337 HIS C 362 HIS ** 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 754 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.067252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049278 restraints weight = 93496.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051137 restraints weight = 52106.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052398 restraints weight = 34195.586| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.339 15181 Z= 0.289 Angle : 0.835 13.652 20649 Z= 0.436 Chirality : 0.049 0.223 2205 Planarity : 0.006 0.063 2656 Dihedral : 7.177 86.549 2143 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1903 helix: 0.23 (0.24), residues: 405 sheet: -0.33 (0.32), residues: 237 loop : -0.39 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 450 HIS 0.010 0.002 HIS B 92 PHE 0.021 0.002 PHE E 821 TYR 0.020 0.003 TYR C 386 ARG 0.008 0.001 ARG D 865 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 5) link_NAG-ASN : angle 2.26159 ( 15) hydrogen bonds : bond 0.04912 ( 577) hydrogen bonds : angle 6.42539 ( 1704) SS BOND : bond 0.00507 ( 53) SS BOND : angle 1.73591 ( 106) covalent geometry : bond 0.00629 (15118) covalent geometry : angle 0.82612 (20528) Misc. bond : bond 0.16763 ( 5) *********************** 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 113 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8509 (pt0) cc_final: 0.7641 (tm-30) REVERT: A 104 CYS cc_start: 0.9115 (m) cc_final: 0.8260 (t) REVERT: B 19 ASN cc_start: 0.9194 (m-40) cc_final: 0.8813 (t0) REVERT: B 65 LYS cc_start: 0.9775 (pptt) cc_final: 0.9003 (mmpt) REVERT: B 141 LEU cc_start: 0.9290 (tp) cc_final: 0.9048 (tp) REVERT: C 175 TRP cc_start: 0.8987 (p90) cc_final: 0.8549 (p90) REVERT: C 349 ASP cc_start: 0.8266 (t0) cc_final: 0.7962 (t0) REVERT: D 449 LEU cc_start: 0.9224 (pp) cc_final: 0.8483 (tp) REVERT: D 822 MET cc_start: 0.6879 (tmm) cc_final: 0.6479 (tmm) REVERT: D 884 MET cc_start: 0.0970 (ppp) cc_final: 0.0017 (tmm) REVERT: D 931 LEU cc_start: 0.7899 (mm) cc_final: 0.7602 (mt) REVERT: E 507 PHE cc_start: 0.8633 (t80) cc_final: 0.8120 (t80) REVERT: E 640 LYS cc_start: 0.8695 (pttt) cc_final: 0.8392 (tptp) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.2506 time to fit residues: 45.0358 Evaluate side-chains 78 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 94 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 HIS ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN D 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.069343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051408 restraints weight = 90035.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053389 restraints weight = 49835.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.054744 restraints weight = 32377.710| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 15181 Z= 0.132 Angle : 0.635 9.235 20649 Z= 0.329 Chirality : 0.044 0.161 2205 Planarity : 0.004 0.057 2656 Dihedral : 6.400 78.685 2143 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1903 helix: 0.88 (0.25), residues: 418 sheet: -0.19 (0.32), residues: 242 loop : -0.25 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 295 HIS 0.006 0.001 HIS D 347 PHE 0.015 0.001 PHE A 117 TYR 0.012 0.001 TYR D 427 ARG 0.004 0.000 ARG D 865 Details of bonding type rmsd link_NAG-ASN : bond 0.00224 ( 5) link_NAG-ASN : angle 1.62099 ( 15) hydrogen bonds : bond 0.03751 ( 577) hydrogen bonds : angle 5.61060 ( 1704) SS BOND : bond 0.00382 ( 53) SS BOND : angle 1.14590 ( 106) covalent geometry : bond 0.00294 (15118) covalent geometry : angle 0.62965 (20528) Misc. bond : bond 0.07834 ( 5) *********************** 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 117 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8427 (pt0) cc_final: 0.7968 (tm-30) REVERT: A 104 CYS cc_start: 0.9058 (m) cc_final: 0.7943 (t) REVERT: B 19 ASN cc_start: 0.9129 (m-40) cc_final: 0.8720 (t0) REVERT: B 106 LEU cc_start: 0.9367 (tt) cc_final: 0.8845 (pp) REVERT: B 141 LEU cc_start: 0.9137 (tp) cc_final: 0.8824 (tp) REVERT: C 179 MET cc_start: 0.8963 (ttm) cc_final: 0.8418 (tmm) REVERT: C 191 LEU cc_start: 0.8528 (tp) cc_final: 0.7901 (mm) REVERT: C 349 ASP cc_start: 0.7870 (t0) cc_final: 0.7419 (t0) REVERT: D 342 ILE cc_start: 0.8828 (mp) cc_final: 0.8607 (tp) REVERT: D 449 LEU cc_start: 0.9126 (pp) cc_final: 0.8380 (tp) REVERT: D 659 MET cc_start: 0.8547 (tpp) cc_final: 0.8229 (tpt) REVERT: D 884 MET cc_start: 0.1073 (ppp) cc_final: -0.0008 (tmm) REVERT: D 903 TRP cc_start: 0.8876 (m-90) cc_final: 0.8465 (m-90) REVERT: E 507 PHE cc_start: 0.8697 (t80) cc_final: 0.8248 (t80) REVERT: E 640 LYS cc_start: 0.8724 (pttt) cc_final: 0.8385 (tptp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2232 time to fit residues: 42.7793 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 : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 181 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ** B 63 HIS ** 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 876 ASN D 932 GLN ** D 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS E 876 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.064320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046573 restraints weight = 93607.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048340 restraints weight = 53136.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049557 restraints weight = 35275.177| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.417 15181 Z= 0.336 Angle : 0.847 15.874 20649 Z= 0.440 Chirality : 0.050 0.247 2205 Planarity : 0.006 0.069 2656 Dihedral : 7.630 89.743 2143 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.06 % Allowed : 6.62 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 1903 helix: 0.23 (0.25), residues: 408 sheet: -0.61 (0.31), residues: 246 loop : -0.67 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 992 HIS 0.014 0.002 HIS D 347 PHE 0.026 0.003 PHE A 36 TYR 0.028 0.003 TYR D 427 ARG 0.013 0.001 ARG D 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 2.67876 ( 15) hydrogen bonds : bond 0.04744 ( 577) hydrogen bonds : angle 6.43923 ( 1704) SS BOND : bond 0.00553 ( 53) SS BOND : angle 1.64941 ( 106) covalent geometry : bond 0.00730 (15118) covalent geometry : angle 0.83835 (20528) Misc. bond : bond 0.20409 ( 5) *********************** 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 93 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8417 (pt0) cc_final: 0.7860 (tm-30) REVERT: A 104 CYS cc_start: 0.9098 (m) cc_final: 0.8254 (t) REVERT: C 349 ASP cc_start: 0.8038 (t0) cc_final: 0.7635 (t0) REVERT: E 507 PHE cc_start: 0.8363 (t80) cc_final: 0.8107 (t80) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.2121 time to fit residues: 32.6282 Evaluate side-chains 62 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 203 ASN D 344 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.066575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048682 restraints weight = 90839.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050579 restraints weight = 50702.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.051879 restraints weight = 33299.895| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.248 15181 Z= 0.155 Angle : 0.653 12.671 20649 Z= 0.338 Chirality : 0.045 0.179 2205 Planarity : 0.005 0.139 2656 Dihedral : 6.891 83.948 2143 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1903 helix: 0.73 (0.25), residues: 409 sheet: -0.56 (0.30), residues: 269 loop : -0.61 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 992 HIS 0.009 0.001 HIS D 347 PHE 0.019 0.002 PHE D 650 TYR 0.022 0.002 TYR D 465 ARG 0.006 0.001 ARG D 865 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 5) link_NAG-ASN : angle 1.77275 ( 15) hydrogen bonds : bond 0.03688 ( 577) hydrogen bonds : angle 5.74667 ( 1704) SS BOND : bond 0.00423 ( 53) SS BOND : angle 1.20585 ( 106) covalent geometry : bond 0.00353 (15118) covalent geometry : angle 0.64724 (20528) Misc. bond : bond 0.11531 ( 5) *********************** 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 99 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8350 (pt0) cc_final: 0.7811 (tm-30) REVERT: A 104 CYS cc_start: 0.9072 (m) cc_final: 0.8079 (t) REVERT: B 19 ASN cc_start: 0.9217 (m-40) cc_final: 0.8707 (t0) REVERT: B 52 ASP cc_start: 0.8973 (m-30) cc_final: 0.8527 (p0) REVERT: B 106 LEU cc_start: 0.9352 (tt) cc_final: 0.8933 (pp) REVERT: C 179 MET cc_start: 0.8925 (ttm) cc_final: 0.8366 (tmm) REVERT: C 191 LEU cc_start: 0.8513 (tp) cc_final: 0.7844 (mm) REVERT: C 203 ASN cc_start: 0.7836 (m110) cc_final: 0.7561 (m-40) REVERT: C 349 ASP cc_start: 0.8007 (t0) cc_final: 0.7545 (t0) REVERT: C 370 TYR cc_start: 0.7450 (m-10) cc_final: 0.7069 (m-80) REVERT: E 507 PHE cc_start: 0.8425 (t80) cc_final: 0.8141 (t80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2186 time to fit residues: 35.7565 Evaluate side-chains 69 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 126 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 158 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048655 restraints weight = 92001.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050520 restraints weight = 51705.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051788 restraints weight = 34043.968| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.266 15181 Z= 0.158 Angle : 0.645 12.245 20649 Z= 0.331 Chirality : 0.044 0.182 2205 Planarity : 0.005 0.094 2656 Dihedral : 6.732 86.451 2143 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1903 helix: 0.94 (0.26), residues: 411 sheet: -0.65 (0.29), residues: 267 loop : -0.55 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 992 HIS 0.009 0.001 HIS D 347 PHE 0.010 0.001 PHE A 98 TYR 0.012 0.001 TYR D 427 ARG 0.008 0.001 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 5) link_NAG-ASN : angle 1.62934 ( 15) hydrogen bonds : bond 0.03548 ( 577) hydrogen bonds : angle 5.58958 ( 1704) SS BOND : bond 0.00309 ( 53) SS BOND : angle 1.11332 ( 106) covalent geometry : bond 0.00365 (15118) covalent geometry : angle 0.64009 (20528) Misc. bond : bond 0.12133 ( 5) *********************** 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 96 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8383 (pt0) cc_final: 0.7835 (tm-30) REVERT: A 104 CYS cc_start: 0.9075 (m) cc_final: 0.8087 (t) REVERT: B 19 ASN cc_start: 0.9212 (m-40) cc_final: 0.8701 (t0) REVERT: B 52 ASP cc_start: 0.9032 (m-30) cc_final: 0.8540 (p0) REVERT: B 99 ASP cc_start: 0.8920 (t0) cc_final: 0.8671 (t0) REVERT: B 106 LEU cc_start: 0.9316 (tt) cc_final: 0.8899 (pp) REVERT: C 179 MET cc_start: 0.8955 (ttm) cc_final: 0.8389 (tmm) REVERT: C 191 LEU cc_start: 0.8527 (tp) cc_final: 0.7914 (mm) REVERT: C 203 ASN cc_start: 0.7415 (m110) cc_final: 0.7203 (m-40) REVERT: C 263 MET cc_start: 0.8733 (tmm) cc_final: 0.8503 (tmm) REVERT: C 343 MET cc_start: 0.8203 (ppp) cc_final: 0.7845 (ppp) REVERT: C 349 ASP cc_start: 0.8022 (t0) cc_final: 0.7667 (t0) REVERT: E 607 LEU cc_start: 0.9292 (tp) cc_final: 0.8830 (mm) REVERT: E 786 MET cc_start: 0.8740 (pmm) cc_final: 0.8447 (pmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2286 time to fit residues: 37.1321 Evaluate side-chains 69 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 183 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 94 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.065653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047757 restraints weight = 92349.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049609 restraints weight = 51881.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050864 restraints weight = 34231.044| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 15181 Z= 0.193 Angle : 0.675 13.924 20649 Z= 0.348 Chirality : 0.045 0.184 2205 Planarity : 0.005 0.085 2656 Dihedral : 6.846 88.190 2143 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 1903 helix: 0.83 (0.26), residues: 410 sheet: -0.85 (0.29), residues: 258 loop : -0.62 (0.18), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 958 HIS 0.012 0.001 HIS D 347 PHE 0.013 0.002 PHE D 283 TYR 0.018 0.002 TYR D 465 ARG 0.007 0.001 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 5) link_NAG-ASN : angle 1.85346 ( 15) hydrogen bonds : bond 0.03704 ( 577) hydrogen bonds : angle 5.77529 ( 1704) SS BOND : bond 0.00480 ( 53) SS BOND : angle 1.33577 ( 106) covalent geometry : bond 0.00438 (15118) covalent geometry : angle 0.66830 (20528) Misc. bond : bond 0.14403 ( 5) *********************** 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 86 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.844 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8432 (pt0) cc_final: 0.7803 (tm-30) REVERT: A 104 CYS cc_start: 0.9069 (m) cc_final: 0.8099 (t) REVERT: B 19 ASN cc_start: 0.9247 (m-40) cc_final: 0.8742 (t0) REVERT: B 52 ASP cc_start: 0.9083 (m-30) cc_final: 0.8576 (p0) REVERT: B 99 ASP cc_start: 0.8940 (t0) cc_final: 0.8634 (t0) REVERT: C 179 MET cc_start: 0.8932 (ttm) cc_final: 0.8333 (tmm) REVERT: C 191 LEU cc_start: 0.8484 (tp) cc_final: 0.7808 (mm) REVERT: C 349 ASP cc_start: 0.8079 (t0) cc_final: 0.7805 (t0) REVERT: D 888 MET cc_start: 0.3695 (tpt) cc_final: 0.2566 (tpt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2499 time to fit residues: 37.6328 Evaluate side-chains 64 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 131 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS ** D 676 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 HIS ** 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 = 0.3574 r_free = 0.3574 target = 0.065669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.047823 restraints weight = 91980.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049658 restraints weight = 51867.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050900 restraints weight = 34301.314| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.288 15181 Z= 0.175 Angle : 0.656 13.193 20649 Z= 0.338 Chirality : 0.045 0.196 2205 Planarity : 0.005 0.066 2656 Dihedral : 6.796 89.510 2143 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1903 helix: 0.90 (0.26), residues: 411 sheet: -1.08 (0.28), residues: 271 loop : -0.61 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 329 HIS 0.010 0.001 HIS D 347 PHE 0.010 0.001 PHE E 438 TYR 0.011 0.001 TYR D 427 ARG 0.006 0.001 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 5) link_NAG-ASN : angle 1.76991 ( 15) hydrogen bonds : bond 0.03560 ( 577) hydrogen bonds : angle 5.69760 ( 1704) SS BOND : bond 0.00328 ( 53) SS BOND : angle 1.25552 ( 106) covalent geometry : bond 0.00404 (15118) covalent geometry : angle 0.65024 (20528) Misc. bond : bond 0.13440 ( 5) *********************** 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 85 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8409 (pt0) cc_final: 0.7804 (tm-30) REVERT: A 104 CYS cc_start: 0.9133 (m) cc_final: 0.8106 (t) REVERT: B 19 ASN cc_start: 0.9284 (m-40) cc_final: 0.8805 (t0) REVERT: B 52 ASP cc_start: 0.9142 (m-30) cc_final: 0.8621 (p0) REVERT: B 99 ASP cc_start: 0.8947 (t0) cc_final: 0.8725 (t0) REVERT: B 106 LEU cc_start: 0.9288 (tt) cc_final: 0.8918 (pp) REVERT: C 179 MET cc_start: 0.8898 (ttm) cc_final: 0.8346 (tmm) REVERT: C 191 LEU cc_start: 0.8508 (tp) cc_final: 0.7968 (mm) REVERT: C 343 MET cc_start: 0.7667 (ptt) cc_final: 0.7436 (ptt) REVERT: C 349 ASP cc_start: 0.8208 (t0) cc_final: 0.7765 (t0) REVERT: D 342 ILE cc_start: 0.8808 (mp) cc_final: 0.8486 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2475 time to fit residues: 35.8898 Evaluate side-chains 68 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 105 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 HIS ** D 676 GLN ** 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 = 0.3627 r_free = 0.3627 target = 0.067711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049971 restraints weight = 89318.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051875 restraints weight = 49919.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053192 restraints weight = 32791.375| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 15181 Z= 0.109 Angle : 0.605 9.091 20649 Z= 0.309 Chirality : 0.043 0.185 2205 Planarity : 0.004 0.065 2656 Dihedral : 6.332 84.698 2143 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1903 helix: 1.20 (0.26), residues: 417 sheet: -0.80 (0.30), residues: 241 loop : -0.50 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 958 HIS 0.006 0.001 HIS A 72 PHE 0.008 0.001 PHE C 173 TYR 0.011 0.001 TYR E 580 ARG 0.003 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 1.30345 ( 15) hydrogen bonds : bond 0.03246 ( 577) hydrogen bonds : angle 5.24987 ( 1704) SS BOND : bond 0.00265 ( 53) SS BOND : angle 1.00524 ( 106) covalent geometry : bond 0.00257 (15118) covalent geometry : angle 0.60160 (20528) Misc. bond : bond 0.06167 ( 5) *********************** 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 103 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8444 (pt0) cc_final: 0.7942 (tm-30) REVERT: A 104 CYS cc_start: 0.9107 (m) cc_final: 0.8116 (t) REVERT: A 136 LEU cc_start: 0.9634 (mm) cc_final: 0.9157 (tp) REVERT: B 19 ASN cc_start: 0.9294 (m-40) cc_final: 0.8673 (p0) REVERT: B 52 ASP cc_start: 0.9072 (m-30) cc_final: 0.8582 (p0) REVERT: B 99 ASP cc_start: 0.8861 (t0) cc_final: 0.8354 (t0) REVERT: B 106 LEU cc_start: 0.9236 (tt) cc_final: 0.8882 (pp) REVERT: C 179 MET cc_start: 0.8838 (ttm) cc_final: 0.8344 (tmm) REVERT: C 191 LEU cc_start: 0.8417 (tp) cc_final: 0.7983 (mm) REVERT: C 343 MET cc_start: 0.7496 (ptt) cc_final: 0.7220 (ptt) REVERT: C 349 ASP cc_start: 0.8081 (t0) cc_final: 0.7678 (t0) REVERT: D 342 ILE cc_start: 0.8756 (mp) cc_final: 0.8440 (tp) REVERT: E 786 MET cc_start: 0.8820 (pmm) cc_final: 0.8249 (pmm) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3393 time to fit residues: 59.2763 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 : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 80 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 23 optimal weight: 0.0570 chunk 152 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 GLN ** 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 = 0.3619 r_free = 0.3619 target = 0.067364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049559 restraints weight = 89389.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051480 restraints weight = 49901.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.052780 restraints weight = 32793.190| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 15181 Z= 0.116 Angle : 0.599 8.951 20649 Z= 0.306 Chirality : 0.043 0.178 2205 Planarity : 0.004 0.064 2656 Dihedral : 6.239 84.935 2143 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1903 helix: 1.30 (0.26), residues: 411 sheet: -0.93 (0.29), residues: 259 loop : -0.47 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 958 HIS 0.005 0.001 HIS A 72 PHE 0.009 0.001 PHE A 98 TYR 0.010 0.001 TYR E 580 ARG 0.004 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 1.43323 ( 15) hydrogen bonds : bond 0.03179 ( 577) hydrogen bonds : angle 5.19066 ( 1704) SS BOND : bond 0.00254 ( 53) SS BOND : angle 1.02470 ( 106) covalent geometry : bond 0.00276 (15118) covalent geometry : angle 0.59453 (20528) Misc. bond : bond 0.07385 ( 5) ********************** 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 99 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8439 (pt0) cc_final: 0.7937 (tm-30) REVERT: A 104 CYS cc_start: 0.9124 (m) cc_final: 0.8137 (t) REVERT: A 136 LEU cc_start: 0.9639 (mm) cc_final: 0.9155 (tp) REVERT: B 19 ASN cc_start: 0.9266 (m-40) cc_final: 0.8835 (t0) REVERT: B 52 ASP cc_start: 0.9070 (m-30) cc_final: 0.8543 (p0) REVERT: B 99 ASP cc_start: 0.8762 (t0) cc_final: 0.8351 (t0) REVERT: B 103 PHE cc_start: 0.9075 (m-10) cc_final: 0.8661 (m-80) REVERT: B 106 LEU cc_start: 0.9209 (tt) cc_final: 0.8877 (pp) REVERT: C 179 MET cc_start: 0.8803 (ttm) cc_final: 0.8332 (tmm) REVERT: C 191 LEU cc_start: 0.8406 (tp) cc_final: 0.7981 (mm) REVERT: C 343 MET cc_start: 0.7434 (ptt) cc_final: 0.7229 (ptt) REVERT: C 349 ASP cc_start: 0.8055 (t0) cc_final: 0.7646 (t0) REVERT: D 342 ILE cc_start: 0.8771 (mp) cc_final: 0.8466 (tp) REVERT: E 786 MET cc_start: 0.8857 (pmm) cc_final: 0.8284 (pmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2724 time to fit residues: 44.7673 Evaluate side-chains 80 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 145 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 117 HIS C 331 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS ** D 676 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 = 0.3591 r_free = 0.3591 target = 0.066371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.048587 restraints weight = 91167.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050458 restraints weight = 50734.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.051716 restraints weight = 33303.937| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.264 15181 Z= 0.160 Angle : 0.633 12.605 20649 Z= 0.326 Chirality : 0.044 0.179 2205 Planarity : 0.004 0.064 2656 Dihedral : 6.443 85.975 2143 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1903 helix: 1.18 (0.26), residues: 410 sheet: -0.87 (0.29), residues: 260 loop : -0.57 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 958 HIS 0.011 0.001 HIS D 495 PHE 0.010 0.001 PHE A 98 TYR 0.010 0.001 TYR D 465 ARG 0.005 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 1.70533 ( 15) hydrogen bonds : bond 0.03355 ( 577) hydrogen bonds : angle 5.36940 ( 1704) SS BOND : bond 0.00291 ( 53) SS BOND : angle 1.07454 ( 106) covalent geometry : bond 0.00371 (15118) covalent geometry : angle 0.62876 (20528) Misc. bond : bond 0.11900 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.04 seconds wall clock time: 87 minutes 28.62 seconds (5248.62 seconds total)