Starting phenix.real_space_refine on Fri May 16 23:10:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/05_2025/9fmu_50570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/05_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_50570/05_2025/9fmu_50570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/05_2025/9fmu_50570.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/05_2025/9fmu_50570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/05_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-5687/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: 8.64, per 1000 atoms: 0.59 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: 4.04 Conformation dependent library (CDL) restraints added in 2.0 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: 2.51 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: 6.68 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6026 1.39 - 1.56: 8929 1.56 - 1.73: 7 1.73 - 1.90: 148 1.90 - 2.07: 8 Bond restraints: 15118 Sorted by residual: bond pdb=" CB CYS D 577 " pdb=" SG CYS D 577 " ideal model delta sigma weight residual 1.808 1.701 0.107 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " ideal model delta sigma weight residual 1.808 1.714 0.094 3.30e-02 9.18e+02 8.07e+00 bond pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.81e+00 bond pdb=" CB CYS D 895 " pdb=" SG CYS D 895 " ideal model delta sigma weight residual 1.808 1.723 0.085 3.30e-02 9.18e+02 6.65e+00 bond pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.15e+00 ... (remaining 15113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 20295 4.22 - 8.45: 196 8.45 - 12.67: 27 12.67 - 16.89: 7 16.89 - 21.11: 3 Bond angle restraints: 20528 Sorted by residual: angle pdb=" CA CYS D 557 " pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " ideal model delta sigma weight residual 114.40 135.51 -21.11 2.30e+00 1.89e-01 8.43e+01 angle pdb=" CA CYS E 547 " pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 114.40 132.19 -17.79 2.30e+00 1.89e-01 5.98e+01 angle pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " pdb=" SG CYS D 547 " ideal model delta sigma weight residual 114.40 131.94 -17.54 2.30e+00 1.89e-01 5.81e+01 angle pdb=" CA CYS D 516 " pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 114.40 129.79 -15.39 2.30e+00 1.89e-01 4.48e+01 angle pdb=" C CYS D 547 " pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " ideal model delta sigma weight residual 109.54 120.92 -11.38 1.84e+00 2.95e-01 3.83e+01 ... (remaining 20523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8260 17.77 - 35.54: 581 35.54 - 53.30: 112 53.30 - 71.07: 32 71.07 - 88.84: 17 Dihedral angle restraints: 9002 sinusoidal: 3631 harmonic: 5371 Sorted by residual: dihedral pdb=" CB CYS D 835 " pdb=" SG CYS D 835 " pdb=" SG CYS D 869 " pdb=" CB CYS D 869 " ideal model delta sinusoidal sigma weight residual 93.00 169.99 -76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS D 335 " pdb=" SG CYS D 335 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 248 " pdb=" CB CYS D 248 " ideal model delta sinusoidal sigma weight residual 93.00 25.60 67.40 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 8999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2000 0.103 - 0.207: 177 0.207 - 0.310: 19 0.310 - 0.413: 7 0.413 - 0.516: 2 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA CYS D 547 " pdb=" N CYS D 547 " pdb=" C CYS D 547 " pdb=" CB CYS D 547 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA CYS E 547 " pdb=" N CYS E 547 " pdb=" C CYS E 547 " pdb=" CB CYS E 547 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2202 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 102 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ASN B 102 " 0.094 2.00e-02 2.50e+03 pdb=" O ASN B 102 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE B 103 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 40 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C ARG B 40 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG B 40 " 0.035 2.00e-02 2.50e+03 pdb=" N PHE B 41 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 25 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLY A 25 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY A 25 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 26 " 0.026 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 160 2.55 - 3.14: 12275 3.14 - 3.72: 23995 3.72 - 4.31: 32449 4.31 - 4.90: 51821 Nonbonded interactions: 120700 Sorted by model distance: nonbonded pdb=" OD2 ASP D 225 " pdb="CA CA D2001 " model vdw 1.959 2.510 nonbonded pdb=" OH TYR D 424 " pdb=" O GLU D 467 " model vdw 1.979 3.040 nonbonded pdb=" OG SER E 879 " pdb=" OD1 ASP E 881 " model vdw 1.993 3.040 nonbonded pdb=" O GLY D 294 " pdb="CA CA D2002 " model vdw 2.104 2.510 nonbonded pdb=" OD1 ASP C 349 " pdb=" N THR C 350 " model vdw 2.124 3.120 ... (remaining 120695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.050 Find NCS groups from input model: 0.230 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- 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 : 1.549 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: 0.2489 time to fit residues: 75.1021 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 : 1.511 ------------------------------------------------------------------------------- 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 = 58)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049264 restraints weight = 93496.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051130 restraints weight = 52179.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052394 restraints weight = 34244.315| |-----------------------------------------------------------------------------| 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 2.26158 ( 15) hydrogen bonds : bond 0.04912 ( 577) hydrogen bonds : angle 6.42539 ( 1704) SS BOND : bond 0.00507 ( 53) SS BOND : angle 1.73588 ( 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 : 1.594 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: 0.8986 (p90) cc_final: 0.8548 (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: 0.6878 (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: 0.7898 (mm) cc_final: 0.7601 (mt) REVERT: E 507 PHE cc_start: 0.8633 (t80) cc_final: 0.8121 (t80) REVERT: E 640 LYS cc_start: 0.8696 (pttt) cc_final: 0.8393 (tptp) outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 0.2424 time to fit residues: 43.2924 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 : 1.722 ------------------------------------------------------------------------------- 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: 0.7980 chunk 150 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 180 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.069799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051856 restraints weight = 88677.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.053874 restraints weight = 49094.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.055249 restraints weight = 31825.314| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 15181 Z= 0.122 Angle : 0.638 9.679 20649 Z= 0.329 Chirality : 0.044 0.164 2205 Planarity : 0.004 0.057 2656 Dihedral : 6.392 79.107 2143 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 0.01 (0.19), residues: 1903 helix: 0.86 (0.25), residues: 419 sheet: -0.06 (0.31), residues: 251 loop : -0.23 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 295 HIS 0.008 0.001 HIS D 347 PHE 0.015 0.001 PHE A 117 TYR 0.011 0.001 TYR D 427 ARG 0.005 0.000 ARG D 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 5) link_NAG-ASN : angle 1.62204 ( 15) hydrogen bonds : bond 0.03805 ( 577) hydrogen bonds : angle 5.62821 ( 1704) SS BOND : bond 0.00341 ( 53) SS BOND : angle 1.15304 ( 106) covalent geometry : bond 0.00268 (15118) covalent geometry : angle 0.63330 (20528) Misc. bond : bond 0.07566 ( 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 120 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8426 (pt0) cc_final: 0.7967 (tm-30) REVERT: A 104 CYS cc_start: 0.9066 (m) cc_final: 0.7923 (t) REVERT: B 19 ASN cc_start: 0.9129 (m-40) cc_final: 0.8773 (t0) REVERT: B 103 PHE cc_start: 0.9161 (m-10) cc_final: 0.8814 (m-80) REVERT: B 106 LEU cc_start: 0.9379 (tt) cc_final: 0.8861 (pp) REVERT: C 179 MET cc_start: 0.8955 (ttm) cc_final: 0.8408 (tmm) REVERT: C 191 LEU cc_start: 0.8563 (tp) cc_final: 0.7851 (mm) REVERT: C 349 ASP cc_start: 0.7920 (t0) cc_final: 0.7491 (t0) REVERT: D 342 ILE cc_start: 0.8825 (mp) cc_final: 0.8597 (tp) REVERT: D 449 LEU cc_start: 0.9094 (pp) cc_final: 0.8374 (tp) REVERT: D 659 MET cc_start: 0.8556 (tpp) cc_final: 0.8246 (tpt) REVERT: D 884 MET cc_start: 0.1032 (ppp) cc_final: -0.0041 (tmm) REVERT: D 903 TRP cc_start: 0.8824 (m-90) cc_final: 0.8469 (m-90) REVERT: E 507 PHE cc_start: 0.8688 (t80) cc_final: 0.8219 (t80) REVERT: E 640 LYS cc_start: 0.8736 (pttt) cc_final: 0.8402 (tptp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2132 time to fit residues: 41.6998 Evaluate side-chains 78 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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: 10.0000 chunk 182 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 250 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.067337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.049439 restraints weight = 91358.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051353 restraints weight = 51022.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052661 restraints weight = 33431.188| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.277 15181 Z= 0.184 Angle : 0.658 12.113 20649 Z= 0.341 Chirality : 0.045 0.183 2205 Planarity : 0.005 0.131 2656 Dihedral : 6.597 81.515 2143 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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: -0.15 (0.19), residues: 1903 helix: 0.81 (0.25), residues: 421 sheet: -0.20 (0.32), residues: 233 loop : -0.36 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 992 HIS 0.010 0.001 HIS D 347 PHE 0.014 0.002 PHE E 821 TYR 0.016 0.002 TYR D 427 ARG 0.008 0.001 ARG D 865 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 5) link_NAG-ASN : angle 1.83799 ( 15) hydrogen bonds : bond 0.03731 ( 577) hydrogen bonds : angle 5.68693 ( 1704) SS BOND : bond 0.00333 ( 53) SS BOND : angle 1.19500 ( 106) covalent geometry : bond 0.00414 (15118) covalent geometry : angle 0.65206 (20528) Misc. bond : bond 0.12671 ( 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 100 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8433 (pt0) cc_final: 0.7957 (tm-30) REVERT: A 104 CYS cc_start: 0.9121 (m) cc_final: 0.8092 (t) REVERT: B 19 ASN cc_start: 0.9214 (m-40) cc_final: 0.8767 (t0) REVERT: B 141 LEU cc_start: 0.9198 (tp) cc_final: 0.8953 (tp) REVERT: C 179 MET cc_start: 0.8944 (ttm) cc_final: 0.8435 (tmm) REVERT: C 349 ASP cc_start: 0.7975 (t0) cc_final: 0.7592 (t0) REVERT: D 659 MET cc_start: 0.8625 (tpp) cc_final: 0.8314 (tpt) REVERT: D 888 MET cc_start: 0.3697 (tpt) cc_final: 0.3354 (tpt) REVERT: E 640 LYS cc_start: 0.8660 (pttt) cc_final: 0.8343 (tmtt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2205 time to fit residues: 36.1734 Evaluate side-chains 71 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 0.0370 chunk 172 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 3.1464 ------------------------------------------------------------------------------- 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** C 203 ASN ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS E 391 GLN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.066224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048326 restraints weight = 93426.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.050178 restraints weight = 52932.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051459 restraints weight = 34995.759| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.308 15181 Z= 0.212 Angle : 0.694 13.393 20649 Z= 0.357 Chirality : 0.045 0.198 2205 Planarity : 0.005 0.089 2656 Dihedral : 6.829 81.382 2143 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.37 % 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: -0.44 (0.19), residues: 1903 helix: 0.82 (0.25), residues: 411 sheet: -0.52 (0.30), residues: 248 loop : -0.61 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 992 HIS 0.009 0.001 HIS D 347 PHE 0.012 0.002 PHE E 821 TYR 0.016 0.002 TYR D 465 ARG 0.008 0.001 ARG D 318 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 5) link_NAG-ASN : angle 1.99956 ( 15) hydrogen bonds : bond 0.03759 ( 577) hydrogen bonds : angle 5.80066 ( 1704) SS BOND : bond 0.00543 ( 53) SS BOND : angle 1.23325 ( 106) covalent geometry : bond 0.00473 (15118) covalent geometry : angle 0.68780 (20528) Misc. bond : bond 0.14368 ( 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 97 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8377 (pt0) cc_final: 0.7854 (tm-30) REVERT: A 104 CYS cc_start: 0.9093 (m) cc_final: 0.8113 (t) REVERT: B 19 ASN cc_start: 0.9264 (m-40) cc_final: 0.8884 (t0) REVERT: B 141 LEU cc_start: 0.9214 (tp) cc_final: 0.8945 (tp) REVERT: C 179 MET cc_start: 0.9014 (ttm) cc_final: 0.8527 (tmm) REVERT: C 203 ASN cc_start: 0.7979 (m110) cc_final: 0.7665 (m-40) REVERT: C 343 MET cc_start: 0.8232 (ppp) cc_final: 0.7913 (ppp) REVERT: C 349 ASP cc_start: 0.7958 (t0) cc_final: 0.7568 (t0) REVERT: D 659 MET cc_start: 0.8675 (tpp) cc_final: 0.8393 (tpt) REVERT: E 786 MET cc_start: 0.8687 (pmm) cc_final: 0.8139 (pmm) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2236 time to fit residues: 35.9113 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 : 1.898 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.067058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049253 restraints weight = 91275.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051176 restraints weight = 50775.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052512 restraints weight = 33275.512| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 15181 Z= 0.145 Angle : 0.624 11.198 20649 Z= 0.321 Chirality : 0.044 0.175 2205 Planarity : 0.004 0.065 2656 Dihedral : 6.485 81.677 2143 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.19), residues: 1903 helix: 1.09 (0.26), residues: 411 sheet: -0.70 (0.29), residues: 259 loop : -0.51 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 958 HIS 0.006 0.001 HIS D 347 PHE 0.011 0.001 PHE A 98 TYR 0.011 0.001 TYR D 427 ARG 0.006 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 5) link_NAG-ASN : angle 1.45250 ( 15) hydrogen bonds : bond 0.03445 ( 577) hydrogen bonds : angle 5.48016 ( 1704) SS BOND : bond 0.00296 ( 53) SS BOND : angle 1.13838 ( 106) covalent geometry : bond 0.00334 (15118) covalent geometry : angle 0.61920 (20528) Misc. bond : bond 0.10402 ( 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 102 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8386 (pt0) cc_final: 0.7855 (tm-30) REVERT: A 104 CYS cc_start: 0.9080 (m) cc_final: 0.8076 (t) REVERT: B 19 ASN cc_start: 0.9243 (m-40) cc_final: 0.8781 (t0) REVERT: B 52 ASP cc_start: 0.8957 (m-30) cc_final: 0.8499 (p0) REVERT: B 106 LEU cc_start: 0.9286 (tt) cc_final: 0.8867 (pp) REVERT: B 141 LEU cc_start: 0.9099 (tp) cc_final: 0.8811 (tp) REVERT: C 179 MET cc_start: 0.8879 (ttm) cc_final: 0.8448 (tmm) REVERT: C 343 MET cc_start: 0.8112 (ppp) cc_final: 0.7827 (ppp) REVERT: C 349 ASP cc_start: 0.8113 (t0) cc_final: 0.7620 (t0) REVERT: D 659 MET cc_start: 0.8648 (tpp) cc_final: 0.8378 (tpt) REVERT: E 507 PHE cc_start: 0.7869 (t80) cc_final: 0.7649 (t80) REVERT: E 786 MET cc_start: 0.8857 (pmm) cc_final: 0.8300 (pmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2018 time to fit residues: 34.6092 Evaluate side-chains 72 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 150 optimal weight: 0.0040 chunk 94 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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** C 203 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.067847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050041 restraints weight = 90468.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051988 restraints weight = 50385.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.053331 restraints weight = 32959.399| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 15181 Z= 0.117 Angle : 0.597 9.108 20649 Z= 0.306 Chirality : 0.043 0.186 2205 Planarity : 0.004 0.063 2656 Dihedral : 6.230 81.161 2143 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.18 (0.19), residues: 1903 helix: 1.25 (0.26), residues: 411 sheet: -0.52 (0.30), residues: 230 loop : -0.49 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 958 HIS 0.006 0.001 HIS D 347 PHE 0.009 0.001 PHE A 98 TYR 0.012 0.001 TYR D 465 ARG 0.004 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 5) link_NAG-ASN : angle 1.32132 ( 15) hydrogen bonds : bond 0.03270 ( 577) hydrogen bonds : angle 5.24003 ( 1704) SS BOND : bond 0.00324 ( 53) SS BOND : angle 1.06031 ( 106) covalent geometry : bond 0.00273 (15118) covalent geometry : angle 0.59273 (20528) Misc. bond : bond 0.07585 ( 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 98 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8402 (pt0) cc_final: 0.7921 (tm-30) REVERT: A 104 CYS cc_start: 0.9095 (m) cc_final: 0.8094 (t) REVERT: B 19 ASN cc_start: 0.9237 (m-40) cc_final: 0.8784 (t0) REVERT: B 52 ASP cc_start: 0.8972 (m-30) cc_final: 0.8485 (p0) REVERT: B 99 ASP cc_start: 0.8852 (t0) cc_final: 0.8652 (t0) REVERT: B 106 LEU cc_start: 0.9287 (tt) cc_final: 0.8948 (pp) REVERT: B 141 LEU cc_start: 0.9041 (tp) cc_final: 0.8727 (tp) REVERT: C 179 MET cc_start: 0.8868 (ttm) cc_final: 0.8413 (tmm) REVERT: C 349 ASP cc_start: 0.8079 (t0) cc_final: 0.7649 (t0) REVERT: D 620 LEU cc_start: 0.9705 (tp) cc_final: 0.9487 (tt) REVERT: D 659 MET cc_start: 0.8718 (tpp) cc_final: 0.8425 (tpt) REVERT: E 786 MET cc_start: 0.8812 (pmm) cc_final: 0.8289 (pmm) REVERT: E 884 MET cc_start: 0.4132 (ppp) cc_final: 0.3878 (ppp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2066 time to fit residues: 34.2770 Evaluate side-chains 74 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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: 0.4980 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 876 ASN E 357 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.067131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049310 restraints weight = 91027.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051196 restraints weight = 50933.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052492 restraints weight = 33506.294| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 15181 Z= 0.144 Angle : 0.613 11.187 20649 Z= 0.315 Chirality : 0.044 0.189 2205 Planarity : 0.004 0.064 2656 Dihedral : 6.310 85.435 2143 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.27 (0.19), residues: 1903 helix: 1.24 (0.26), residues: 410 sheet: -0.76 (0.28), residues: 255 loop : -0.53 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 958 HIS 0.008 0.001 HIS D 347 PHE 0.013 0.001 PHE E 507 TYR 0.009 0.001 TYR D 427 ARG 0.007 0.001 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 5) link_NAG-ASN : angle 1.52255 ( 15) hydrogen bonds : bond 0.03340 ( 577) hydrogen bonds : angle 5.30428 ( 1704) SS BOND : bond 0.00269 ( 53) SS BOND : angle 1.15419 ( 106) covalent geometry : bond 0.00335 (15118) covalent geometry : angle 0.60825 (20528) Misc. bond : bond 0.10473 ( 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 95 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8407 (pt0) cc_final: 0.7916 (tm-30) REVERT: A 104 CYS cc_start: 0.9172 (m) cc_final: 0.8198 (t) REVERT: B 19 ASN cc_start: 0.9285 (m-40) cc_final: 0.8844 (t0) REVERT: B 52 ASP cc_start: 0.9062 (m-30) cc_final: 0.8570 (p0) REVERT: B 106 LEU cc_start: 0.9267 (tt) cc_final: 0.9007 (pp) REVERT: C 179 MET cc_start: 0.8942 (ttm) cc_final: 0.8433 (tmm) REVERT: C 343 MET cc_start: 0.7642 (ptt) cc_final: 0.7300 (ptt) REVERT: C 349 ASP cc_start: 0.8263 (t0) cc_final: 0.7826 (t0) REVERT: D 620 LEU cc_start: 0.9703 (tp) cc_final: 0.9471 (tt) REVERT: D 659 MET cc_start: 0.8676 (tpp) cc_final: 0.8423 (tpt) REVERT: D 888 MET cc_start: 0.3418 (tpt) cc_final: 0.3012 (tpt) REVERT: E 786 MET cc_start: 0.8852 (pmm) cc_final: 0.8276 (pmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2074 time to fit residues: 33.1619 Evaluate side-chains 76 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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: 5.9990 chunk 80 optimal weight: 0.3980 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 D 618 HIS ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.068096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050286 restraints weight = 89994.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052207 restraints weight = 50428.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.053536 restraints weight = 33101.038| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 15181 Z= 0.111 Angle : 0.588 8.836 20649 Z= 0.300 Chirality : 0.043 0.186 2205 Planarity : 0.004 0.064 2656 Dihedral : 6.105 84.119 2143 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.13 (0.19), residues: 1903 helix: 1.37 (0.26), residues: 411 sheet: -0.65 (0.30), residues: 233 loop : -0.45 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 958 HIS 0.004 0.001 HIS A 72 PHE 0.009 0.001 PHE E 438 TYR 0.013 0.001 TYR D 465 ARG 0.004 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 5) link_NAG-ASN : angle 1.30924 ( 15) hydrogen bonds : bond 0.03157 ( 577) hydrogen bonds : angle 5.14298 ( 1704) SS BOND : bond 0.00243 ( 53) SS BOND : angle 1.00803 ( 106) covalent geometry : bond 0.00262 (15118) covalent geometry : angle 0.58450 (20528) Misc. bond : bond 0.06963 ( 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 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8391 (pt0) cc_final: 0.7909 (tm-30) REVERT: A 104 CYS cc_start: 0.9135 (m) cc_final: 0.8135 (t) REVERT: B 19 ASN cc_start: 0.9244 (m-40) cc_final: 0.8777 (t0) REVERT: B 52 ASP cc_start: 0.9014 (m-30) cc_final: 0.8504 (p0) REVERT: B 106 LEU cc_start: 0.9239 (tt) cc_final: 0.8982 (pp) REVERT: B 141 LEU cc_start: 0.9019 (tp) cc_final: 0.8678 (tp) REVERT: C 179 MET cc_start: 0.8847 (ttm) cc_final: 0.8415 (tmm) REVERT: C 343 MET cc_start: 0.7492 (ptt) cc_final: 0.7205 (ptt) REVERT: C 349 ASP cc_start: 0.8259 (t0) cc_final: 0.7758 (t0) REVERT: D 342 ILE cc_start: 0.8867 (mp) cc_final: 0.8581 (tp) REVERT: D 450 TRP cc_start: 0.8542 (m-10) cc_final: 0.8227 (m-10) REVERT: D 659 MET cc_start: 0.8783 (tpp) cc_final: 0.8453 (tpt) REVERT: D 888 MET cc_start: 0.4220 (tpt) cc_final: 0.3912 (tpt) REVERT: E 786 MET cc_start: 0.8761 (pmm) cc_final: 0.8216 (pmm) REVERT: E 884 MET cc_start: 0.3856 (ppp) cc_final: 0.3549 (ppp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2088 time to fit residues: 36.3864 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 : 1.522 ------------------------------------------------------------------------------- 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: 0.0170 chunk 178 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 HIS ** E 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.067715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049910 restraints weight = 89523.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051838 restraints weight = 49853.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053163 restraints weight = 32654.763| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 15181 Z= 0.122 Angle : 0.590 9.316 20649 Z= 0.301 Chirality : 0.043 0.180 2205 Planarity : 0.004 0.062 2656 Dihedral : 6.107 84.350 2143 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.19), residues: 1903 helix: 1.39 (0.26), residues: 410 sheet: -0.72 (0.30), residues: 231 loop : -0.47 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 958 HIS 0.006 0.001 HIS D 347 PHE 0.012 0.001 PHE E 507 TYR 0.008 0.001 TYR E 580 ARG 0.005 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 5) link_NAG-ASN : angle 1.40374 ( 15) hydrogen bonds : bond 0.03191 ( 577) hydrogen bonds : angle 5.10950 ( 1704) SS BOND : bond 0.00241 ( 53) SS BOND : angle 1.04135 ( 106) covalent geometry : bond 0.00288 (15118) covalent geometry : angle 0.58572 (20528) Misc. bond : bond 0.08029 ( 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 101 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8389 (pt0) cc_final: 0.7877 (tm-30) REVERT: A 104 CYS cc_start: 0.9141 (m) cc_final: 0.8176 (t) REVERT: B 19 ASN cc_start: 0.9220 (m-40) cc_final: 0.8747 (t0) REVERT: B 52 ASP cc_start: 0.9036 (m-30) cc_final: 0.8555 (p0) REVERT: B 99 ASP cc_start: 0.8748 (t0) cc_final: 0.8459 (t0) REVERT: B 103 PHE cc_start: 0.9053 (m-10) cc_final: 0.8754 (m-80) REVERT: B 106 LEU cc_start: 0.9233 (tt) cc_final: 0.8866 (pp) REVERT: C 179 MET cc_start: 0.8827 (ttm) cc_final: 0.8400 (tmm) REVERT: D 342 ILE cc_start: 0.8804 (mp) cc_final: 0.8495 (tp) REVERT: D 659 MET cc_start: 0.8754 (tpp) cc_final: 0.8455 (tpt) REVERT: D 888 MET cc_start: 0.4017 (tpt) cc_final: 0.3685 (tpt) REVERT: E 786 MET cc_start: 0.8783 (pmm) cc_final: 0.8215 (pmm) REVERT: E 884 MET cc_start: 0.3906 (ppp) cc_final: 0.3642 (ppp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2137 time to fit residues: 35.5044 Evaluate side-chains 78 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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: 0.7980 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 68 optimal weight: 0.0000 chunk 26 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN D 464 HIS D 618 HIS E 754 HIS ** E 876 ASN ** 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 = 0.3634 r_free = 0.3634 target = 0.068125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050344 restraints weight = 89751.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.052299 restraints weight = 50128.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.053642 restraints weight = 32822.216| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 15181 Z= 0.109 Angle : 0.584 8.439 20649 Z= 0.298 Chirality : 0.043 0.176 2205 Planarity : 0.004 0.063 2656 Dihedral : 6.020 83.831 2143 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.19), residues: 1903 helix: 1.42 (0.26), residues: 413 sheet: -0.67 (0.30), residues: 231 loop : -0.45 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 958 HIS 0.004 0.001 HIS D 347 PHE 0.009 0.001 PHE E 438 TYR 0.009 0.001 TYR D 465 ARG 0.004 0.000 ARG D 476 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 5) link_NAG-ASN : angle 1.31385 ( 15) hydrogen bonds : bond 0.03141 ( 577) hydrogen bonds : angle 5.03842 ( 1704) SS BOND : bond 0.00252 ( 53) SS BOND : angle 1.00884 ( 106) covalent geometry : bond 0.00256 (15118) covalent geometry : angle 0.57990 (20528) Misc. bond : bond 0.06684 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4135.05 seconds wall clock time: 73 minutes 45.74 seconds (4425.74 seconds total)