Starting phenix.real_space_refine on Tue Dec 31 06:03:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fmu_50570/12_2024/9fmu_50570.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fmu_50570/12_2024/9fmu_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_50570/12_2024/9fmu_50570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fmu_50570/12_2024/9fmu_50570.map" model { file = "/net/cci-nas-00/data/ceres_data/9fmu_50570/12_2024/9fmu_50570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fmu_50570/12_2024/9fmu_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-5532/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: 8.60, per 1000 atoms: 0.58 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: 4.67 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: 2.17 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: 6.75 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6026 1.39 - 1.56: 8929 1.56 - 1.73: 7 1.73 - 1.90: 148 1.90 - 2.07: 8 Bond restraints: 15118 Sorted by residual: bond pdb=" CB CYS D 577 " pdb=" SG CYS D 577 " ideal model delta sigma weight residual 1.808 1.701 0.107 3.30e-02 9.18e+02 1.04e+01 bond pdb=" CB CYS D 228 " pdb=" SG CYS D 228 " ideal model delta sigma weight residual 1.808 1.714 0.094 3.30e-02 9.18e+02 8.07e+00 bond pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 1.808 1.716 0.092 3.30e-02 9.18e+02 7.81e+00 bond pdb=" CB CYS D 895 " pdb=" SG CYS D 895 " ideal model delta sigma weight residual 1.808 1.723 0.085 3.30e-02 9.18e+02 6.65e+00 bond pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.15e+00 ... (remaining 15113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 20295 4.22 - 8.45: 196 8.45 - 12.67: 27 12.67 - 16.89: 7 16.89 - 21.11: 3 Bond angle restraints: 20528 Sorted by residual: angle pdb=" CA CYS D 557 " pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " ideal model delta sigma weight residual 114.40 135.51 -21.11 2.30e+00 1.89e-01 8.43e+01 angle pdb=" CA CYS E 547 " pdb=" CB CYS E 547 " pdb=" SG CYS E 547 " ideal model delta sigma weight residual 114.40 132.19 -17.79 2.30e+00 1.89e-01 5.98e+01 angle pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " pdb=" SG CYS D 547 " ideal model delta sigma weight residual 114.40 131.94 -17.54 2.30e+00 1.89e-01 5.81e+01 angle pdb=" CA CYS D 516 " pdb=" CB CYS D 516 " pdb=" SG CYS D 516 " ideal model delta sigma weight residual 114.40 129.79 -15.39 2.30e+00 1.89e-01 4.48e+01 angle pdb=" C CYS D 547 " pdb=" CA CYS D 547 " pdb=" CB CYS D 547 " ideal model delta sigma weight residual 109.54 120.92 -11.38 1.84e+00 2.95e-01 3.83e+01 ... (remaining 20523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8260 17.77 - 35.54: 581 35.54 - 53.30: 112 53.30 - 71.07: 32 71.07 - 88.84: 17 Dihedral angle restraints: 9002 sinusoidal: 3631 harmonic: 5371 Sorted by residual: dihedral pdb=" CB CYS D 835 " pdb=" SG CYS D 835 " pdb=" SG CYS D 869 " pdb=" CB CYS D 869 " ideal model delta sinusoidal sigma weight residual 93.00 169.99 -76.99 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CB CYS D 335 " pdb=" SG CYS D 335 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 23.89 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 248 " pdb=" CB CYS D 248 " ideal model delta sinusoidal sigma weight residual 93.00 25.60 67.40 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 8999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2000 0.103 - 0.207: 177 0.207 - 0.310: 19 0.310 - 0.413: 7 0.413 - 0.516: 2 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA CYS D 547 " pdb=" N CYS D 547 " pdb=" C CYS D 547 " pdb=" CB CYS D 547 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA CYS E 547 " pdb=" N CYS E 547 " pdb=" C CYS E 547 " pdb=" CB CYS E 547 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA CYS D 228 " pdb=" N CYS D 228 " pdb=" C CYS D 228 " pdb=" CB CYS D 228 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2202 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 102 " -0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ASN B 102 " 0.094 2.00e-02 2.50e+03 pdb=" O ASN B 102 " -0.035 2.00e-02 2.50e+03 pdb=" N PHE B 103 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 40 " 0.027 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C ARG B 40 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG B 40 " 0.035 2.00e-02 2.50e+03 pdb=" N PHE B 41 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 25 " 0.023 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLY A 25 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY A 25 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA A 26 " 0.026 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 160 2.55 - 3.14: 12275 3.14 - 3.72: 23995 3.72 - 4.31: 32449 4.31 - 4.90: 51821 Nonbonded interactions: 120700 Sorted by model distance: nonbonded pdb=" OD2 ASP D 225 " pdb="CA CA D2001 " model vdw 1.959 2.510 nonbonded pdb=" OH TYR D 424 " pdb=" O GLU D 467 " model vdw 1.979 3.040 nonbonded pdb=" OG SER E 879 " pdb=" OD1 ASP E 881 " model vdw 1.993 3.040 nonbonded pdb=" O GLY D 294 " pdb="CA CA D2002 " model vdw 2.104 2.510 nonbonded pdb=" OD1 ASP C 349 " pdb=" N THR C 350 " model vdw 2.124 3.120 ... (remaining 120695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.010 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.440 Find NCS groups from input model: 0.250 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- 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 : 0.005 0.107 15118 Z= 0.361 Angle : 1.182 21.112 20528 Z= 0.655 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 *********************** 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 : 1.743 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: 0.2731 time to fit residues: 81.7124 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 : 1.880 ------------------------------------------------------------------------------- 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: 3.9990 chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** B 139 ASN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 15118 Z= 0.442 Angle : 0.843 13.416 20528 Z= 0.444 Chirality : 0.050 0.227 2205 Planarity : 0.006 0.062 2656 Dihedral : 7.248 86.861 2143 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.19 % Allowed : 6.49 % Favored : 93.32 % 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: -0.50 (0.18), residues: 1903 helix: 0.14 (0.24), residues: 412 sheet: -0.30 (0.33), residues: 225 loop : -0.46 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 450 HIS 0.011 0.002 HIS B 92 PHE 0.021 0.003 PHE E 821 TYR 0.021 0.003 TYR D 354 ARG 0.008 0.001 ARG D 865 *********************** 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 112 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8662 (pt0) cc_final: 0.7930 (tm-30) REVERT: A 104 CYS cc_start: 0.9174 (m) cc_final: 0.8423 (t) REVERT: B 19 ASN cc_start: 0.9071 (m-40) cc_final: 0.8613 (t0) REVERT: B 65 LYS cc_start: 0.9731 (pptt) cc_final: 0.8991 (mmpt) REVERT: C 175 TRP cc_start: 0.9119 (p90) cc_final: 0.8382 (p90) REVERT: C 349 ASP cc_start: 0.8069 (t0) cc_final: 0.7756 (t0) REVERT: D 449 LEU cc_start: 0.9129 (pp) cc_final: 0.8447 (tp) REVERT: D 884 MET cc_start: 0.1222 (ppp) cc_final: 0.0467 (tmm) REVERT: D 931 LEU cc_start: 0.7358 (mm) cc_final: 0.7098 (mt) REVERT: D 961 ASP cc_start: 0.9457 (m-30) cc_final: 0.9131 (p0) REVERT: E 507 PHE cc_start: 0.8764 (t80) cc_final: 0.8251 (t80) REVERT: E 640 LYS cc_start: 0.8850 (pttt) cc_final: 0.8492 (tptp) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.2482 time to fit residues: 43.8270 Evaluate side-chains 79 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 171 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN D 250 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15118 Z= 0.261 Angle : 0.660 10.833 20528 Z= 0.346 Chirality : 0.045 0.173 2205 Planarity : 0.005 0.056 2656 Dihedral : 6.681 77.968 2143 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -0.25 (0.19), residues: 1903 helix: 0.66 (0.25), residues: 417 sheet: -0.31 (0.31), residues: 238 loop : -0.39 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 295 HIS 0.007 0.001 HIS D 347 PHE 0.017 0.002 PHE A 117 TYR 0.017 0.002 TYR D 427 ARG 0.013 0.001 ARG D 318 *********************** 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 105 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8622 (pt0) cc_final: 0.8176 (tm-30) REVERT: A 36 PHE cc_start: 0.9037 (m-80) cc_final: 0.8750 (m-10) REVERT: A 104 CYS cc_start: 0.9162 (m) cc_final: 0.8234 (t) REVERT: B 19 ASN cc_start: 0.9049 (m-40) cc_final: 0.8618 (t0) REVERT: B 141 LEU cc_start: 0.9353 (tp) cc_final: 0.9070 (tp) REVERT: C 179 MET cc_start: 0.9186 (ttm) cc_final: 0.8549 (tmm) REVERT: C 349 ASP cc_start: 0.7644 (t0) cc_final: 0.7178 (t0) REVERT: D 884 MET cc_start: 0.1350 (ppp) cc_final: 0.0630 (tmm) REVERT: E 507 PHE cc_start: 0.8685 (t80) cc_final: 0.8210 (t80) REVERT: E 884 MET cc_start: 0.5964 (tmm) cc_final: 0.5723 (ppp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2375 time to fit residues: 40.5716 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 : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 HIS ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN E 648 HIS E 876 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 15118 Z= 0.346 Angle : 0.720 14.577 20528 Z= 0.373 Chirality : 0.046 0.210 2205 Planarity : 0.005 0.065 2656 Dihedral : 7.069 85.918 2143 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % 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: -0.51 (0.19), residues: 1903 helix: 0.63 (0.25), residues: 411 sheet: -0.50 (0.31), residues: 244 loop : -0.63 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 992 HIS 0.010 0.002 HIS D 347 PHE 0.014 0.002 PHE D 283 TYR 0.019 0.002 TYR D 465 ARG 0.010 0.001 ARG D 392 *********************** 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: 2 poor density : 98 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8529 (pt0) cc_final: 0.8050 (tm-30) REVERT: A 104 CYS cc_start: 0.9118 (m) cc_final: 0.8202 (t) REVERT: C 187 THR cc_start: 0.9205 (m) cc_final: 0.8785 (t) REVERT: C 349 ASP cc_start: 0.7961 (t0) cc_final: 0.7531 (t0) REVERT: C 370 TYR cc_start: 0.7631 (m-80) cc_final: 0.7275 (m-10) REVERT: D 822 MET cc_start: 0.7046 (tmm) cc_final: 0.6743 (tmm) REVERT: D 888 MET cc_start: 0.4031 (tpt) cc_final: 0.3417 (tpt) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2179 time to fit residues: 36.3588 Evaluate side-chains 62 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 chunk 75 optimal weight: 0.3980 chunk 156 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN D 464 HIS D 946 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15118 Z= 0.208 Angle : 0.620 11.069 20528 Z= 0.320 Chirality : 0.044 0.162 2205 Planarity : 0.005 0.129 2656 Dihedral : 6.545 80.718 2143 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1903 helix: 1.04 (0.26), residues: 411 sheet: -0.43 (0.30), residues: 244 loop : -0.58 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 295 HIS 0.008 0.001 HIS D 347 PHE 0.015 0.001 PHE A 36 TYR 0.010 0.001 TYR D 427 ARG 0.007 0.000 ARG D 865 *********************** 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 104 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8530 (pt0) cc_final: 0.8057 (tm-30) REVERT: A 104 CYS cc_start: 0.9158 (m) cc_final: 0.8217 (t) REVERT: B 19 ASN cc_start: 0.8999 (m-40) cc_final: 0.8514 (t0) REVERT: B 99 ASP cc_start: 0.8581 (t0) cc_final: 0.8335 (t0) REVERT: B 106 LEU cc_start: 0.9400 (tt) cc_final: 0.9032 (pp) REVERT: C 179 MET cc_start: 0.9163 (ttm) cc_final: 0.8518 (tmm) REVERT: C 343 MET cc_start: 0.7913 (ppp) cc_final: 0.7547 (ppp) REVERT: C 349 ASP cc_start: 0.7964 (t0) cc_final: 0.7462 (t0) REVERT: D 822 MET cc_start: 0.7018 (tmm) cc_final: 0.6761 (tmm) REVERT: E 507 PHE cc_start: 0.8680 (t80) cc_final: 0.8354 (t80) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2132 time to fit residues: 37.4248 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 : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.0970 chunk 165 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 15118 Z= 0.155 Angle : 0.588 8.158 20528 Z= 0.301 Chirality : 0.043 0.159 2205 Planarity : 0.004 0.073 2656 Dihedral : 6.191 81.858 2143 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1903 helix: 1.42 (0.26), residues: 413 sheet: -0.44 (0.31), residues: 236 loop : -0.48 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 295 HIS 0.005 0.001 HIS A 72 PHE 0.010 0.001 PHE A 36 TYR 0.013 0.001 TYR D 465 ARG 0.005 0.000 ARG D 318 *********************** 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 119 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8548 (pt0) cc_final: 0.8041 (tm-30) REVERT: A 46 PHE cc_start: 0.8101 (m-10) cc_final: 0.7857 (m-80) REVERT: A 104 CYS cc_start: 0.9171 (m) cc_final: 0.8175 (t) REVERT: B 19 ASN cc_start: 0.9034 (m-40) cc_final: 0.8584 (t0) REVERT: B 52 ASP cc_start: 0.9110 (m-30) cc_final: 0.8698 (p0) REVERT: B 99 ASP cc_start: 0.8514 (t0) cc_final: 0.8269 (t0) REVERT: B 106 LEU cc_start: 0.9346 (tt) cc_final: 0.9005 (pp) REVERT: B 141 LEU cc_start: 0.9231 (tp) cc_final: 0.8907 (tp) REVERT: C 179 MET cc_start: 0.9133 (ttm) cc_final: 0.8556 (tmm) REVERT: C 349 ASP cc_start: 0.7921 (t0) cc_final: 0.7426 (t0) REVERT: C 370 TYR cc_start: 0.7478 (m-10) cc_final: 0.7275 (m-10) REVERT: D 822 MET cc_start: 0.6924 (tmm) cc_final: 0.6583 (tmm) REVERT: E 786 MET cc_start: 0.8314 (pmm) cc_final: 0.7848 (pmm) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2184 time to fit residues: 42.8903 Evaluate side-chains 75 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 618 HIS E 391 GLN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15118 Z= 0.177 Angle : 0.585 9.332 20528 Z= 0.301 Chirality : 0.043 0.183 2205 Planarity : 0.004 0.062 2656 Dihedral : 6.143 81.798 2143 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1903 helix: 1.41 (0.26), residues: 412 sheet: -0.48 (0.30), residues: 238 loop : -0.42 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 295 HIS 0.007 0.001 HIS D 347 PHE 0.015 0.001 PHE E 507 TYR 0.008 0.001 TYR D 354 ARG 0.005 0.000 ARG D 476 *********************** 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 106 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8582 (pt0) cc_final: 0.8056 (tm-30) REVERT: A 104 CYS cc_start: 0.9180 (m) cc_final: 0.8199 (t) REVERT: B 52 ASP cc_start: 0.9141 (m-30) cc_final: 0.8686 (p0) REVERT: B 106 LEU cc_start: 0.9332 (tt) cc_final: 0.9022 (pp) REVERT: C 179 MET cc_start: 0.9101 (ttm) cc_final: 0.8498 (tmm) REVERT: C 343 MET cc_start: 0.7697 (ptt) cc_final: 0.7262 (ptt) REVERT: C 349 ASP cc_start: 0.8010 (t0) cc_final: 0.7451 (t0) REVERT: D 822 MET cc_start: 0.6930 (tmm) cc_final: 0.6550 (tmm) REVERT: D 888 MET cc_start: 0.4681 (tpt) cc_final: 0.4354 (tpt) REVERT: E 786 MET cc_start: 0.8457 (pmm) cc_final: 0.8024 (pmm) REVERT: E 884 MET cc_start: 0.4910 (ppp) cc_final: 0.4629 (ppp) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2377 time to fit residues: 42.0823 Evaluate side-chains 75 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15118 Z= 0.250 Angle : 0.631 12.663 20528 Z= 0.326 Chirality : 0.044 0.187 2205 Planarity : 0.004 0.070 2656 Dihedral : 6.427 85.847 2143 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -0.23 (0.19), residues: 1903 helix: 1.27 (0.26), residues: 411 sheet: -0.73 (0.28), residues: 270 loop : -0.49 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 295 HIS 0.011 0.001 HIS D 347 PHE 0.012 0.001 PHE D 283 TYR 0.011 0.001 TYR C 386 ARG 0.008 0.001 ARG D 476 *********************** 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 : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8585 (pt0) cc_final: 0.8108 (tm-30) REVERT: A 104 CYS cc_start: 0.9265 (m) cc_final: 0.8321 (t) REVERT: B 52 ASP cc_start: 0.9207 (m-30) cc_final: 0.8751 (p0) REVERT: C 179 MET cc_start: 0.9140 (ttm) cc_final: 0.8510 (tmm) REVERT: D 888 MET cc_start: 0.4160 (tpt) cc_final: 0.3797 (tpt) REVERT: E 786 MET cc_start: 0.8608 (pmm) cc_final: 0.8124 (pmm) REVERT: E 884 MET cc_start: 0.5223 (ppp) cc_final: 0.4983 (ppp) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2178 time to fit residues: 35.2277 Evaluate side-chains 67 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 HIS C 195 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15118 Z= 0.266 Angle : 0.648 12.992 20528 Z= 0.334 Chirality : 0.044 0.182 2205 Planarity : 0.005 0.065 2656 Dihedral : 6.554 83.444 2143 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1903 helix: 1.18 (0.26), residues: 408 sheet: -1.04 (0.29), residues: 251 loop : -0.59 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 295 HIS 0.013 0.001 HIS E 754 PHE 0.013 0.002 PHE E 507 TYR 0.018 0.002 TYR D 465 ARG 0.008 0.001 ARG D 476 *********************** 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 93 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 2.188 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8585 (pt0) cc_final: 0.8118 (tm-30) REVERT: A 104 CYS cc_start: 0.9198 (m) cc_final: 0.8326 (t) REVERT: A 116 GLU cc_start: 0.8883 (pm20) cc_final: 0.8643 (pm20) REVERT: B 52 ASP cc_start: 0.9273 (m-30) cc_final: 0.8802 (p0) REVERT: B 99 ASP cc_start: 0.8643 (t0) cc_final: 0.8342 (t0) REVERT: B 106 LEU cc_start: 0.9367 (tt) cc_final: 0.9039 (pp) REVERT: C 179 MET cc_start: 0.9138 (ttm) cc_final: 0.8505 (tmm) REVERT: D 329 TRP cc_start: 0.8789 (m100) cc_final: 0.8070 (m100) REVERT: E 786 MET cc_start: 0.8714 (pmm) cc_final: 0.8226 (pmm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2301 time to fit residues: 36.6402 Evaluate side-chains 69 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 15118 Z= 0.330 Angle : 0.696 14.288 20528 Z= 0.359 Chirality : 0.045 0.182 2205 Planarity : 0.005 0.063 2656 Dihedral : 6.948 89.859 2143 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.66 (0.19), residues: 1903 helix: 0.98 (0.26), residues: 405 sheet: -1.20 (0.28), residues: 264 loop : -0.75 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1013 HIS 0.012 0.002 HIS D 347 PHE 0.013 0.002 PHE D 283 TYR 0.013 0.002 TYR C 386 ARG 0.009 0.001 ARG D 476 ********************** 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 89 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.762 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8602 (pt0) cc_final: 0.8198 (tm-30) REVERT: A 136 LEU cc_start: 0.9643 (mm) cc_final: 0.9223 (tp) REVERT: B 52 ASP cc_start: 0.9383 (m-30) cc_final: 0.8893 (p0) REVERT: B 99 ASP cc_start: 0.8759 (t0) cc_final: 0.8469 (t0) REVERT: C 179 MET cc_start: 0.9148 (ttm) cc_final: 0.8507 (tmm) REVERT: D 329 TRP cc_start: 0.8768 (m100) cc_final: 0.7879 (m100) REVERT: D 420 LEU cc_start: 0.8400 (mm) cc_final: 0.8182 (mm) REVERT: D 465 TYR cc_start: 0.6974 (m-80) cc_final: 0.6462 (m-80) REVERT: D 888 MET cc_start: 0.4464 (tpt) cc_final: 0.4035 (tpt) REVERT: D 914 LEU cc_start: 0.9216 (pt) cc_final: 0.8886 (tt) REVERT: E 786 MET cc_start: 0.8829 (pmm) cc_final: 0.8305 (pmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2079 time to fit residues: 31.8911 Evaluate side-chains 70 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.067629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049952 restraints weight = 89556.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.051824 restraints weight = 50063.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053115 restraints weight = 32841.315| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.6567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 15118 Z= 0.165 Angle : 0.602 9.796 20528 Z= 0.308 Chirality : 0.044 0.168 2205 Planarity : 0.004 0.064 2656 Dihedral : 6.306 82.292 2143 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1903 helix: 1.33 (0.26), residues: 418 sheet: -0.82 (0.30), residues: 238 loop : -0.58 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 295 HIS 0.006 0.001 HIS A 72 PHE 0.018 0.001 PHE E 507 TYR 0.011 0.001 TYR E 580 ARG 0.003 0.000 ARG D 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.88 seconds wall clock time: 47 minutes 15.30 seconds (2835.30 seconds total)