Starting phenix.real_space_refine on Fri Aug 7 22:03:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29te_57361/08_2026/29te_57361.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 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 1 9.91 5 S 32 5.16 5 C 7413 2.51 5 N 1928 2.21 5 O 2336 1.98 5 H 11104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22814 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 14776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 14776 Classifications: {'peptide': 957} Link IDs: {'PCIS': 3, 'PTRANS': 71, 'TRANS': 882} Chain breaks: 1 Chain: "B" Number of atoms: 7655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7655 Classifications: {'peptide': 500} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 474} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {' CA': 1, 'BMA': 1, 'KIF': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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 Time building chain proxies: 3.99, per 1000 atoms: 0.17 Number of scatterers: 22814 At special positions: 0 Unit cell: (125.25, 125.25, 120.24, 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) Ca 1 19.99 S 32 16.00 O 2336 8.00 N 1928 7.00 C 7413 6.00 H 11104 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS A 647 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 963 " - pdb=" SG CYS A 985 " distance=2.03 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 86 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " MAN D 1 " - " MAN D 2 " " MAN F 1 " - " MAN F 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 520.7 milliseconds 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 14 sheets defined 36.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 63 through 88 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 122 through 136 removed outlier: 4.026A pdb=" N ILE A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Processing helix chain 'A' and resid 189 through 208 Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.617A pdb=" N ARG A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.700A pdb=" N TYR A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 Processing helix chain 'A' and resid 324 through 340 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.589A pdb=" N HIS A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 419 through 437 Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 467 through 477 removed outlier: 4.360A pdb=" N GLY A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 removed outlier: 3.737A pdb=" N LEU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 535 Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.611A pdb=" N LEU A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 removed outlier: 6.248A pdb=" N THR A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 585 " --> pdb=" O GLY A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.750A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 667 Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.623A pdb=" N ARG A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 748 through 755 removed outlier: 4.148A pdb=" N GLN A 752 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASN A 753 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 933 Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 986 through 994 removed outlier: 3.603A pdb=" N ILE A 994 " --> pdb=" O LYS A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 Processing helix chain 'A' and resid 1078 through 1082 removed outlier: 3.698A pdb=" N ILE A1081 " --> pdb=" O VAL A1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 38 removed outlier: 4.174A pdb=" N ASP B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.783A pdb=" N LYS B 54 " --> pdb=" O CYS B 50 " (cutoff:3.500A) Proline residue: B 58 - end of helix Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.579A pdb=" N CYS B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.586A pdb=" N GLU B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.615A pdb=" N ALA B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 190 removed outlier: 3.709A pdb=" N GLU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 226 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.525A pdb=" N GLY B 245 " --> pdb=" O TYR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 272 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 288 through 294 removed outlier: 4.014A pdb=" N GLY B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 361 through 369 removed outlier: 4.245A pdb=" N ASN B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 405 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 406 through 409 removed outlier: 4.588A pdb=" N ASP B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 409' Processing helix chain 'B' and resid 452 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.786A pdb=" N VAL A 187 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 301 through 303 removed outlier: 3.579A pdb=" N VAL A 351 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 363 removed outlier: 4.154A pdb=" N VAL A 450 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ASN A 449 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 440 Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA8, first strand: chain 'A' and resid 562 through 565 removed outlier: 3.840A pdb=" N GLY A 562 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLU A 570 " --> pdb=" O GLN A 564 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 745 through 746 Processing sheet with id=AB1, first strand: chain 'A' and resid 956 through 958 removed outlier: 5.847A pdb=" N ILE A 978 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1010 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 980 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A1007 " --> pdb=" O VAL A1045 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A1047 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A1009 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 823 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A1068 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A1062 " --> pdb=" O LEU A 829 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.868A pdb=" N ILE B 24 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP B 78 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 42 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 77 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU B 44 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB4, first strand: chain 'B' and resid 282 through 283 removed outlier: 5.145A pdb=" N ILE B 282 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 251 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.907A pdb=" N ASP B 417 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 376 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 378 " --> pdb=" O LYS B 434 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1089 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: 4.99 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11099 1.03 - 1.23: 21 1.23 - 1.42: 5034 1.42 - 1.62: 6892 1.62 - 1.81: 50 Bond restraints: 23096 Sorted by residual: bond pdb=" C SER A1019 " pdb=" N GLY A1020 " ideal model delta sigma weight residual 1.335 1.326 0.009 7.50e-03 1.78e+04 1.35e+00 bond pdb=" CA GLY A 693 " pdb=" C GLY A 693 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.23e+00 bond pdb=" CA VAL A 74 " pdb=" HA VAL A 74 " ideal model delta sigma weight residual 0.970 0.948 0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CA TRP B 384 " pdb=" CB TRP B 384 " ideal model delta sigma weight residual 1.536 1.520 0.016 1.58e-02 4.01e+03 1.03e+00 bond pdb=" N GLY A 693 " pdb=" CA GLY A 693 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.02e+00 ... (remaining 23091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 39327 1.22 - 2.43: 2151 2.43 - 3.65: 177 3.65 - 4.86: 26 4.86 - 6.08: 4 Bond angle restraints: 41685 Sorted by residual: angle pdb=" N VAL A 637 " pdb=" CA VAL A 637 " pdb=" C VAL A 637 " ideal model delta sigma weight residual 110.42 115.27 -4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" N SER B 497 " pdb=" CA SER B 497 " pdb=" CB SER B 497 " ideal model delta sigma weight residual 114.17 110.42 3.75 1.14e+00 7.69e-01 1.08e+01 angle pdb=" N THR A 636 " pdb=" CA THR A 636 " pdb=" C THR A 636 " ideal model delta sigma weight residual 108.07 112.42 -4.35 1.38e+00 5.25e-01 9.94e+00 angle pdb=" N ARG A 179 " pdb=" CA ARG A 179 " pdb=" C ARG A 179 " ideal model delta sigma weight residual 112.97 109.69 3.28 1.06e+00 8.90e-01 9.59e+00 angle pdb=" CA ARG A 151 " pdb=" CB ARG A 151 " pdb=" CG ARG A 151 " ideal model delta sigma weight residual 114.10 120.18 -6.08 2.00e+00 2.50e-01 9.24e+00 ... (remaining 41680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 10386 17.34 - 34.68: 706 34.68 - 52.01: 227 52.01 - 69.35: 74 69.35 - 86.69: 17 Dihedral angle restraints: 11410 sinusoidal: 6482 harmonic: 4928 Sorted by residual: dihedral pdb=" CA THR A 636 " pdb=" C THR A 636 " pdb=" N VAL A 637 " pdb=" CA VAL A 637 " ideal model delta harmonic sigma weight residual -180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS A 963 " pdb=" SG CYS A 963 " pdb=" SG CYS A 985 " pdb=" CB CYS A 985 " ideal model delta sinusoidal sigma weight residual 93.00 47.50 45.50 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CA PHE A 747 " pdb=" C PHE A 747 " pdb=" N MET A 748 " pdb=" CA MET A 748 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 11407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1219 0.032 - 0.064: 460 0.064 - 0.095: 103 0.095 - 0.127: 87 0.127 - 0.159: 6 Chirality restraints: 1875 Sorted by residual: chirality pdb=" CA ILE B 246 " pdb=" N ILE B 246 " pdb=" C ILE B 246 " pdb=" CB ILE B 246 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE B 413 " pdb=" N ILE B 413 " pdb=" C ILE B 413 " pdb=" CB ILE B 413 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE A 980 " pdb=" N ILE A 980 " pdb=" C ILE A 980 " pdb=" CB ILE A 980 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 1872 not shown) Planarity restraints: 3440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 595 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO A 596 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 724 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 725 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 725 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 725 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 194 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" C ILE A 194 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 194 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 195 " 0.011 2.00e-02 2.50e+03 ... (remaining 3437 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 9093 2.37 - 2.93: 53621 2.93 - 3.48: 60971 3.48 - 4.04: 81905 4.04 - 4.60: 121164 Nonbonded interactions: 326754 Sorted by model distance: nonbonded pdb="HE21 GLN A 752 " pdb=" OE1 GLU A 755 " model vdw 1.810 2.450 nonbonded pdb="HE21 GLN A 328 " pdb="HH22 ARG A 332 " model vdw 1.817 2.100 nonbonded pdb="HD21 ASN A 120 " pdb=" HG SER A 185 " model vdw 1.821 2.100 nonbonded pdb=" HZ2 TRP B 384 " pdb=" HE2 PHE B 430 " model vdw 1.866 2.100 nonbonded pdb=" H SER A 122 " pdb=" HH TYR A 164 " model vdw 1.870 2.100 ... (remaining 326749 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'H' } 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 individual isotropic 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: 0.550 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: 0.130 Extract box with map and model: 0.260 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.330 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 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 : 0.003 0.029 12011 Z= 0.148 Angle : 0.653 6.450 16371 Z= 0.373 Chirality : 0.040 0.159 1875 Planarity : 0.004 0.049 2084 Dihedral : 11.504 86.688 4896 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1451 helix: 0.50 (0.25), residues: 465 sheet: -1.19 (0.47), residues: 129 loop : -0.95 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.017 0.001 TYR B 395 PHE 0.014 0.001 PHE A 77 TRP 0.031 0.001 TRP A 427 HIS 0.007 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (11992) covalent geometry : angle 0.64179 / 0.37 (16318) SS BOND : bond 0.00259 / 0.17 ( 4) SS BOND : angle 0.88639 / 0.49 ( 8) hydrogen bonds : bond 0.16401 / 11.12 ( 391) hydrogen bonds : angle 8.18240 / 5.97 ( 1089) link_ALPHA1-3 : bond 0.01064 / 0.70 ( 3) link_ALPHA1-3 : angle 1.45275 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00787 / 0.55 ( 2) link_ALPHA1-6 : angle 1.47140 / 1.04 ( 6) link_BETA1-4 : bond 0.00751 / 0.41 ( 10) link_BETA1-4 : angle 2.72723 / 1.68 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.9100 (tpt) cc_final: 0.8654 (tpt) REVERT: B 428 MET cc_start: 0.5226 (ptt) cc_final: 0.4837 (ptt) REVERT: B 462 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8619 (pt0) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.2264 time to fit residues: 31.6188 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 477 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 50.0000 chunk 55 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.119165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.091142 restraints weight = 93862.396| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 6.42 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12011 Z= 0.237 Angle : 0.658 9.658 16371 Z= 0.339 Chirality : 0.042 0.166 1875 Planarity : 0.005 0.051 2084 Dihedral : 5.830 59.978 2195 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.49 % Allowed : 3.21 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.22), residues: 1451 helix: 0.04 (0.23), residues: 473 sheet: -1.54 (0.43), residues: 142 loop : -1.06 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 574 TYR 0.018 0.002 TYR A 79 PHE 0.024 0.002 PHE A 77 TRP 0.015 0.002 TRP A 427 HIS 0.007 0.002 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 (11992) covalent geometry : angle 0.65174 / 0.34 (16318) SS BOND : bond 0.00204 / 0.10 ( 4) SS BOND : angle 1.07863 / 0.61 ( 8) hydrogen bonds : bond 0.04943 / 3.37 ( 391) hydrogen bonds : angle 7.03827 / 5.08 ( 1089) link_ALPHA1-3 : bond 0.00745 / 0.52 ( 3) link_ALPHA1-3 : angle 1.53631 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00476 / 0.34 ( 2) link_ALPHA1-6 : angle 1.81842 / 1.37 ( 6) link_BETA1-4 : bond 0.00466 / 0.27 ( 10) link_BETA1-4 : angle 1.83655 / 1.21 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.9121 (tpt) cc_final: 0.8636 (tpt) REVERT: B 365 TYR cc_start: 0.6923 (t80) cc_final: 0.6608 (t80) REVERT: B 428 MET cc_start: 0.5406 (ptt) cc_final: 0.5068 (ptt) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.2373 time to fit residues: 27.9747 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain B residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 21 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 144 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.122478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.091671 restraints weight = 99588.897| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 6.92 r_work: 0.4197 rms_B_bonded: 6.80 restraints_weight: 2.0000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12011 Z= 0.131 Angle : 0.560 6.870 16371 Z= 0.285 Chirality : 0.040 0.155 1875 Planarity : 0.004 0.047 2084 Dihedral : 5.553 51.928 2193 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.25 % Allowed : 4.53 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1451 helix: 0.37 (0.24), residues: 465 sheet: -1.15 (0.46), residues: 133 loop : -1.06 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.012 0.001 TYR A 79 PHE 0.013 0.001 PHE A 77 TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11992) covalent geometry : angle 0.55382 / 0.28 (16318) SS BOND : bond 0.00344 / 0.24 ( 4) SS BOND : angle 0.68635 / 0.51 ( 8) hydrogen bonds : bond 0.04344 / 2.93 ( 391) hydrogen bonds : angle 6.66300 / 4.79 ( 1089) link_ALPHA1-3 : bond 0.00608 / 0.41 ( 3) link_ALPHA1-3 : angle 1.48869 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00412 / 0.29 ( 2) link_ALPHA1-6 : angle 1.76365 / 1.32 ( 6) link_BETA1-4 : bond 0.00417 / 0.21 ( 10) link_BETA1-4 : angle 1.71214 / 1.15 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6141 (mt-10) REVERT: B 122 MET cc_start: 0.9243 (tpt) cc_final: 0.8729 (tpt) outliers start: 3 outliers final: 3 residues processed: 77 average time/residue: 0.2361 time to fit residues: 26.9931 Evaluate side-chains 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 462 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 87 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 84 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 0.2980 chunk 102 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.123748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.092948 restraints weight = 98416.990| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 6.89 r_work: 0.4231 rms_B_bonded: 6.79 restraints_weight: 2.0000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12011 Z= 0.115 Angle : 0.535 5.731 16371 Z= 0.271 Chirality : 0.040 0.149 1875 Planarity : 0.004 0.045 2084 Dihedral : 5.346 50.573 2193 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.41 % Allowed : 4.36 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1451 helix: 0.51 (0.24), residues: 466 sheet: -1.07 (0.46), residues: 133 loop : -1.03 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.017 0.001 TYR B 365 PHE 0.012 0.001 PHE A 77 TRP 0.010 0.001 TRP A 427 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11992) covalent geometry : angle 0.52867 / 0.27 (16318) SS BOND : bond 0.00385 / 0.27 ( 4) SS BOND : angle 0.71583 / 0.58 ( 8) hydrogen bonds : bond 0.03822 / 2.57 ( 391) hydrogen bonds : angle 6.37945 / 4.57 ( 1089) link_ALPHA1-3 : bond 0.00554 / 0.37 ( 3) link_ALPHA1-3 : angle 1.47692 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00410 / 0.29 ( 2) link_ALPHA1-6 : angle 1.68410 / 1.23 ( 6) link_BETA1-4 : bond 0.00397 / 0.21 ( 10) link_BETA1-4 : angle 1.61858 / 1.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 THR cc_start: 0.8020 (m) cc_final: 0.7816 (p) REVERT: B 122 MET cc_start: 0.9246 (tpt) cc_final: 0.8718 (tpt) REVERT: B 365 TYR cc_start: 0.6860 (t80) cc_final: 0.6632 (t80) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.2545 time to fit residues: 29.5087 Evaluate side-chains 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 56 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 92 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 27 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4892 r_free = 0.4892 target = 0.123939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.093283 restraints weight = 98096.028| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 6.86 r_work: 0.4232 rms_B_bonded: 6.73 restraints_weight: 2.0000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12011 Z= 0.117 Angle : 0.528 6.293 16371 Z= 0.267 Chirality : 0.040 0.143 1875 Planarity : 0.004 0.045 2084 Dihedral : 5.258 51.432 2193 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.33 % Allowed : 4.94 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1451 helix: 0.56 (0.24), residues: 467 sheet: -1.09 (0.46), residues: 134 loop : -1.01 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.013 0.001 TYR A 531 PHE 0.009 0.001 PHE A 77 TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (11992) covalent geometry : angle 0.52249 / 0.27 (16318) SS BOND : bond 0.00506 / 0.36 ( 4) SS BOND : angle 0.82646 / 0.52 ( 8) hydrogen bonds : bond 0.03705 / 2.49 ( 391) hydrogen bonds : angle 6.24482 / 4.48 ( 1089) link_ALPHA1-3 : bond 0.00550 / 0.37 ( 3) link_ALPHA1-3 : angle 1.46340 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00433 / 0.30 ( 2) link_ALPHA1-6 : angle 1.65875 / 1.21 ( 6) link_BETA1-4 : bond 0.00392 / 0.21 ( 10) link_BETA1-4 : angle 1.56431 / 1.07 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.9213 (tpt) cc_final: 0.8676 (tpt) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.2514 time to fit residues: 28.5562 Evaluate side-chains 76 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 56 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 67 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4812 r_free = 0.4812 target = 0.115204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.086903 restraints weight = 94725.368| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 6.44 r_work: 0.4138 rms_B_bonded: 6.38 restraints_weight: 2.0000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12011 Z= 0.253 Angle : 0.656 8.366 16371 Z= 0.340 Chirality : 0.042 0.150 1875 Planarity : 0.005 0.051 2084 Dihedral : 5.869 59.195 2193 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.66 % Allowed : 5.43 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.21), residues: 1451 helix: -0.17 (0.23), residues: 473 sheet: -1.45 (0.44), residues: 140 loop : -1.24 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 574 TYR 0.022 0.003 TYR A 469 PHE 0.019 0.002 PHE A 334 TRP 0.013 0.002 TRP A 335 HIS 0.009 0.002 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (11992) covalent geometry : angle 0.65052 / 0.34 (16318) SS BOND : bond 0.00171 / 0.11 ( 4) SS BOND : angle 1.43722 / 0.76 ( 8) hydrogen bonds : bond 0.04551 / 3.11 ( 391) hydrogen bonds : angle 6.64079 / 4.75 ( 1089) link_ALPHA1-3 : bond 0.00600 / 0.42 ( 3) link_ALPHA1-3 : angle 1.48165 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00583 / 0.42 ( 2) link_ALPHA1-6 : angle 1.90842 / 1.46 ( 6) link_BETA1-4 : bond 0.00469 / 0.27 ( 10) link_BETA1-4 : angle 1.67763 / 1.08 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 MET cc_start: 0.9165 (tpt) cc_final: 0.8653 (tpt) REVERT: B 365 TYR cc_start: 0.6491 (t80) cc_final: 0.6280 (t80) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.2246 time to fit residues: 25.6700 Evaluate side-chains 78 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 456 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 69 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4848 r_free = 0.4848 target = 0.118827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.089854 restraints weight = 92721.436| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 6.21 r_work: 0.4195 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12011 Z= 0.139 Angle : 0.561 6.466 16371 Z= 0.287 Chirality : 0.040 0.139 1875 Planarity : 0.005 0.050 2084 Dihedral : 5.677 54.239 2193 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.74 % Allowed : 5.76 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.22), residues: 1451 helix: 0.22 (0.24), residues: 465 sheet: -1.41 (0.44), residues: 141 loop : -1.13 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 325 TYR 0.012 0.002 TYR B 365 PHE 0.012 0.001 PHE B 331 TRP 0.010 0.001 TRP A 493 HIS 0.005 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11992) covalent geometry : angle 0.55518 / 0.29 (16318) SS BOND : bond 0.00272 / 0.19 ( 4) SS BOND : angle 0.78669 / 0.49 ( 8) hydrogen bonds : bond 0.03843 / 2.58 ( 391) hydrogen bonds : angle 6.31462 / 4.51 ( 1089) link_ALPHA1-3 : bond 0.00584 / 0.39 ( 3) link_ALPHA1-3 : angle 1.48396 / 0.87 ( 9) link_ALPHA1-6 : bond 0.00473 / 0.33 ( 2) link_ALPHA1-6 : angle 1.73254 / 1.30 ( 6) link_BETA1-4 : bond 0.00388 / 0.19 ( 10) link_BETA1-4 : angle 1.57715 / 1.05 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7662 (mm-30) REVERT: A 313 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6200 (mt-10) REVERT: A 374 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7355 (tm-30) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.2015 time to fit residues: 23.9548 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 456 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 97 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 94 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4833 r_free = 0.4833 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.087315 restraints weight = 100812.564| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 6.44 r_work: 0.4151 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12011 Z= 0.173 Angle : 0.581 6.937 16371 Z= 0.298 Chirality : 0.040 0.135 1875 Planarity : 0.005 0.054 2084 Dihedral : 5.686 57.371 2193 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.66 % Allowed : 6.09 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.22), residues: 1451 helix: 0.16 (0.24), residues: 472 sheet: -1.40 (0.44), residues: 138 loop : -1.13 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 574 TYR 0.015 0.002 TYR B 365 PHE 0.011 0.001 PHE B 331 TRP 0.011 0.001 TRP A 335 HIS 0.004 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (11992) covalent geometry : angle 0.57508 / 0.30 (16318) SS BOND : bond 0.00215 / 0.15 ( 4) SS BOND : angle 1.14535 / 0.60 ( 8) hydrogen bonds : bond 0.03961 / 2.67 ( 391) hydrogen bonds : angle 6.33341 / 4.52 ( 1089) link_ALPHA1-3 : bond 0.00613 / 0.42 ( 3) link_ALPHA1-3 : angle 1.46429 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00521 / 0.37 ( 2) link_ALPHA1-6 : angle 1.73594 / 1.31 ( 6) link_BETA1-4 : bond 0.00398 / 0.20 ( 10) link_BETA1-4 : angle 1.55537 / 1.02 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 313 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6443 (mt-10) REVERT: A 374 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7438 (tm-30) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.2246 time to fit residues: 26.6244 Evaluate side-chains 80 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 456 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 87 optimal weight: 40.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4805 r_free = 0.4805 target = 0.113657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.085608 restraints weight = 98770.807| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 6.48 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12011 Z= 0.218 Angle : 0.636 9.019 16371 Z= 0.330 Chirality : 0.041 0.141 1875 Planarity : 0.005 0.060 2084 Dihedral : 6.096 59.121 2193 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.66 % Allowed : 6.26 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.22), residues: 1451 helix: -0.19 (0.23), residues: 477 sheet: -1.48 (0.44), residues: 138 loop : -1.26 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 325 TYR 0.019 0.002 TYR A 469 PHE 0.015 0.002 PHE A 334 TRP 0.013 0.002 TRP A 493 HIS 0.007 0.002 HIS A 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (11992) covalent geometry : angle 0.63006 / 0.33 (16318) SS BOND : bond 0.00129 / 0.07 ( 4) SS BOND : angle 1.42581 / 0.75 ( 8) hydrogen bonds : bond 0.04336 / 2.93 ( 391) hydrogen bonds : angle 6.47896 / 4.63 ( 1089) link_ALPHA1-3 : bond 0.00666 / 0.46 ( 3) link_ALPHA1-3 : angle 1.45303 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00601 / 0.43 ( 2) link_ALPHA1-6 : angle 1.79866 / 1.39 ( 6) link_BETA1-4 : bond 0.00440 / 0.22 ( 10) link_BETA1-4 : angle 1.62551 / 1.04 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: A 672 ARG cc_start: 0.8725 (ttp80) cc_final: 0.7803 (tpt170) outliers start: 8 outliers final: 7 residues processed: 73 average time/residue: 0.2787 time to fit residues: 29.6614 Evaluate side-chains 75 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 477 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4852 r_free = 0.4852 target = 0.118278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.087656 restraints weight = 98322.539| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 6.72 r_work: 0.4155 rms_B_bonded: 6.54 restraints_weight: 2.0000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12011 Z= 0.118 Angle : 0.568 8.152 16371 Z= 0.289 Chirality : 0.040 0.145 1875 Planarity : 0.005 0.059 2084 Dihedral : 5.751 52.561 2193 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.58 % Allowed : 6.50 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1451 helix: 0.19 (0.23), residues: 479 sheet: -1.27 (0.45), residues: 136 loop : -1.10 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 113 TYR 0.015 0.002 TYR A 668 PHE 0.014 0.001 PHE B 331 TRP 0.013 0.001 TRP A 706 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11992) covalent geometry : angle 0.56291 / 0.29 (16318) SS BOND : bond 0.00367 / 0.26 ( 4) SS BOND : angle 0.73740 / 0.50 ( 8) hydrogen bonds : bond 0.03679 / 2.44 ( 391) hydrogen bonds : angle 6.13161 / 4.38 ( 1089) link_ALPHA1-3 : bond 0.00582 / 0.39 ( 3) link_ALPHA1-3 : angle 1.50187 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00540 / 0.38 ( 2) link_ALPHA1-6 : angle 1.59250 / 1.17 ( 6) link_BETA1-4 : bond 0.00406 / 0.20 ( 10) link_BETA1-4 : angle 1.54230 / 1.04 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.9105 (mt) cc_final: 0.8779 (mm) REVERT: A 313 GLU cc_start: 0.6364 (mt-10) cc_final: 0.6129 (mt-10) REVERT: A 672 ARG cc_start: 0.8622 (ttp80) cc_final: 0.7690 (tpt170) outliers start: 7 outliers final: 7 residues processed: 78 average time/residue: 0.2607 time to fit residues: 30.2209 Evaluate side-chains 79 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 477 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 55 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 328 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 = 0.4828 r_free = 0.4828 target = 0.116478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.087650 restraints weight = 94943.386| |-----------------------------------------------------------------------------| r_work (start): 0.4305 rms_B_bonded: 6.49 r_work: 0.4149 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12011 Z= 0.168 Angle : 0.581 7.588 16371 Z= 0.298 Chirality : 0.040 0.136 1875 Planarity : 0.005 0.058 2084 Dihedral : 5.739 57.489 2193 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.74 % Allowed : 6.34 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1451 helix: 0.14 (0.23), residues: 479 sheet: -1.09 (0.46), residues: 127 loop : -1.18 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.026 0.002 TYR A 541 PHE 0.013 0.001 PHE A 423 TRP 0.012 0.001 TRP A 493 HIS 0.004 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (11992) covalent geometry : angle 0.57638 / 0.30 (16318) SS BOND : bond 0.00160 / 0.10 ( 4) SS BOND : angle 0.85416 / 0.47 ( 8) hydrogen bonds : bond 0.03906 / 2.63 ( 391) hydrogen bonds : angle 6.19200 / 4.43 ( 1089) link_ALPHA1-3 : bond 0.00626 / 0.43 ( 3) link_ALPHA1-3 : angle 1.45838 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00567 / 0.40 ( 2) link_ALPHA1-6 : angle 1.65465 / 1.25 ( 6) link_BETA1-4 : bond 0.00400 / 0.20 ( 10) link_BETA1-4 : angle 1.52013 / 1.01 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5737.47 seconds wall clock time: 98 minutes 26.84 seconds (5906.84 seconds total)