Starting phenix.real_space_refine on Wed Mar 4 03:52:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804.map" model { file = "/net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q4e_13804/03_2026/7q4e_13804_trim.cif" } resolution = 3.63 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= 0.001 sd= 0.043 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 Zn 1 6.06 5 S 19 5.16 5 C 3386 2.51 5 N 868 2.21 5 O 1044 1.98 5 H 4731 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10049 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 9690 Classifications: {'peptide': 608} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 569} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" 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: "D" 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: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" 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: "G" 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: "H" 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 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: 1.85, per 1000 atoms: 0.18 Number of scatterers: 10049 At special positions: 0 Unit cell: (86.92, 90.1, 93.28, 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) Zn 1 29.99 S 19 16.00 O 1044 8.00 N 868 7.00 C 3386 6.00 H 4731 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " distance=2.02 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 6 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " BETA1-2 " MAN C 4 " - " NAG C 5 " " MAN E 4 " - " NAG E 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " BETA1-6 " NAG C 1 " - " FUC C 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1302 " - " ASN A 416 " " NAG B 1 " - " ASN A 117 " " NAG C 1 " - " ASN A 289 " " NAG D 1 " - " ASN A 45 " " NAG E 1 " - " ASN A 25 " " NAG F 1 " - " ASN A 480 " " NAG G 1 " - " ASN A 9 " " NAG H 1 " - " ASN A 82 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 278.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 71.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.518A pdb=" N LEU A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 3.914A pdb=" N LYS A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 124 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.666A pdb=" N LEU A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.742A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 removed outlier: 3.545A pdb=" N GLU A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.539A pdb=" N GLY A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 3.954A pdb=" N GLY A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.605A pdb=" N PHE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.741A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 removed outlier: 3.611A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 4.305A pdb=" N LEU A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 451 removed outlier: 4.027A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.605A pdb=" N LYS A 489 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.684A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.561A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.001A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 336 286 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4730 1.03 - 1.23: 24 1.23 - 1.42: 2363 1.42 - 1.62: 3057 1.62 - 1.81: 31 Bond restraints: 10205 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.358 0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.465 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C2 BMA E 3 " pdb=" C3 BMA E 3 " ideal model delta sigma weight residual 1.544 1.497 0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C1 MAN C 6 " pdb=" C2 MAN C 6 " ideal model delta sigma weight residual 1.526 1.572 -0.046 2.00e-02 2.50e+03 5.34e+00 ... (remaining 10200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 17041 1.43 - 2.87: 967 2.87 - 4.30: 142 4.30 - 5.74: 38 5.74 - 7.17: 20 Bond angle restraints: 18208 Sorted by residual: angle pdb=" CA ARG A 380 " pdb=" CB ARG A 380 " pdb=" CG ARG A 380 " ideal model delta sigma weight residual 114.10 106.93 7.17 2.00e+00 2.50e-01 1.29e+01 angle pdb=" CA TYR A 372 " pdb=" CB TYR A 372 " pdb=" CG TYR A 372 " ideal model delta sigma weight residual 113.90 120.13 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CA GLU A 389 " pdb=" CB GLU A 389 " pdb=" CG GLU A 389 " ideal model delta sigma weight residual 114.10 107.20 6.90 2.00e+00 2.50e-01 1.19e+01 angle pdb=" C HIS A 360 " pdb=" N HIS A 361 " pdb=" CA HIS A 361 " ideal model delta sigma weight residual 120.29 116.10 4.19 1.42e+00 4.96e-01 8.71e+00 angle pdb=" CB ARG A 380 " pdb=" CG ARG A 380 " pdb=" CD ARG A 380 " ideal model delta sigma weight residual 111.30 117.65 -6.35 2.30e+00 1.89e-01 7.61e+00 ... (remaining 18203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 4797 21.18 - 42.36: 275 42.36 - 63.54: 115 63.54 - 84.73: 48 84.73 - 105.91: 29 Dihedral angle restraints: 5264 sinusoidal: 3029 harmonic: 2235 Sorted by residual: dihedral pdb=" CA PRO A 604 " pdb=" C PRO A 604 " pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta harmonic sigma weight residual 180.00 -154.90 -25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA A 383 " pdb=" C ALA A 383 " pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA CYS A 528 " pdb=" C CYS A 528 " pdb=" N ASP A 529 " pdb=" CA ASP A 529 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 796 0.092 - 0.184: 53 0.184 - 0.276: 2 0.276 - 0.368: 6 0.368 - 0.461: 1 Chirality restraints: 858 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 855 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " -0.565 9.50e-02 1.11e+02 1.91e-01 5.27e+01 pdb=" NE ARG A 96 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.035 2.00e-02 2.50e+03 pdb="HH11 ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 96 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A 96 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 96 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 467 " -0.562 9.50e-02 1.11e+02 1.89e-01 4.61e+01 pdb=" NE ARG A 467 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 467 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 467 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 467 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG A 467 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 467 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 467 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 467 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 413 " 0.211 9.50e-02 1.11e+02 8.01e-02 3.75e+01 pdb=" NE ARG A 413 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 413 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 413 " -0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG A 413 " 0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 413 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 413 " 0.074 2.00e-02 2.50e+03 pdb="HH21 ARG A 413 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 413 " -0.011 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1028 2.25 - 2.83: 22011 2.83 - 3.42: 26588 3.42 - 4.01: 35815 4.01 - 4.60: 55658 Nonbonded interactions: 141100 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 107 " pdb=" OE2 GLU A 184 " model vdw 1.657 2.450 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.667 2.450 nonbonded pdb=" HE1 TRP A 464 " pdb=" OD2 ASP A 485 " model vdw 1.675 2.450 nonbonded pdb=" HG1 THR A 47 " pdb=" OD1 ASN A 50 " model vdw 1.681 2.450 nonbonded pdb=" O PHE A 83 " pdb="HH11 ARG A 89 " model vdw 1.701 2.450 ... (remaining 141095 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 'B' selection = chain 'F' selection = chain 'G' } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.470 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.008 0.054 5506 Z= 0.380 Angle : 1.058 13.493 7550 Z= 0.502 Chirality : 0.057 0.461 858 Planarity : 0.014 0.255 927 Dihedral : 19.121 105.908 2412 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.91 (0.29), residues: 606 helix: -1.32 (0.22), residues: 343 sheet: 0.65 (1.57), residues: 10 loop : -1.06 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.005 ARG A 467 TYR 0.030 0.006 TYR A 372 PHE 0.024 0.003 PHE A 387 TRP 0.025 0.004 TRP A 68 HIS 0.011 0.003 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00819 ( 5474) covalent geometry : angle 0.98525 ( 7460) SS BOND : bond 0.00499 ( 3) SS BOND : angle 1.54181 ( 6) hydrogen bonds : bond 0.22354 ( 286) hydrogen bonds : angle 8.85943 ( 816) metal coordination : bond 0.04727 ( 1) link_ALPHA1-3 : bond 0.00800 ( 2) link_ALPHA1-3 : angle 2.16397 ( 6) link_ALPHA1-6 : bond 0.00082 ( 2) link_ALPHA1-6 : angle 1.67961 ( 6) link_BETA1-2 : bond 0.01097 ( 2) link_BETA1-2 : angle 1.42918 ( 6) link_BETA1-4 : bond 0.00737 ( 13) link_BETA1-4 : angle 3.58617 ( 39) link_BETA1-6 : bond 0.00258 ( 1) link_BETA1-6 : angle 4.86683 ( 3) link_NAG-ASN : bond 0.00976 ( 8) link_NAG-ASN : angle 4.84772 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.253 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: A 155 MET cc_start: 0.8416 (tpt) cc_final: 0.8089 (mmp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1993 time to fit residues: 24.9168 Evaluate side-chains 52 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN A 508 GLN A 545 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089647 restraints weight = 31000.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093005 restraints weight = 12399.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095219 restraints weight = 6728.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.096646 restraints weight = 4420.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097615 restraints weight = 3314.864| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5506 Z= 0.177 Angle : 0.801 6.666 7550 Z= 0.392 Chirality : 0.043 0.289 858 Planarity : 0.006 0.055 927 Dihedral : 13.907 71.789 1233 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.76 % Allowed : 7.07 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.33 (0.31), residues: 606 helix: 0.13 (0.25), residues: 365 sheet: 1.62 (1.54), residues: 10 loop : -0.69 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 413 TYR 0.026 0.002 TYR A 372 PHE 0.022 0.002 PHE A 387 TRP 0.024 0.001 TRP A 163 HIS 0.009 0.002 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5474) covalent geometry : angle 0.76747 ( 7460) SS BOND : bond 0.03472 ( 3) SS BOND : angle 2.62708 ( 6) hydrogen bonds : bond 0.06640 ( 286) hydrogen bonds : angle 5.47949 ( 816) metal coordination : bond 0.00063 ( 1) link_ALPHA1-3 : bond 0.00872 ( 2) link_ALPHA1-3 : angle 3.03041 ( 6) link_ALPHA1-6 : bond 0.00603 ( 2) link_ALPHA1-6 : angle 1.69550 ( 6) link_BETA1-2 : bond 0.00464 ( 2) link_BETA1-2 : angle 1.53328 ( 6) link_BETA1-4 : bond 0.00380 ( 13) link_BETA1-4 : angle 2.39964 ( 39) link_BETA1-6 : bond 0.00192 ( 1) link_BETA1-6 : angle 2.17212 ( 3) link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 1.88179 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.7476 (t0) cc_final: 0.6952 (m-40) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.1752 time to fit residues: 12.9402 Evaluate side-chains 46 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 477 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.104002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087696 restraints weight = 31909.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091066 restraints weight = 13273.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093301 restraints weight = 7471.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094798 restraints weight = 5059.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095662 restraints weight = 3851.134| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5506 Z= 0.207 Angle : 0.719 7.258 7550 Z= 0.354 Chirality : 0.041 0.280 858 Planarity : 0.005 0.048 927 Dihedral : 10.197 61.593 1233 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.38 % Allowed : 9.94 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.03 (0.32), residues: 606 helix: 0.47 (0.25), residues: 368 sheet: 1.68 (1.68), residues: 10 loop : -0.77 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.022 0.002 TYR A 372 PHE 0.044 0.002 PHE A 83 TRP 0.016 0.001 TRP A 163 HIS 0.008 0.002 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 5474) covalent geometry : angle 0.69210 ( 7460) SS BOND : bond 0.00726 ( 3) SS BOND : angle 1.86908 ( 6) hydrogen bonds : bond 0.05775 ( 286) hydrogen bonds : angle 5.15097 ( 816) metal coordination : bond 0.00341 ( 1) link_ALPHA1-3 : bond 0.01005 ( 2) link_ALPHA1-3 : angle 1.99837 ( 6) link_ALPHA1-6 : bond 0.00737 ( 2) link_ALPHA1-6 : angle 1.62857 ( 6) link_BETA1-2 : bond 0.00430 ( 2) link_BETA1-2 : angle 1.11581 ( 6) link_BETA1-4 : bond 0.00478 ( 13) link_BETA1-4 : angle 2.19607 ( 39) link_BETA1-6 : bond 0.00054 ( 1) link_BETA1-6 : angle 1.97055 ( 3) link_NAG-ASN : bond 0.00370 ( 8) link_NAG-ASN : angle 1.63605 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ASN cc_start: 0.7536 (t0) cc_final: 0.6914 (m-40) REVERT: A 362 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7790 (mm-30) outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.1251 time to fit residues: 9.7362 Evaluate side-chains 42 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089030 restraints weight = 31612.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092441 restraints weight = 12972.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094706 restraints weight = 7263.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096172 restraints weight = 4905.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097176 restraints weight = 3739.078| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5506 Z= 0.139 Angle : 0.638 6.516 7550 Z= 0.312 Chirality : 0.038 0.255 858 Planarity : 0.005 0.048 927 Dihedral : 8.380 50.309 1233 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.76 % Allowed : 10.71 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.49 (0.33), residues: 606 helix: 0.89 (0.26), residues: 367 sheet: 1.78 (1.78), residues: 10 loop : -0.56 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.021 0.002 TYR A 372 PHE 0.018 0.002 PHE A 83 TRP 0.018 0.001 TRP A 163 HIS 0.006 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5474) covalent geometry : angle 0.61757 ( 7460) SS BOND : bond 0.00356 ( 3) SS BOND : angle 0.96810 ( 6) hydrogen bonds : bond 0.05041 ( 286) hydrogen bonds : angle 4.83801 ( 816) metal coordination : bond 0.00336 ( 1) link_ALPHA1-3 : bond 0.00927 ( 2) link_ALPHA1-3 : angle 2.09168 ( 6) link_ALPHA1-6 : bond 0.00901 ( 2) link_ALPHA1-6 : angle 1.43136 ( 6) link_BETA1-2 : bond 0.00309 ( 2) link_BETA1-2 : angle 0.99613 ( 6) link_BETA1-4 : bond 0.00348 ( 13) link_BETA1-4 : angle 1.81008 ( 39) link_BETA1-6 : bond 0.00104 ( 1) link_BETA1-6 : angle 1.76074 ( 3) link_NAG-ASN : bond 0.00185 ( 8) link_NAG-ASN : angle 1.37886 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 243 ASN cc_start: 0.7440 (t0) cc_final: 0.6857 (m-40) REVERT: A 362 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7826 (mm-30) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1010 time to fit residues: 7.2514 Evaluate side-chains 46 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086565 restraints weight = 31734.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089936 restraints weight = 13206.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092125 restraints weight = 7447.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093577 restraints weight = 5082.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094465 restraints weight = 3906.701| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5506 Z= 0.223 Angle : 0.669 6.963 7550 Z= 0.334 Chirality : 0.039 0.258 858 Planarity : 0.005 0.046 927 Dihedral : 7.804 48.535 1233 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.76 % Allowed : 11.47 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.33 (0.33), residues: 606 helix: 0.81 (0.26), residues: 368 sheet: 1.41 (1.70), residues: 10 loop : -0.70 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 446 TYR 0.022 0.002 TYR A 372 PHE 0.017 0.002 PHE A 387 TRP 0.012 0.001 TRP A 163 HIS 0.011 0.002 HIS A 491 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 5474) covalent geometry : angle 0.64875 ( 7460) SS BOND : bond 0.00316 ( 3) SS BOND : angle 1.15159 ( 6) hydrogen bonds : bond 0.05056 ( 286) hydrogen bonds : angle 4.91150 ( 816) metal coordination : bond 0.00674 ( 1) link_ALPHA1-3 : bond 0.00770 ( 2) link_ALPHA1-3 : angle 2.00455 ( 6) link_ALPHA1-6 : bond 0.00900 ( 2) link_ALPHA1-6 : angle 1.24016 ( 6) link_BETA1-2 : bond 0.00312 ( 2) link_BETA1-2 : angle 1.09069 ( 6) link_BETA1-4 : bond 0.00356 ( 13) link_BETA1-4 : angle 1.80523 ( 39) link_BETA1-6 : bond 0.00144 ( 1) link_BETA1-6 : angle 1.82674 ( 3) link_NAG-ASN : bond 0.00335 ( 8) link_NAG-ASN : angle 1.48994 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: A 243 ASN cc_start: 0.7523 (t0) cc_final: 0.6892 (m-40) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1103 time to fit residues: 7.1953 Evaluate side-chains 44 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 600 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 24 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088854 restraints weight = 31779.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092324 restraints weight = 12963.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.094597 restraints weight = 7236.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096062 restraints weight = 4889.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097103 restraints weight = 3728.974| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5506 Z= 0.126 Angle : 0.585 6.378 7550 Z= 0.287 Chirality : 0.036 0.233 858 Planarity : 0.004 0.042 927 Dihedral : 6.931 58.501 1233 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.34 % Allowed : 11.66 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.33), residues: 606 helix: 1.09 (0.26), residues: 372 sheet: 0.95 (1.61), residues: 10 loop : -0.42 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.019 0.002 TYR A 372 PHE 0.011 0.001 PHE A 387 TRP 0.013 0.001 TRP A 163 HIS 0.006 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5474) covalent geometry : angle 0.56883 ( 7460) SS BOND : bond 0.00139 ( 3) SS BOND : angle 1.01183 ( 6) hydrogen bonds : bond 0.04647 ( 286) hydrogen bonds : angle 4.60488 ( 816) metal coordination : bond 0.00321 ( 1) link_ALPHA1-3 : bond 0.00971 ( 2) link_ALPHA1-3 : angle 1.56706 ( 6) link_ALPHA1-6 : bond 0.01079 ( 2) link_ALPHA1-6 : angle 1.33368 ( 6) link_BETA1-2 : bond 0.00276 ( 2) link_BETA1-2 : angle 0.97648 ( 6) link_BETA1-4 : bond 0.00365 ( 13) link_BETA1-4 : angle 1.51509 ( 39) link_BETA1-6 : bond 0.00240 ( 1) link_BETA1-6 : angle 1.55620 ( 3) link_NAG-ASN : bond 0.00173 ( 8) link_NAG-ASN : angle 1.26151 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: A 243 ASN cc_start: 0.7463 (t0) cc_final: 0.6867 (m-40) REVERT: A 298 GLU cc_start: 0.7609 (tt0) cc_final: 0.7331 (tm-30) REVERT: A 498 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.6503 (t80) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.1071 time to fit residues: 7.5201 Evaluate side-chains 46 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 590 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089007 restraints weight = 31609.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092463 restraints weight = 13047.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094702 restraints weight = 7331.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096173 restraints weight = 4971.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097134 restraints weight = 3795.105| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5506 Z= 0.140 Angle : 0.580 6.024 7550 Z= 0.285 Chirality : 0.035 0.230 858 Planarity : 0.004 0.039 927 Dihedral : 6.422 52.559 1233 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 12.05 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.78 (0.33), residues: 606 helix: 1.16 (0.26), residues: 378 sheet: 0.62 (1.57), residues: 10 loop : -0.54 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.019 0.002 TYR A 372 PHE 0.011 0.001 PHE A 387 TRP 0.019 0.001 TRP A 261 HIS 0.007 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5474) covalent geometry : angle 0.56255 ( 7460) SS BOND : bond 0.00204 ( 3) SS BOND : angle 1.00079 ( 6) hydrogen bonds : bond 0.04529 ( 286) hydrogen bonds : angle 4.56119 ( 816) metal coordination : bond 0.00384 ( 1) link_ALPHA1-3 : bond 0.00827 ( 2) link_ALPHA1-3 : angle 1.53581 ( 6) link_ALPHA1-6 : bond 0.01078 ( 2) link_ALPHA1-6 : angle 1.61184 ( 6) link_BETA1-2 : bond 0.00314 ( 2) link_BETA1-2 : angle 1.03573 ( 6) link_BETA1-4 : bond 0.00311 ( 13) link_BETA1-4 : angle 1.53835 ( 39) link_BETA1-6 : bond 0.00241 ( 1) link_BETA1-6 : angle 1.59363 ( 3) link_NAG-ASN : bond 0.00209 ( 8) link_NAG-ASN : angle 1.23082 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 129 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8660 (tt) REVERT: A 243 ASN cc_start: 0.7487 (t0) cc_final: 0.7097 (t0) REVERT: A 298 GLU cc_start: 0.7629 (tt0) cc_final: 0.7253 (tm-30) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.1356 time to fit residues: 9.9109 Evaluate side-chains 49 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089274 restraints weight = 31207.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092750 restraints weight = 12834.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095019 restraints weight = 7182.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096457 restraints weight = 4868.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097452 restraints weight = 3725.325| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5506 Z= 0.131 Angle : 0.568 5.925 7550 Z= 0.281 Chirality : 0.035 0.228 858 Planarity : 0.004 0.036 927 Dihedral : 6.076 47.873 1233 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.91 % Allowed : 12.05 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.88 (0.33), residues: 606 helix: 1.27 (0.26), residues: 379 sheet: 0.49 (1.51), residues: 10 loop : -0.57 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.020 0.002 TYR A 241 PHE 0.011 0.001 PHE A 387 TRP 0.011 0.001 TRP A 163 HIS 0.007 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5474) covalent geometry : angle 0.55209 ( 7460) SS BOND : bond 0.00159 ( 3) SS BOND : angle 0.87506 ( 6) hydrogen bonds : bond 0.04420 ( 286) hydrogen bonds : angle 4.47628 ( 816) metal coordination : bond 0.00333 ( 1) link_ALPHA1-3 : bond 0.00821 ( 2) link_ALPHA1-3 : angle 1.40601 ( 6) link_ALPHA1-6 : bond 0.01107 ( 2) link_ALPHA1-6 : angle 1.72916 ( 6) link_BETA1-2 : bond 0.00294 ( 2) link_BETA1-2 : angle 1.03093 ( 6) link_BETA1-4 : bond 0.00315 ( 13) link_BETA1-4 : angle 1.46542 ( 39) link_BETA1-6 : bond 0.00235 ( 1) link_BETA1-6 : angle 1.52520 ( 3) link_NAG-ASN : bond 0.00196 ( 8) link_NAG-ASN : angle 1.14530 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.263 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: A 14 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 129 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 243 ASN cc_start: 0.7464 (t0) cc_final: 0.7122 (t0) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1345 time to fit residues: 9.9099 Evaluate side-chains 53 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 590 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088785 restraints weight = 31350.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092217 restraints weight = 12852.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094485 restraints weight = 7204.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095937 restraints weight = 4876.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096756 restraints weight = 3737.519| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5506 Z= 0.141 Angle : 0.565 5.122 7550 Z= 0.282 Chirality : 0.035 0.220 858 Planarity : 0.004 0.031 927 Dihedral : 5.743 44.114 1233 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.91 % Allowed : 12.05 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.92 (0.33), residues: 606 helix: 1.38 (0.26), residues: 379 sheet: -0.13 (1.38), residues: 10 loop : -0.69 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.016 0.002 TYR A 372 PHE 0.012 0.001 PHE A 387 TRP 0.009 0.001 TRP A 163 HIS 0.007 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5474) covalent geometry : angle 0.54785 ( 7460) SS BOND : bond 0.00203 ( 3) SS BOND : angle 0.97826 ( 6) hydrogen bonds : bond 0.04371 ( 286) hydrogen bonds : angle 4.42929 ( 816) metal coordination : bond 0.00386 ( 1) link_ALPHA1-3 : bond 0.00703 ( 2) link_ALPHA1-3 : angle 1.41225 ( 6) link_ALPHA1-6 : bond 0.01084 ( 2) link_ALPHA1-6 : angle 1.69856 ( 6) link_BETA1-2 : bond 0.00301 ( 2) link_BETA1-2 : angle 1.07343 ( 6) link_BETA1-4 : bond 0.00314 ( 13) link_BETA1-4 : angle 1.48272 ( 39) link_BETA1-6 : bond 0.00255 ( 1) link_BETA1-6 : angle 1.57789 ( 3) link_NAG-ASN : bond 0.00192 ( 8) link_NAG-ASN : angle 1.14922 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.278 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: A 14 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 129 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8629 (tt) REVERT: A 240 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7321 (ptm-80) REVERT: A 243 ASN cc_start: 0.7468 (t0) cc_final: 0.7122 (t0) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.1509 time to fit residues: 10.8284 Evaluate side-chains 48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088907 restraints weight = 31398.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092268 restraints weight = 12878.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094515 restraints weight = 7256.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095999 restraints weight = 4909.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096834 restraints weight = 3742.231| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5506 Z= 0.138 Angle : 0.557 5.260 7550 Z= 0.278 Chirality : 0.035 0.218 858 Planarity : 0.004 0.031 927 Dihedral : 5.620 42.883 1233 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 12.43 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.99 (0.33), residues: 606 helix: 1.47 (0.26), residues: 379 sheet: -0.66 (1.26), residues: 10 loop : -0.70 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.016 0.001 TYR A 372 PHE 0.013 0.001 PHE A 178 TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5474) covalent geometry : angle 0.54076 ( 7460) SS BOND : bond 0.00209 ( 3) SS BOND : angle 0.90636 ( 6) hydrogen bonds : bond 0.04361 ( 286) hydrogen bonds : angle 4.40438 ( 816) metal coordination : bond 0.00399 ( 1) link_ALPHA1-3 : bond 0.00672 ( 2) link_ALPHA1-3 : angle 1.38877 ( 6) link_ALPHA1-6 : bond 0.00991 ( 2) link_ALPHA1-6 : angle 1.65283 ( 6) link_BETA1-2 : bond 0.00284 ( 2) link_BETA1-2 : angle 1.08518 ( 6) link_BETA1-4 : bond 0.00302 ( 13) link_BETA1-4 : angle 1.45620 ( 39) link_BETA1-6 : bond 0.00256 ( 1) link_BETA1-6 : angle 1.50757 ( 3) link_NAG-ASN : bond 0.00203 ( 8) link_NAG-ASN : angle 1.10154 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 129 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 240 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7069 (ptm-80) REVERT: A 243 ASN cc_start: 0.7540 (t0) cc_final: 0.7187 (t0) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.1509 time to fit residues: 10.4863 Evaluate side-chains 48 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.105083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088810 restraints weight = 31516.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092260 restraints weight = 12928.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094513 restraints weight = 7227.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.095978 restraints weight = 4891.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096931 restraints weight = 3737.289| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5506 Z= 0.133 Angle : 0.554 5.106 7550 Z= 0.276 Chirality : 0.035 0.217 858 Planarity : 0.004 0.031 927 Dihedral : 5.511 41.970 1233 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.72 % Allowed : 12.62 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.07 (0.33), residues: 606 helix: 1.55 (0.26), residues: 379 sheet: -0.48 (1.37), residues: 10 loop : -0.71 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 89 TYR 0.016 0.002 TYR A 372 PHE 0.013 0.001 PHE A 178 TRP 0.011 0.001 TRP A 160 HIS 0.012 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5474) covalent geometry : angle 0.53833 ( 7460) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.92828 ( 6) hydrogen bonds : bond 0.04318 ( 286) hydrogen bonds : angle 4.38326 ( 816) metal coordination : bond 0.00371 ( 1) link_ALPHA1-3 : bond 0.00654 ( 2) link_ALPHA1-3 : angle 1.39838 ( 6) link_ALPHA1-6 : bond 0.00974 ( 2) link_ALPHA1-6 : angle 1.63823 ( 6) link_BETA1-2 : bond 0.00285 ( 2) link_BETA1-2 : angle 1.09135 ( 6) link_BETA1-4 : bond 0.00297 ( 13) link_BETA1-4 : angle 1.45498 ( 39) link_BETA1-6 : bond 0.00269 ( 1) link_BETA1-6 : angle 1.50414 ( 3) link_NAG-ASN : bond 0.00188 ( 8) link_NAG-ASN : angle 1.09999 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1839.06 seconds wall clock time: 31 minutes 59.41 seconds (1919.41 seconds total)