Starting phenix.real_space_refine on Wed Feb 14 21:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_13804_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_13804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_13804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_13804_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/02_2024/7q4e_13804_trim.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 4.81, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 8.29 Conformation dependent library (CDL) restraints added in 937.2 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: 0.77 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: 3.62 Time building geometry restraints manager: 8.59 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: 97.84 - 105.08: 138 105.08 - 112.31: 11119 112.31 - 119.54: 2744 119.54 - 126.78: 4084 126.78 - 134.01: 123 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 1.850 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.667 1.850 nonbonded pdb=" HE1 TRP A 464 " pdb=" OD2 ASP A 485 " model vdw 1.675 1.850 nonbonded pdb=" HG1 THR A 47 " pdb=" OD1 ASN A 50 " model vdw 1.681 1.850 nonbonded pdb=" O PHE A 83 " pdb="HH11 ARG A 89 " model vdw 1.701 1.850 ... (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 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: 0.010 Normalize map: mean=0, sd=1: 3.440 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: 0.150 Extract box with map and model: 10.210 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 37.120 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.150 ------------------------------------------------------------------------------- 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 5474 Z= 0.533 Angle : 0.985 7.170 7460 Z= 0.487 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.025 0.004 TRP A 68 HIS 0.011 0.003 HIS A 234 PHE 0.024 0.003 PHE A 387 TYR 0.030 0.006 TYR A 372 ARG 0.042 0.005 ARG A 467 *********************** 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 fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.738 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: 0.4168 time to fit residues: 52.3279 Evaluate side-chains 52 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN A 545 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5474 Z= 0.255 Angle : 0.759 6.694 7460 Z= 0.380 Chirality : 0.043 0.317 858 Planarity : 0.006 0.063 927 Dihedral : 14.004 72.044 1233 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.76 % Allowed : 7.27 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 606 helix: 0.09 (0.24), residues: 365 sheet: 1.52 (1.52), residues: 10 loop : -0.63 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.009 0.002 HIS A 365 PHE 0.022 0.002 PHE A 387 TYR 0.026 0.002 TYR A 372 ARG 0.003 0.001 ARG A 467 *********************** 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 54 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.3885 time to fit residues: 27.6458 Evaluate side-chains 52 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 317 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 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5474 Z= 0.219 Angle : 0.642 6.923 7460 Z= 0.318 Chirality : 0.040 0.298 858 Planarity : 0.005 0.063 927 Dihedral : 9.772 60.683 1233 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.76 % Allowed : 10.13 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.33), residues: 606 helix: 0.72 (0.25), residues: 367 sheet: 1.72 (1.66), residues: 10 loop : -0.41 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.008 0.001 HIS A 361 PHE 0.012 0.001 PHE A 178 TYR 0.020 0.002 TYR A 372 ARG 0.006 0.000 ARG A 340 *********************** 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 57 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8003 (ttm110) REVERT: A 264 ILE cc_start: 0.8191 (pt) cc_final: 0.7953 (tp) REVERT: A 362 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7613 (mm-30) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.2935 time to fit residues: 23.5099 Evaluate side-chains 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 357 SER 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 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5474 Z= 0.315 Angle : 0.664 7.092 7460 Z= 0.334 Chirality : 0.040 0.288 858 Planarity : 0.005 0.046 927 Dihedral : 8.181 45.146 1233 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 12.05 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.33), residues: 606 helix: 0.78 (0.26), residues: 367 sheet: 1.62 (1.68), residues: 10 loop : -0.51 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.010 0.002 HIS A 404 PHE 0.018 0.002 PHE A 387 TYR 0.022 0.002 TYR A 372 ARG 0.004 0.000 ARG A 340 *********************** 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 54 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.861 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 89 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8282 (ttp-110) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.2998 time to fit residues: 23.0413 Evaluate side-chains 49 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.0870 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5474 Z= 0.180 Angle : 0.573 6.367 7460 Z= 0.287 Chirality : 0.037 0.272 858 Planarity : 0.004 0.043 927 Dihedral : 7.336 51.460 1233 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.76 % Allowed : 12.43 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.34), residues: 606 helix: 1.14 (0.26), residues: 367 sheet: 1.27 (1.63), residues: 10 loop : -0.23 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.007 0.001 HIS A 360 PHE 0.012 0.001 PHE A 387 TYR 0.018 0.002 TYR A 372 ARG 0.001 0.000 ARG A 295 *********************** 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 49 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.3246 time to fit residues: 21.9387 Evaluate side-chains 47 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 590 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5474 Z= 0.222 Angle : 0.573 6.173 7460 Z= 0.290 Chirality : 0.036 0.256 858 Planarity : 0.004 0.041 927 Dihedral : 6.679 57.108 1233 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.76 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.33), residues: 606 helix: 1.17 (0.26), residues: 376 sheet: 0.72 (1.54), residues: 10 loop : -0.27 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.008 0.001 HIS A 361 PHE 0.012 0.001 PHE A 387 TYR 0.020 0.002 TYR A 498 ARG 0.005 0.000 ARG A 240 *********************** 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 50 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.3206 time to fit residues: 22.0457 Evaluate side-chains 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5474 Z= 0.192 Angle : 0.555 5.883 7460 Z= 0.279 Chirality : 0.035 0.247 858 Planarity : 0.004 0.039 927 Dihedral : 6.231 49.825 1233 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.15 % Allowed : 13.77 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.34), residues: 606 helix: 1.32 (0.26), residues: 376 sheet: 0.31 (1.47), residues: 10 loop : -0.21 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 163 HIS 0.007 0.001 HIS A 361 PHE 0.036 0.002 PHE A 178 TYR 0.017 0.002 TYR A 372 ARG 0.002 0.000 ARG A 446 *********************** 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 51 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.3386 time to fit residues: 24.9881 Evaluate side-chains 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5474 Z= 0.285 Angle : 0.591 5.738 7460 Z= 0.302 Chirality : 0.036 0.246 858 Planarity : 0.004 0.039 927 Dihedral : 6.242 46.417 1233 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.53 % Allowed : 14.15 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.33), residues: 606 helix: 1.25 (0.26), residues: 377 sheet: -0.12 (1.40), residues: 10 loop : -0.44 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.009 0.002 HIS A 404 PHE 0.025 0.002 PHE A 178 TYR 0.017 0.002 TYR A 372 ARG 0.003 0.000 ARG A 446 *********************** 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 51 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.2680 time to fit residues: 19.4109 Evaluate side-chains 47 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5474 Z= 0.154 Angle : 0.537 5.518 7460 Z= 0.269 Chirality : 0.035 0.227 858 Planarity : 0.004 0.032 927 Dihedral : 5.711 43.657 1233 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.76 % Allowed : 14.91 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.34), residues: 606 helix: 1.54 (0.26), residues: 378 sheet: -0.42 (1.34), residues: 10 loop : -0.21 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.009 0.001 HIS A 164 PHE 0.024 0.002 PHE A 178 TYR 0.015 0.001 TYR A 372 ARG 0.002 0.000 ARG A 479 *********************** 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 49 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ILE cc_start: 0.8212 (pt) cc_final: 0.7947 (tp) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.2536 time to fit residues: 18.6317 Evaluate side-chains 44 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 HIS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5474 Z= 0.203 Angle : 0.548 5.430 7460 Z= 0.278 Chirality : 0.035 0.231 858 Planarity : 0.004 0.033 927 Dihedral : 5.620 43.241 1233 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.96 % Allowed : 15.11 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.34), residues: 606 helix: 1.60 (0.26), residues: 379 sheet: -0.42 (1.43), residues: 10 loop : -0.31 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.008 0.001 HIS A 361 PHE 0.031 0.002 PHE A 505 TYR 0.016 0.002 TYR A 372 ARG 0.002 0.000 ARG A 446 ********************** 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 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ILE cc_start: 0.8262 (pt) cc_final: 0.7964 (tp) outliers start: 5 outliers final: 3 residues processed: 46 average time/residue: 0.2509 time to fit residues: 17.7135 Evaluate side-chains 43 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089720 restraints weight = 31324.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093133 restraints weight = 12907.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095369 restraints weight = 7233.852| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5474 Z= 0.178 Angle : 0.534 5.246 7460 Z= 0.270 Chirality : 0.035 0.223 858 Planarity : 0.004 0.030 927 Dihedral : 5.423 41.728 1233 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.76 % Allowed : 15.30 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.34), residues: 606 helix: 1.67 (0.26), residues: 379 sheet: -0.60 (1.37), residues: 10 loop : -0.33 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.007 0.001 HIS A 361 PHE 0.023 0.002 PHE A 505 TYR 0.015 0.001 TYR A 372 ARG 0.002 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2854.47 seconds wall clock time: 51 minutes 19.82 seconds (3079.82 seconds total)