Starting phenix.real_space_refine on Wed Nov 15 02:28:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/11_2023/7q4e_13804_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/11_2023/7q4e_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_13804/11_2023/7q4e_13804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/11_2023/7q4e_13804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/11_2023/7q4e_13804_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4e_13804/11_2023/7q4e_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-1.21rc1-5144/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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.51 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: 8.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.72 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: 3.44 Time building geometry restraints manager: 8.96 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 - 17.47: 3648 17.47 - 34.93: 274 34.93 - 52.40: 45 52.40 - 69.86: 41 69.86 - 87.33: 8 Dihedral angle restraints: 4016 sinusoidal: 1781 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 4013 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: 0.000 Normalize map: mean=0, sd=1: 11.420 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: 0.000 Extract box with map and model: 14.840 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 39.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 68.670 ------------------------------------------------------------------------------- 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 : 13.940 87.329 1848 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 *********************** 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 : 0.872 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: 0 outliers final: 0 residues processed: 101 average time/residue: 0.4311 time to fit residues: 54.9791 Evaluate side-chains 52 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9907 ------------------------------------------------------------------------------- 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: 0.9990 chunk 45 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5474 Z= 0.209 Angle : 0.716 6.592 7460 Z= 0.368 Chirality : 0.038 0.270 858 Planarity : 0.006 0.068 927 Dihedral : 6.001 19.900 669 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.57 % Allowed : 7.46 % 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: -0.18 (0.31), residues: 606 helix: 0.21 (0.25), residues: 365 sheet: 1.50 (1.52), residues: 10 loop : -0.55 (0.40), residues: 231 *********************** 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: 3 poor density : 51 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.3861 time to fit residues: 27.4650 Evaluate side-chains 50 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1149 time to fit residues: 1.5518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5474 Z= 0.221 Angle : 0.637 7.109 7460 Z= 0.318 Chirality : 0.036 0.256 858 Planarity : 0.004 0.042 927 Dihedral : 5.291 19.248 669 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.57 % Allowed : 9.37 % Favored : 90.06 % 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: 0.46 (0.33), residues: 606 helix: 0.77 (0.26), residues: 365 sheet: 1.78 (1.63), residues: 10 loop : -0.39 (0.41), residues: 231 *********************** 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 59 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.2933 time to fit residues: 24.4352 Evaluate side-chains 47 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1393 time to fit residues: 1.7551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5474 Z= 0.223 Angle : 0.611 6.910 7460 Z= 0.307 Chirality : 0.035 0.228 858 Planarity : 0.004 0.041 927 Dihedral : 5.038 18.543 669 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.38 % Allowed : 11.47 % Favored : 88.15 % 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: 0.77 (0.33), residues: 606 helix: 1.02 (0.26), residues: 369 sheet: 1.77 (1.72), residues: 10 loop : -0.26 (0.42), residues: 227 *********************** 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 53 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2572 time to fit residues: 20.0308 Evaluate side-chains 47 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.792 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1163 time to fit residues: 1.3994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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: 0.7729 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5474 Z= 0.223 Angle : 0.588 6.745 7460 Z= 0.295 Chirality : 0.035 0.219 858 Planarity : 0.004 0.039 927 Dihedral : 4.840 18.452 669 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.57 % Allowed : 11.28 % Favored : 88.15 % 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: 368 sheet: 1.08 (1.58), residues: 10 loop : -0.25 (0.41), residues: 228 *********************** 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 47 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.3239 time to fit residues: 20.6097 Evaluate side-chains 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1759 time to fit residues: 1.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7747 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5474 Z= 0.238 Angle : 0.593 6.468 7460 Z= 0.297 Chirality : 0.035 0.204 858 Planarity : 0.004 0.037 927 Dihedral : 4.759 18.241 669 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % 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: 1.22 (0.26), residues: 370 sheet: 0.68 (1.52), residues: 10 loop : -0.32 (0.41), residues: 226 *********************** 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 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2774 time to fit residues: 18.7651 Evaluate side-chains 42 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.4572 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= 0.197 Angle : 0.566 6.261 7460 Z= 0.282 Chirality : 0.034 0.197 858 Planarity : 0.004 0.035 927 Dihedral : 4.650 17.962 669 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.57 % Allowed : 13.19 % Favored : 86.23 % 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: 1.02 (0.34), residues: 606 helix: 1.31 (0.26), residues: 376 sheet: 0.30 (1.41), residues: 10 loop : -0.31 (0.42), residues: 220 *********************** 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 48 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 48 average time/residue: 0.2688 time to fit residues: 18.9865 Evaluate side-chains 42 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1097 time to fit residues: 1.1871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 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: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 494 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5474 Z= 0.228 Angle : 0.578 6.078 7460 Z= 0.290 Chirality : 0.035 0.189 858 Planarity : 0.004 0.034 927 Dihedral : 4.578 18.022 669 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.38 % Allowed : 13.38 % Favored : 86.23 % 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: 0.95 (0.34), residues: 606 helix: 1.32 (0.26), residues: 378 sheet: -0.43 (1.33), residues: 10 loop : -0.45 (0.42), residues: 218 *********************** 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 45 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.2372 time to fit residues: 16.4198 Evaluate side-chains 43 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1834 time to fit residues: 1.3297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 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: 0.7748 moved from start: 0.4978 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= 0.192 Angle : 0.559 5.895 7460 Z= 0.278 Chirality : 0.034 0.184 858 Planarity : 0.004 0.033 927 Dihedral : 4.498 17.943 669 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.19 % Allowed : 13.58 % Favored : 86.23 % 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: 1.09 (0.34), residues: 606 helix: 1.46 (0.26), residues: 378 sheet: -0.78 (1.30), residues: 10 loop : -0.44 (0.42), residues: 218 *********************** 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 46 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.2818 time to fit residues: 19.5376 Evaluate side-chains 42 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.5111 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= 0.168 Angle : 0.545 5.658 7460 Z= 0.271 Chirality : 0.033 0.179 858 Planarity : 0.004 0.027 927 Dihedral : 4.419 17.538 669 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.19 % Allowed : 13.96 % Favored : 85.85 % 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: 1.22 (0.34), residues: 606 helix: 1.60 (0.26), residues: 378 sheet: -1.11 (1.32), residues: 10 loop : -0.44 (0.42), residues: 218 ********************** 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 44 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.2435 time to fit residues: 16.1516 Evaluate side-chains 41 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.104898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.089089 restraints weight = 31370.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092468 restraints weight = 12941.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094700 restraints weight = 7275.766| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5474 Z= 0.221 Angle : 0.564 5.626 7460 Z= 0.283 Chirality : 0.034 0.182 858 Planarity : 0.004 0.028 927 Dihedral : 4.393 17.672 669 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 14.34 % 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 (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: 1.17 (0.34), residues: 606 helix: 1.56 (0.26), residues: 379 sheet: -1.09 (1.31), residues: 10 loop : -0.47 (0.42), residues: 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.15 seconds wall clock time: 51 minutes 29.76 seconds (3089.76 seconds total)