Starting phenix.real_space_refine on Tue Sep 24 05:10:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/09_2024/7r0z_14225.cif" } resolution = 3.5 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= 0.002 sd= 0.074 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4404 2.51 5 N 1131 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6891 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1977 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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 Time building chain proxies: 4.85, per 1000 atoms: 0.70 Number of scatterers: 6891 At special positions: 0 Unit cell: (72.226, 99.176, 140.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 39 16.00 O 1316 8.00 N 1131 7.00 C 4404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 432 " " NAG D 906 " - " ASN D 546 " " NAG D 907 " - " ASN D 103 " Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 51.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.845A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.804A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.678A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.756A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 223 removed outlier: 3.706A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 223' Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.042A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.526A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.183A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.800A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.505A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.627A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.061A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.521A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.234A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.652A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.982A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.185A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.741A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.162A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.999A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.952A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 310 hydrogen bonds defined for protein. 879 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: 1.92 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2194 1.34 - 1.46: 1764 1.46 - 1.58: 3057 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7075 Sorted by residual: bond pdb=" C1 NAG D 907 " pdb=" O5 NAG D 907 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C1 NAG D 906 " pdb=" O5 NAG D 906 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.42e+00 ... (remaining 7070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 9332 1.64 - 3.27: 237 3.27 - 4.91: 34 4.91 - 6.54: 6 6.54 - 8.18: 4 Bond angle restraints: 9613 Sorted by residual: angle pdb=" C ILE D 233 " pdb=" CA ILE D 233 " pdb=" CB ILE D 233 " ideal model delta sigma weight residual 111.29 104.99 6.30 1.64e+00 3.72e-01 1.48e+01 angle pdb=" C HIS D 34 " pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.62e+00 angle pdb=" N GLU D 224 " pdb=" CA GLU D 224 " pdb=" C GLU D 224 " ideal model delta sigma weight residual 109.86 106.08 3.78 1.55e+00 4.16e-01 5.94e+00 angle pdb=" N HIS D 401 " pdb=" CA HIS D 401 " pdb=" C HIS D 401 " ideal model delta sigma weight residual 113.12 110.21 2.91 1.25e+00 6.40e-01 5.42e+00 angle pdb=" N ILE D 233 " pdb=" CA ILE D 233 " pdb=" CB ILE D 233 " ideal model delta sigma weight residual 111.23 114.94 -3.71 1.65e+00 3.67e-01 5.06e+00 ... (remaining 9608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3851 17.02 - 34.04: 350 34.04 - 51.07: 59 51.07 - 68.09: 16 68.09 - 85.11: 10 Dihedral angle restraints: 4286 sinusoidal: 1829 harmonic: 2457 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 31.45 61.55 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual 93.00 129.07 -36.07 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -119.29 33.29 1 1.00e+01 1.00e-02 1.58e+01 ... (remaining 4283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 910 0.067 - 0.135: 125 0.135 - 0.202: 5 0.202 - 0.269: 1 0.269 - 0.336: 1 Chirality restraints: 1042 Sorted by residual: chirality pdb=" C1 NAG D 907 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D 907 " pdb=" O5 NAG D 907 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.51e-01 ... (remaining 1039 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU D 35 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU D 35 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA D 36 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO D 146 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " 0.004 2.00e-02 2.50e+03 2.13e-02 5.66e+00 pdb=" CG ASN D 103 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG D 907 " 0.021 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 6443 3.28 - 3.82: 10488 3.82 - 4.36: 12373 4.36 - 4.90: 22418 Nonbonded interactions: 52431 Sorted by model distance: nonbonded pdb=" OD1 ASN D 103 " pdb=" OG SER D 106 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.255 2.230 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.291 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.393 3.040 ... (remaining 52426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:4.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7075 Z= 0.331 Angle : 0.640 8.181 9613 Z= 0.331 Chirality : 0.047 0.336 1042 Planarity : 0.005 0.061 1231 Dihedral : 13.556 85.110 2684 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.47 (0.28), residues: 831 helix: 1.31 (0.28), residues: 356 sheet: 0.93 (0.58), residues: 70 loop : -0.70 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 165 HIS 0.009 0.001 HIS D 378 PHE 0.027 0.002 PHE D 369 TYR 0.020 0.002 TYR A 495 ARG 0.008 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8988 (t) cc_final: 0.8701 (t) REVERT: A 574 ASP cc_start: 0.6738 (m-30) cc_final: 0.6344 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1977 time to fit residues: 28.5331 Evaluate side-chains 71 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 overall best weight: 0.1474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7075 Z= 0.131 Angle : 0.503 6.882 9613 Z= 0.259 Chirality : 0.041 0.198 1042 Planarity : 0.004 0.035 1231 Dihedral : 6.399 56.363 1076 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.41 % Allowed : 6.22 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.81 (0.28), residues: 831 helix: 1.52 (0.27), residues: 373 sheet: 1.14 (0.59), residues: 70 loop : -0.53 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 401 PHE 0.012 0.001 PHE D 369 TYR 0.017 0.001 TYR D 183 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 SER cc_start: 0.8916 (t) cc_final: 0.8535 (t) outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.1466 time to fit residues: 18.2487 Evaluate side-chains 76 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.0020 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 60 optimal weight: 0.0870 overall best weight: 0.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7075 Z= 0.128 Angle : 0.468 6.488 9613 Z= 0.240 Chirality : 0.040 0.190 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.961 55.402 1076 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.81 % Allowed : 9.07 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.07 (0.29), residues: 831 helix: 1.82 (0.27), residues: 368 sheet: 1.15 (0.58), residues: 71 loop : -0.43 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.000 HIS D 378 PHE 0.011 0.001 PHE D 369 TYR 0.013 0.001 TYR D 183 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.7915 (m) cc_final: 0.7569 (m) REVERT: D 383 MET cc_start: 0.8898 (mtt) cc_final: 0.8608 (mtp) REVERT: D 471 ASP cc_start: 0.7588 (t0) cc_final: 0.7154 (t0) REVERT: A 358 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7956 (mt) REVERT: A 438 SER cc_start: 0.8924 (t) cc_final: 0.8509 (t) outliers start: 6 outliers final: 3 residues processed: 87 average time/residue: 0.1442 time to fit residues: 18.5899 Evaluate side-chains 82 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.0030 overall best weight: 0.4348 ------------------------------------------------------------------------------- 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: 0.7852 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7075 Z= 0.193 Angle : 0.497 6.701 9613 Z= 0.257 Chirality : 0.041 0.186 1042 Planarity : 0.004 0.035 1231 Dihedral : 6.030 57.198 1076 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.62 % Allowed : 9.74 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.00 (0.28), residues: 831 helix: 1.76 (0.27), residues: 368 sheet: 1.29 (0.58), residues: 71 loop : -0.51 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS D 378 PHE 0.018 0.001 PHE D 327 TYR 0.014 0.001 TYR A 495 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.8027 (m) cc_final: 0.7687 (m) REVERT: D 383 MET cc_start: 0.8997 (mtt) cc_final: 0.8635 (mtp) REVERT: D 471 ASP cc_start: 0.7580 (t0) cc_final: 0.7106 (t0) REVERT: A 358 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.7961 (mt) REVERT: A 438 SER cc_start: 0.8998 (t) cc_final: 0.8583 (t) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.1380 time to fit residues: 17.9586 Evaluate side-chains 78 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 26 optimal weight: 0.1980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7075 Z= 0.164 Angle : 0.483 6.408 9613 Z= 0.247 Chirality : 0.040 0.189 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.936 56.572 1076 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.22 % Allowed : 10.83 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.06 (0.29), residues: 831 helix: 1.79 (0.27), residues: 368 sheet: 1.29 (0.58), residues: 71 loop : -0.45 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 PHE 0.015 0.001 PHE D 369 TYR 0.012 0.001 TYR D 183 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.7972 (m) cc_final: 0.7647 (m) REVERT: D 471 ASP cc_start: 0.7564 (t0) cc_final: 0.7036 (t0) REVERT: A 358 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7954 (mt) REVERT: A 438 SER cc_start: 0.8970 (t) cc_final: 0.8537 (t) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.1344 time to fit residues: 17.2868 Evaluate side-chains 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7075 Z= 0.148 Angle : 0.471 6.185 9613 Z= 0.241 Chirality : 0.040 0.185 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.847 56.167 1076 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.62 % Allowed : 10.69 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.12 (0.29), residues: 831 helix: 1.87 (0.28), residues: 368 sheet: 1.29 (0.58), residues: 71 loop : -0.45 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.014 0.001 PHE D 369 TYR 0.011 0.001 TYR D 183 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7937 (m) cc_final: 0.7612 (m) REVERT: D 383 MET cc_start: 0.8985 (mtt) cc_final: 0.8699 (mtp) REVERT: D 471 ASP cc_start: 0.7585 (t0) cc_final: 0.7033 (t0) REVERT: A 358 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7891 (mt) REVERT: A 438 SER cc_start: 0.8962 (t) cc_final: 0.8516 (t) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.1415 time to fit residues: 18.2267 Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 0.0270 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 0.0170 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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: 0.7828 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7075 Z= 0.148 Angle : 0.485 8.708 9613 Z= 0.245 Chirality : 0.040 0.188 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.834 56.167 1076 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 11.64 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.15 (0.29), residues: 831 helix: 1.89 (0.28), residues: 368 sheet: 1.26 (0.58), residues: 71 loop : -0.42 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.014 0.001 PHE D 369 TYR 0.011 0.001 TYR D 183 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.703 Fit side-chains REVERT: D 78 THR cc_start: 0.7924 (m) cc_final: 0.7598 (m) REVERT: D 383 MET cc_start: 0.8973 (mtt) cc_final: 0.8701 (mtp) REVERT: D 471 ASP cc_start: 0.7653 (t0) cc_final: 0.7112 (t0) REVERT: A 358 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7892 (mt) REVERT: A 438 SER cc_start: 0.8963 (t) cc_final: 0.8507 (t) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.1399 time to fit residues: 17.7552 Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 50 optimal weight: 0.0570 chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 72 optimal weight: 0.0170 chunk 76 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN A 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7075 Z= 0.115 Angle : 0.454 6.182 9613 Z= 0.232 Chirality : 0.039 0.189 1042 Planarity : 0.003 0.033 1231 Dihedral : 5.698 55.364 1076 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.95 % Allowed : 12.58 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 2.02 (0.28), residues: 368 sheet: 1.36 (0.59), residues: 71 loop : -0.35 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.010 0.001 PHE D 369 TYR 0.010 0.001 TYR D 183 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.777 Fit side-chains REVERT: D 57 GLU cc_start: 0.6663 (tm-30) cc_final: 0.5762 (tm-30) REVERT: D 78 THR cc_start: 0.7822 (m) cc_final: 0.7521 (m) REVERT: D 383 MET cc_start: 0.8876 (mtt) cc_final: 0.8634 (mtp) REVERT: D 471 ASP cc_start: 0.7659 (t0) cc_final: 0.7104 (t0) REVERT: A 438 SER cc_start: 0.8921 (t) cc_final: 0.8472 (t) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.1336 time to fit residues: 16.8422 Evaluate side-chains 79 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.5980 chunk 76 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 0.0270 chunk 22 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7075 Z= 0.146 Angle : 0.481 9.299 9613 Z= 0.243 Chirality : 0.040 0.187 1042 Planarity : 0.003 0.033 1231 Dihedral : 5.744 55.949 1076 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 12.58 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.26 (0.29), residues: 831 helix: 2.00 (0.28), residues: 368 sheet: 1.33 (0.59), residues: 71 loop : -0.38 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.001 HIS D 378 PHE 0.013 0.001 PHE D 369 TYR 0.010 0.001 TYR D 252 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 0.779 Fit side-chains REVERT: D 57 GLU cc_start: 0.6690 (tm-30) cc_final: 0.5771 (tm-30) REVERT: D 78 THR cc_start: 0.7886 (m) cc_final: 0.7558 (m) REVERT: D 383 MET cc_start: 0.8944 (mtt) cc_final: 0.8696 (mtp) REVERT: D 471 ASP cc_start: 0.7669 (t0) cc_final: 0.7116 (t0) REVERT: A 438 SER cc_start: 0.8952 (t) cc_final: 0.8498 (t) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.1319 time to fit residues: 16.7578 Evaluate side-chains 82 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.0570 chunk 82 optimal weight: 0.0870 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 7075 Z= 0.135 Angle : 0.472 6.930 9613 Z= 0.240 Chirality : 0.040 0.188 1042 Planarity : 0.003 0.033 1231 Dihedral : 5.711 55.656 1076 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.95 % Allowed : 12.99 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 2.04 (0.28), residues: 368 sheet: 1.38 (0.59), residues: 71 loop : -0.35 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.003 0.000 HIS D 378 PHE 0.011 0.001 PHE D 369 TYR 0.016 0.001 TYR D 252 ARG 0.002 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.702 Fit side-chains REVERT: D 57 GLU cc_start: 0.6666 (tm-30) cc_final: 0.5753 (tm-30) REVERT: D 78 THR cc_start: 0.7855 (m) cc_final: 0.7529 (m) REVERT: D 383 MET cc_start: 0.8882 (mtt) cc_final: 0.8645 (mtp) REVERT: D 471 ASP cc_start: 0.7684 (t0) cc_final: 0.7140 (t0) REVERT: A 438 SER cc_start: 0.8935 (t) cc_final: 0.8487 (t) REVERT: A 574 ASP cc_start: 0.6564 (m-30) cc_final: 0.5767 (t0) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.1321 time to fit residues: 16.3128 Evaluate side-chains 80 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 0.0770 chunk 75 optimal weight: 0.0670 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.187973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.174972 restraints weight = 7722.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.160044 restraints weight = 14344.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.157300 restraints weight = 13542.653| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7075 Z= 0.208 Angle : 0.544 17.997 9613 Z= 0.275 Chirality : 0.041 0.229 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.873 56.522 1076 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.08 % Allowed : 13.13 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.95 (0.28), residues: 368 sheet: 1.23 (0.59), residues: 71 loop : -0.44 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 PHE 0.024 0.001 PHE D 314 TYR 0.012 0.001 TYR D 252 ARG 0.002 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.79 seconds wall clock time: 31 minutes 13.15 seconds (1873.15 seconds total)