Starting phenix.real_space_refine on Mon Mar 11 03:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/03_2024/7r0z_14225.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/03_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_14225/03_2024/7r0z_14225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/03_2024/7r0z_14225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/03_2024/7r0z_14225.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r0z_14225/03_2024/7r0z_14225.pdb" } 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 Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "A ASP 428": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.22, per 1000 atoms: 0.61 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 - 3.50 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 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 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: 0.77 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: 1.82 Time building geometry restraints manager: 2.83 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: 99.44 - 106.36: 206 106.36 - 113.27: 3742 113.27 - 120.19: 2646 120.19 - 127.11: 2921 127.11 - 134.02: 98 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 2.440 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.245 2.520 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 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.393 2.440 ... (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 ========== 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: 4.480 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: 9.510 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 23.980 Find NCS groups from input model: 0.200 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.310 ------------------------------------------------------------------------------- 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 : 1.081 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: 0.1780 time to fit residues: 24.4996 Evaluate side-chains 71 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 0.2980 chunk 62 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 75 optimal weight: 0.0970 overall best weight: 0.1352 ------------------------------------------------------------------------------- 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: 0.7798 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 0.026 7075 Z= 0.132 Angle : 0.491 6.810 9613 Z= 0.251 Chirality : 0.040 0.201 1042 Planarity : 0.004 0.035 1231 Dihedral : 6.688 58.927 1076 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 6.36 % Favored : 93.10 % 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: 0.87 (0.28), residues: 831 helix: 1.64 (0.27), residues: 367 sheet: 1.11 (0.59), residues: 70 loop : -0.53 (0.29), residues: 394 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 0.004 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 89 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 THR cc_start: 0.7963 (m) cc_final: 0.7599 (m) REVERT: D 471 ASP cc_start: 0.7612 (t0) cc_final: 0.7238 (t0) REVERT: A 438 SER cc_start: 0.8859 (t) cc_final: 0.8522 (t) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.1553 time to fit residues: 19.8873 Evaluate side-chains 76 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR 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: 0.6980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 81 optimal weight: 0.0470 chunk 67 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 overall best weight: 0.0832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN D 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1446 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= 0.106 Angle : 0.445 6.198 9613 Z= 0.227 Chirality : 0.039 0.187 1042 Planarity : 0.003 0.033 1231 Dihedral : 6.247 55.667 1076 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.81 % Allowed : 9.61 % Favored : 89.58 % 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: 1.20 (0.29), residues: 831 helix: 1.94 (0.27), residues: 368 sheet: 1.15 (0.58), residues: 71 loop : -0.37 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.009 0.001 PHE D 369 TYR 0.013 0.001 TYR D 183 ARG 0.005 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 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7850 (m) cc_final: 0.7510 (m) REVERT: D 383 MET cc_start: 0.8826 (mtt) cc_final: 0.8565 (mtp) REVERT: D 406 GLU cc_start: 0.8218 (tp30) cc_final: 0.7984 (tp30) REVERT: D 471 ASP cc_start: 0.7641 (t0) cc_final: 0.7177 (t0) REVERT: A 358 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 438 SER cc_start: 0.8800 (t) cc_final: 0.8455 (t) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.1588 time to fit residues: 21.5632 Evaluate side-chains 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7075 Z= 0.235 Angle : 0.515 6.399 9613 Z= 0.266 Chirality : 0.042 0.188 1042 Planarity : 0.004 0.036 1231 Dihedral : 6.498 58.517 1076 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.49 % Allowed : 10.55 % 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: 1.02 (0.29), residues: 831 helix: 1.78 (0.28), residues: 368 sheet: 1.22 (0.58), residues: 71 loop : -0.49 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.007 0.001 HIS D 378 PHE 0.022 0.002 PHE D 327 TYR 0.014 0.002 TYR A 453 ARG 0.003 0.000 ARG D 357 *********************** 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 87 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.8029 (m) cc_final: 0.7674 (m) REVERT: D 471 ASP cc_start: 0.7681 (t0) cc_final: 0.7182 (t0) REVERT: A 358 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 438 SER cc_start: 0.8927 (t) cc_final: 0.8598 (t) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.1354 time to fit residues: 17.5877 Evaluate side-chains 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7075 Z= 0.331 Angle : 0.579 8.052 9613 Z= 0.300 Chirality : 0.045 0.198 1042 Planarity : 0.004 0.045 1231 Dihedral : 6.699 59.150 1076 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 11.37 % 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: 0.61 (0.28), residues: 831 helix: 1.37 (0.28), residues: 370 sheet: 1.08 (0.58), residues: 71 loop : -0.66 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.008 0.001 HIS D 378 PHE 0.028 0.002 PHE D 327 TYR 0.015 0.002 TYR D 587 ARG 0.004 0.001 ARG D 357 *********************** 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 80 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: D 471 ASP cc_start: 0.7742 (t0) cc_final: 0.7234 (t0) REVERT: A 358 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8001 (mt) REVERT: A 438 SER cc_start: 0.8939 (t) cc_final: 0.8619 (t) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1497 time to fit residues: 16.9332 Evaluate side-chains 75 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 198 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.0050 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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: 0.7897 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7075 Z= 0.206 Angle : 0.505 6.781 9613 Z= 0.259 Chirality : 0.041 0.195 1042 Planarity : 0.004 0.037 1231 Dihedral : 6.445 58.450 1076 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.76 % Allowed : 12.45 % 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: 0.69 (0.29), residues: 831 helix: 1.48 (0.28), residues: 369 sheet: 1.05 (0.58), residues: 71 loop : -0.64 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS D 378 PHE 0.018 0.001 PHE D 369 TYR 0.012 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 82 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: D 78 THR cc_start: 0.7990 (m) cc_final: 0.7634 (m) REVERT: D 471 ASP cc_start: 0.7657 (t0) cc_final: 0.7119 (t0) REVERT: A 358 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 438 SER cc_start: 0.8896 (t) cc_final: 0.8576 (t) outliers start: 13 outliers final: 5 residues processed: 78 average time/residue: 0.1386 time to fit residues: 16.4702 Evaluate side-chains 73 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 401 HIS 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: 0.7980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7075 Z= 0.225 Angle : 0.524 8.105 9613 Z= 0.266 Chirality : 0.042 0.192 1042 Planarity : 0.004 0.037 1231 Dihedral : 6.355 58.559 1076 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.62 % Allowed : 12.45 % Favored : 85.93 % 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: 0.70 (0.29), residues: 831 helix: 1.50 (0.28), residues: 369 sheet: 1.07 (0.58), residues: 71 loop : -0.65 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS D 378 PHE 0.020 0.002 PHE D 369 TYR 0.012 0.001 TYR D 183 ARG 0.003 0.000 ARG D 357 *********************** 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 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.735 Fit side-chains REVERT: D 57 GLU cc_start: 0.6936 (tm-30) cc_final: 0.5978 (tm-30) REVERT: D 78 THR cc_start: 0.7996 (m) cc_final: 0.7659 (m) REVERT: D 471 ASP cc_start: 0.7675 (t0) cc_final: 0.7143 (t0) REVERT: A 358 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8055 (mt) REVERT: A 438 SER cc_start: 0.8892 (t) cc_final: 0.8580 (t) outliers start: 12 outliers final: 8 residues processed: 78 average time/residue: 0.1314 time to fit residues: 15.6207 Evaluate side-chains 78 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 415 THR 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: 0.5980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 39 optimal weight: 0.0670 chunk 7 optimal weight: 0.0980 chunk 62 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 overall best weight: 0.1716 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7075 Z= 0.120 Angle : 0.457 5.974 9613 Z= 0.232 Chirality : 0.039 0.195 1042 Planarity : 0.003 0.035 1231 Dihedral : 5.943 55.594 1076 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.81 % Allowed : 13.94 % Favored : 85.25 % 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: 0.97 (0.29), residues: 831 helix: 1.77 (0.28), residues: 368 sheet: 1.16 (0.59), residues: 71 loop : -0.54 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.010 0.001 PHE D 369 TYR 0.011 0.001 TYR D 183 ARG 0.003 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 87 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.807 Fit side-chains REVERT: D 57 GLU cc_start: 0.6924 (tm-30) cc_final: 0.5964 (tm-30) REVERT: D 78 THR cc_start: 0.7857 (m) cc_final: 0.7524 (m) REVERT: D 383 MET cc_start: 0.8955 (mtt) cc_final: 0.8688 (mtp) REVERT: D 406 GLU cc_start: 0.8240 (tp30) cc_final: 0.8029 (tp30) REVERT: D 471 ASP cc_start: 0.7649 (t0) cc_final: 0.7100 (t0) REVERT: A 438 SER cc_start: 0.8776 (t) cc_final: 0.8443 (t) outliers start: 6 outliers final: 4 residues processed: 85 average time/residue: 0.1426 time to fit residues: 18.2291 Evaluate side-chains 75 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 440 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.0020 chunk 67 optimal weight: 0.0070 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 overall best weight: 0.1618 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7075 Z= 0.117 Angle : 0.474 10.349 9613 Z= 0.237 Chirality : 0.039 0.189 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.761 55.206 1076 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.08 % Allowed : 14.34 % Favored : 84.57 % 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: 1.23 (0.29), residues: 831 helix: 2.05 (0.28), residues: 362 sheet: 1.25 (0.59), residues: 71 loop : -0.42 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.011 0.001 PHE D 369 TYR 0.028 0.001 TYR D 279 ARG 0.001 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 84 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.841 Fit side-chains REVERT: D 57 GLU cc_start: 0.6875 (tm-30) cc_final: 0.5912 (tm-30) REVERT: D 78 THR cc_start: 0.7829 (m) cc_final: 0.7512 (m) REVERT: D 383 MET cc_start: 0.8925 (mtt) cc_final: 0.8692 (mtp) REVERT: D 406 GLU cc_start: 0.8201 (tp30) cc_final: 0.7996 (tp30) REVERT: D 471 ASP cc_start: 0.7609 (t0) cc_final: 0.7055 (t0) REVERT: A 438 SER cc_start: 0.8749 (t) cc_final: 0.8449 (t) outliers start: 8 outliers final: 7 residues processed: 81 average time/residue: 0.1408 time to fit residues: 17.2697 Evaluate side-chains 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 574 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7075 Z= 0.196 Angle : 0.495 5.864 9613 Z= 0.252 Chirality : 0.041 0.188 1042 Planarity : 0.003 0.035 1231 Dihedral : 5.915 56.580 1076 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.08 % Allowed : 13.94 % Favored : 84.98 % 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: 1.97 (0.28), residues: 362 sheet: 1.32 (0.59), residues: 71 loop : -0.52 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 PHE 0.017 0.001 PHE D 369 TYR 0.023 0.001 TYR D 279 ARG 0.002 0.000 ARG D 357 ********************** 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: 8 poor density : 75 time to evaluate : 0.798 Fit side-chains REVERT: D 57 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6577 (tm-30) REVERT: D 78 THR cc_start: 0.7948 (m) cc_final: 0.7614 (m) REVERT: D 406 GLU cc_start: 0.8252 (tp30) cc_final: 0.8016 (tp30) REVERT: D 471 ASP cc_start: 0.7609 (t0) cc_final: 0.7058 (t0) REVERT: A 358 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7908 (mt) REVERT: A 438 SER cc_start: 0.8842 (t) cc_final: 0.8551 (t) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.1392 time to fit residues: 16.8467 Evaluate side-chains 81 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 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 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE 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: 1.9990 chunk 18 optimal weight: 0.1980 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.188286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.172401 restraints weight = 7798.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.158602 restraints weight = 12728.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.157651 restraints weight = 10279.541| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 7075 Z= 0.196 Angle : 0.532 17.440 9613 Z= 0.268 Chirality : 0.041 0.236 1042 Planarity : 0.003 0.034 1231 Dihedral : 5.928 56.163 1076 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.62 % Allowed : 13.80 % Favored : 84.57 % 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: 1.11 (0.29), residues: 831 helix: 1.95 (0.28), residues: 362 sheet: 1.22 (0.59), residues: 71 loop : -0.50 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 165 HIS 0.004 0.001 HIS D 378 PHE 0.015 0.001 PHE D 369 TYR 0.023 0.001 TYR D 279 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: 1667.50 seconds wall clock time: 31 minutes 4.98 seconds (1864.98 seconds total)