Starting phenix.real_space_refine on Thu Jul 18 23:33:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x1n_37997/07_2024/8x1n_37997_neut.cif" } resolution = 3.31 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= 0.000 sd= 0.047 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 40 5.16 5 C 3008 2.51 5 N 792 2.21 5 O 922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4763 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4651 Classifications: {'peptide': 591} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 569} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' ZN': 1, 'PLM': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.39, per 1000 atoms: 0.71 Number of scatterers: 4763 At special positions: 0 Unit cell: (70.484, 93.628, 103.096, 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 40 16.00 O 922 8.00 N 792 7.00 C 3008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 393 " distance=2.04 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 462 " distance=2.04 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 501 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 591 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 251 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 735.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 268 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 264 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 22 " 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.729A pdb=" N CYS A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 108 removed outlier: 3.762A pdb=" N LEU A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 146 through 154 removed outlier: 4.292A pdb=" N GLU A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 170 removed outlier: 3.894A pdb=" N ARG A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.525A pdb=" N ILE A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 197 through 247 removed outlier: 3.788A pdb=" N ALA A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ARG A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 271 removed outlier: 3.855A pdb=" N LYS A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.546A pdb=" N GLN A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.515A pdb=" N THR A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 343 through 362 removed outlier: 3.911A pdb=" N ARG A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.534A pdb=" N PHE A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.586A pdb=" N CYS A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.611A pdb=" N GLN A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.813A pdb=" N CYS A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 4.103A pdb=" N ALA A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.924A pdb=" N CYS A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.759A pdb=" N ILE A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.687A pdb=" N GLN A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.812A pdb=" N PHE A 552 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 584 removed outlier: 4.165A pdb=" N GLN A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 608 removed outlier: 4.452A pdb=" N GLN A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) 295 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: 1.26 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1570 1.35 - 1.47: 1031 1.47 - 1.59: 2193 1.59 - 1.71: 0 1.71 - 1.83: 48 Bond restraints: 4842 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 PLM A 704 " pdb=" C2 PLM A 704 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 PLM A 703 " pdb=" C2 PLM A 703 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 4837 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.59: 110 106.59 - 113.41: 2614 113.41 - 120.24: 1867 120.24 - 127.06: 1879 127.06 - 133.89: 43 Bond angle restraints: 6513 Sorted by residual: angle pdb=" CA CYS A 472 " pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " ideal model delta sigma weight residual 114.40 121.49 -7.09 2.30e+00 1.89e-01 9.50e+00 angle pdb=" N CYS A 461 " pdb=" CA CYS A 461 " pdb=" C CYS A 461 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.34e+00 5.57e-01 8.88e+00 angle pdb=" N CYS A 462 " pdb=" CA CYS A 462 " pdb=" C CYS A 462 " ideal model delta sigma weight residual 113.01 109.47 3.54 1.20e+00 6.94e-01 8.70e+00 angle pdb=" CA GLN A 291 " pdb=" C GLN A 291 " pdb=" N GLN A 292 " ideal model delta sigma weight residual 114.76 117.84 -3.08 1.14e+00 7.69e-01 7.30e+00 angle pdb=" CB MET A 159 " pdb=" CG MET A 159 " pdb=" SD MET A 159 " ideal model delta sigma weight residual 112.70 120.36 -7.66 3.00e+00 1.11e-01 6.52e+00 ... (remaining 6508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 2802 22.13 - 44.27: 221 44.27 - 66.40: 31 66.40 - 88.53: 14 88.53 - 110.66: 7 Dihedral angle restraints: 3075 sinusoidal: 1338 harmonic: 1737 Sorted by residual: dihedral pdb=" CB CYS A 461 " pdb=" SG CYS A 461 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 583 " pdb=" CB CYS A 583 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 591 " pdb=" CB CYS A 591 " ideal model delta sinusoidal sigma weight residual -86.00 -167.52 81.52 1 1.00e+01 1.00e-02 8.18e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 638 0.056 - 0.111: 87 0.111 - 0.167: 6 0.167 - 0.223: 0 0.223 - 0.278: 2 Chirality restraints: 733 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 251 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA CYS A 461 " pdb=" N CYS A 461 " pdb=" C CYS A 461 " pdb=" CB CYS A 461 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 730 not shown) Planarity restraints: 843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 132 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 133 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 494 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 495 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 336 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ASP A 336 " -0.018 2.00e-02 2.50e+03 pdb=" O ASP A 336 " 0.007 2.00e-02 2.50e+03 pdb=" N ARG A 337 " 0.006 2.00e-02 2.50e+03 ... (remaining 840 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1013 2.78 - 3.31: 4403 3.31 - 3.84: 7369 3.84 - 4.37: 7898 4.37 - 4.90: 14920 Nonbonded interactions: 35603 Sorted by model distance: nonbonded pdb=" O SER A 34 " pdb=" OG SER A 34 " model vdw 2.251 2.440 nonbonded pdb=" ND2 ASN A 329 " pdb=" OD1 ASN A 331 " model vdw 2.285 2.520 nonbonded pdb=" OE2 GLU A 392 " pdb=" NZ LYS A 396 " model vdw 2.326 2.520 nonbonded pdb=" O LEU A 432 " pdb=" OG1 THR A 436 " model vdw 2.352 2.440 nonbonded pdb=" O GLU A 88 " pdb=" NE2 GLN A 90 " model vdw 2.395 2.520 ... (remaining 35598 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 individual isotropic 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: 0.430 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.003 0.051 4842 Z= 0.204 Angle : 0.594 7.660 6513 Z= 0.327 Chirality : 0.040 0.278 733 Planarity : 0.003 0.041 842 Dihedral : 16.855 110.663 1897 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.01 (0.36), residues: 589 helix: 1.99 (0.27), residues: 397 sheet: None (None), residues: 0 loop : -0.01 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.010 0.001 PHE A 339 TYR 0.010 0.001 TYR A 435 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2218 time to fit residues: 13.1029 Evaluate side-chains 46 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4842 Z= 0.208 Angle : 0.502 5.929 6513 Z= 0.261 Chirality : 0.039 0.194 733 Planarity : 0.003 0.039 842 Dihedral : 9.721 62.548 747 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.14 % Allowed : 11.07 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.36), residues: 589 helix: 1.97 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 268 PHE 0.009 0.001 PHE A 575 TYR 0.012 0.002 TYR A 435 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.546 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.1836 time to fit residues: 13.6300 Evaluate side-chains 52 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4842 Z= 0.171 Angle : 0.475 5.988 6513 Z= 0.247 Chirality : 0.039 0.189 733 Planarity : 0.003 0.037 842 Dihedral : 8.123 58.646 747 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 12.82 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.05 (0.36), residues: 589 helix: 2.09 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.004 0.001 HIS A 268 PHE 0.008 0.001 PHE A 575 TYR 0.011 0.001 TYR A 435 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6845 (pt0) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1815 time to fit residues: 13.7838 Evaluate side-chains 54 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 0.0000 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 331 ASN A 483 HIS A 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4842 Z= 0.134 Angle : 0.432 5.367 6513 Z= 0.227 Chirality : 0.037 0.186 733 Planarity : 0.003 0.037 842 Dihedral : 6.823 58.721 747 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.72 % Allowed : 13.20 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.28 (0.36), residues: 589 helix: 2.29 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.30 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.002 0.001 HIS A 128 PHE 0.008 0.001 PHE A 592 TYR 0.008 0.001 TYR A 151 ARG 0.001 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.529 Fit side-chains REVERT: A 400 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6942 (pt0) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.1860 time to fit residues: 14.2714 Evaluate side-chains 58 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4842 Z= 0.298 Angle : 0.517 5.408 6513 Z= 0.269 Chirality : 0.041 0.217 733 Planarity : 0.003 0.039 842 Dihedral : 7.452 58.437 747 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.33 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.06 (0.36), residues: 589 helix: 2.06 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.26 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.006 0.001 HIS A 268 PHE 0.011 0.001 PHE A 385 TYR 0.012 0.002 TYR A 425 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6975 (pt0) outliers start: 12 outliers final: 11 residues processed: 57 average time/residue: 0.1743 time to fit residues: 13.0077 Evaluate side-chains 54 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.005 0.058 4842 Z= 0.307 Angle : 0.539 6.334 6513 Z= 0.281 Chirality : 0.041 0.213 733 Planarity : 0.003 0.040 842 Dihedral : 7.783 59.052 747 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.30 % Allowed : 13.40 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: 1.83 (0.36), residues: 589 helix: 1.90 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -0.38 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 181 HIS 0.006 0.001 HIS A 268 PHE 0.011 0.001 PHE A 385 TYR 0.012 0.002 TYR A 425 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6979 (pt0) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.1782 time to fit residues: 13.2810 Evaluate side-chains 57 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 44 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4842 Z= 0.193 Angle : 0.476 6.336 6513 Z= 0.250 Chirality : 0.038 0.207 733 Planarity : 0.003 0.040 842 Dihedral : 7.422 57.233 747 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.11 % Allowed : 14.17 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.02 (0.36), residues: 589 helix: 2.05 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.36 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.007 0.001 PHE A 385 TYR 0.008 0.001 TYR A 426 ARG 0.001 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6935 (pt0) outliers start: 16 outliers final: 16 residues processed: 57 average time/residue: 0.1801 time to fit residues: 13.3915 Evaluate side-chains 60 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 4842 Z= 0.309 Angle : 0.531 7.162 6513 Z= 0.275 Chirality : 0.041 0.215 733 Planarity : 0.003 0.041 842 Dihedral : 7.781 59.578 747 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.50 % Allowed : 13.79 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.36), residues: 589 helix: 1.91 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.28 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.005 0.001 HIS A 268 PHE 0.011 0.001 PHE A 385 TYR 0.012 0.002 TYR A 435 ARG 0.001 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7252 (t0) cc_final: 0.6960 (t0) REVERT: A 383 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7747 (tttm) REVERT: A 400 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6970 (pt0) outliers start: 18 outliers final: 14 residues processed: 59 average time/residue: 0.1830 time to fit residues: 13.9879 Evaluate side-chains 57 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4842 Z= 0.186 Angle : 0.517 14.681 6513 Z= 0.266 Chirality : 0.039 0.230 733 Planarity : 0.003 0.040 842 Dihedral : 7.555 57.816 747 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.91 % Allowed : 13.98 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: 2.05 (0.36), residues: 589 helix: 2.06 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.32 (0.49), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.003 0.001 HIS A 268 PHE 0.007 0.001 PHE A 385 TYR 0.008 0.001 TYR A 164 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7213 (t0) cc_final: 0.6927 (t0) REVERT: A 400 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6946 (pt0) outliers start: 15 outliers final: 15 residues processed: 57 average time/residue: 0.1844 time to fit residues: 13.7094 Evaluate side-chains 58 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 185 TYR Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 563 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 13 optimal weight: 0.3980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4842 Z= 0.136 Angle : 0.467 12.455 6513 Z= 0.242 Chirality : 0.037 0.201 733 Planarity : 0.003 0.041 842 Dihedral : 6.677 56.246 747 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.14 % Allowed : 14.17 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.29 (0.36), residues: 589 helix: 2.26 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -0.27 (0.48), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.002 0.001 HIS A 488 PHE 0.008 0.001 PHE A 512 TYR 0.006 0.001 TYR A 151 ARG 0.001 0.000 ARG A 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7120 (t0) cc_final: 0.6842 (t0) REVERT: A 400 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6919 (pt0) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.1702 time to fit residues: 12.2666 Evaluate side-chains 52 residues out of total 515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 462 CYS Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 522 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.155065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112287 restraints weight = 5379.539| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.26 r_work: 0.2803 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 4842 Z= 0.328 Angle : 0.584 12.199 6513 Z= 0.298 Chirality : 0.043 0.226 733 Planarity : 0.004 0.042 842 Dihedral : 7.399 59.139 747 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.33 % Allowed : 14.37 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 2.01 (0.36), residues: 589 helix: 1.99 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.26 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 181 HIS 0.008 0.001 HIS A 268 PHE 0.013 0.001 PHE A 385 TYR 0.011 0.002 TYR A 164 ARG 0.002 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.64 seconds wall clock time: 22 minutes 37.49 seconds (1357.49 seconds total)